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Code Issues 14 Pull requests 2 Packages Activity Actions

[BUG]: Coordinates transforms to native space using ANTs are off #388

Merged
synchon merged 5 commits from fix/coords-ants into main 2024-11-19 12:25:12 +00:00
Conversation 9 Commits 5 Files changed 3 +15 -4
synchon commented 2024-11-13 12:07:21 +00:00 (Migrated from github.com)
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Is there an existing issue for this?

  • I have searched the existing issues

Current Behavior

When computing any marker on coordinates in native space, the coordinates in native space do not match the corresponding landmark in MNI space.

These are two examples in which the left (MNI space) do not match the right (T1w space).

In this first example, the coordinates are off-brain:

Screenshot 2024-11-06 at 10 04 17 (2)

In this second example, the coordinates are in the brain, but not in the same landmark:

Screenshot 2024-11-06 at 10 06 17 (2)

Expected Behavior

I expect that the coordinates point to the right landmark.

Steps To Reproduce

  1. With latest junifer (main branch)
  2. Modify the WorkdirManager code so that temporary directories are not cleaned.
  3. Compute (f)ALFF on Aomic's sub-0001 using "Power2011" using this script:
# %%
import pickle
from junifer.datagrabber.aomic import DataladAOMICID1000
from junifer.utils import configure_logging
from junifer.pipeline import WorkDirManager

configure_logging(level="DEBUG")

WorkDirManager(
    workdir="/home/fraimondo/dev/scratch/test_junifer_native/temp",
    cleanup=False,
)

element = "sub-0001"
# %% Load data

dg = DataladAOMICID1000(
    native_t1w=True,
    datadir="/home/fraimondo/test_datasets/aomic_id1000/",
    types=["BOLD", "T1w", "Warp"]
)

with dg:
    data = dg[element]

    # %% Read data
    from junifer.datareader import DefaultDataReader

    reader = DefaultDataReader()
    data = reader.fit_transform(data)

    pickle.dump(data, open(f"aomic_{element}_read.pkl", "wb"))
    # # %% Preprocess
    from junifer.preprocess import fMRIPrepConfoundRemover

    confound = fMRIPrepConfoundRemover(
        detrend=True,
        standardize=True,
        strategy={
            "motion": "full",
            "wm_csf": "full",
            "global_signal": "full",
        },
        # masks=["inherit", "compute_epi_mask", {"threshold": 0}],
        masks=["inherit"],
    )

    data = confound.fit_transform(data)

    pickle.dump(data, open(f"aomic_{element}_deconfounded.pkl", "wb"))

    # %% Warp
    from junifer.preprocess import SpaceWarper

    warper = SpaceWarper(reference="T1w", on="BOLD", using="ants")

    data = warper.fit_transform(data)
    pickle.dump(data, open(f"aomic_{element}_warped.pkl", "wb"))
  
    # %%  Compute marker
    # data = pickle.load(open(f"aomic_{element}_warped.pkl", "rb"))
    from junifer.markers import ALFFSpheres


    marker = ALFFSpheres(
        coords="Power2011",
        radius=5,
        allow_overlap=True,
        using="afni",
        agg_method="mean",
        highpass=0.01,
        lowpass=0.08,
        masks="inherit",
    )
    out = marker.fit_transform(data)

    pickle.dump(out, open(f"aomic_{element}_out.pkl", "wb"))
  1. Check the output and temporary directory and find the pretransformed and transformed coordinates. Visualize them in the MNI and T1w images.

Environment

junifer:
  version: 0.0.6.dev176
python:
  version: 3.12.6
  implementation: CPython
dependencies:
  click: 8.1.7
  numpy: 1.26.4
  scipy: 1.14.1
  datalad: 1.1.3
  pandas: 2.2.2
  nibabel: 5.2.1
  ruamel.yaml: 0.17.40
  looseversion: None
system:
  platform: Linux-6.6.13+bpo-amd64-x86_64-with-glibc2.36
environment:
  PATH:
    /data/group/appliedml/tools/ants_2.5.0/binaries:/home/fraimondo/miniconda3/envs/junifer/bin:/home/fraimondo/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/games

Relevant log output

[WARNING] Requested extension 'next' is not available
2024-11-05 11:23:10,090 - JUNIFER - INFO - ===== Lib Versions =====
2024-11-05 11:23:10,090 - JUNIFER - INFO - numpy: 1.26.4
2024-11-05 11:23:10,090 - JUNIFER - INFO - junifer: 0.0.6.dev176
2024-11-05 11:23:10,090 - JUNIFER - INFO - ========================
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - Initializing PatternDataladDataGrabber
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - 	types = ['BOLD', 'T1w', 'Warp']
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - 	datadir = /home/fraimondo/test_datasets/aomic_id1000/
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - 	uri = https://github.com/OpenNeuroDatasets/ds003097.git
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - 	patterns = {'BOLD': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'space': 'MNI152NLin2009cAsym', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'confounds': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_desc-confounds_regressors.tsv', 'format': 'fmriprep'}}, 'T1w': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-preproc_T1w.nii.gz', 'space': 'native', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-brain_mask.nii.gz', 'space': 'native'}}, 'VBM_CSF': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_GM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_WM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'DWI': {'pattern': 'derivatives/dwipreproc/{subject}/dwi/{subject}_desc-preproc_dwi.nii.gz'}, 'FreeSurfer': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]', 'aseg': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]'}, 'norm': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]'}, 'lh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]'}, 'rh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]'}, 'lh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]'}, 'rh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]'}}, 'Warp': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'src': 'MNI152NLin2009cAsym', 'dst': 'native'}}
2024-11-05 11:23:10,090 - JUNIFER - DEBUG - 	replacements = ['subject']
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - 	confounds_format = fmriprep
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for BOLD
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mask` found for BOLD
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD.mask
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for BOLD.mask
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `confounds` found for BOLD
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD.confounds
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `format` found for BOLD.confounds
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mappings` found for BOLD.confounds
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for T1w
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for T1w
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mask` found for T1w
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for T1w.mask
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for T1w.mask
2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_CSF
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_CSF
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_GM
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_GM
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_WM
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_WM
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for DWI
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `aseg` found for FreeSurfer
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.aseg
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `norm` found for FreeSurfer
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.norm
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `lh_white` found for FreeSurfer
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.lh_white
2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `rh_white` found for FreeSurfer
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.rh_white
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Optional key: `lh_pial` found for FreeSurfer
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.lh_pial
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Optional key: `rh_pial` found for FreeSurfer
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.rh_pial
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for Warp
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `src` found for Warp
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `dst` found for Warp
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing BaseDataGrabber
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - 	_datadir = /home/fraimondo/test_datasets/aomic_id1000
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - 	types = ['BOLD', 'T1w', 'Warp']
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing PatternDataGrabber
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - 	patterns = {'BOLD': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'space': 'MNI152NLin2009cAsym', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'confounds': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_desc-confounds_regressors.tsv', 'format': 'fmriprep'}}, 'T1w': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-preproc_T1w.nii.gz', 'space': 'native', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-brain_mask.nii.gz', 'space': 'native'}}, 'VBM_CSF': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_GM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_WM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'DWI': {'pattern': 'derivatives/dwipreproc/{subject}/dwi/{subject}_desc-preproc_dwi.nii.gz'}, 'FreeSurfer': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]', 'aseg': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]'}, 'norm': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]'}, 'lh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]'}, 'rh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]'}, 'lh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]'}, 'rh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]'}}, 'Warp': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'src': 'MNI152NLin2009cAsym', 'dst': 'native'}}
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - 	replacements = ['subject']
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - 	confounds_format = fmriprep
2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing DataladDataGrabber
2024-11-05 11:23:10,094 - JUNIFER - DEBUG - 	uri = https://github.com/OpenNeuroDatasets/ds003097.git
2024-11-05 11:23:10,094 - JUNIFER - DEBUG - 	_rootdir = .
[DEBUG  ] Run ['git', 'version'] (protocol_class=StdOutErrCapture) (cwd=None)
[DEBUG  ] Finished ['git', 'version'] with status 0
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] with status 0
2024-11-05 11:23:10,106 - JUNIFER - DEBUG - Dataset already installed
2024-11-05 11:23:10,106 - JUNIFER - DEBUG - Querying https://github.com/OpenNeuroDatasets/ds003097.git for dataset ID
[DEBUG  ] Git clone from https://github.com/OpenNeuroDatasets/ds003097.git to /tmp/tmpuuwkuaq4
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'clone', '--progress', '-n', '--depth=1', 'https://github.com/OpenNeuroDatasets/ds003097.git', '/tmp/tmpuuwkuaq4'] (protocol_class=GitProgress) (cwd=None)
[DEBUG  ] Non-progress stderr: b"Cloning into '/tmp/tmpuuwkuaq4'...\n"
[DEBUG  ] Non-progress stderr: b'remote: Total 362591 (delta 6578), reused 362588 (delta 6578), pack-reused 0 (from 0)        \n'
[DEBUG  ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'clone', '--progress', '-n', '--depth=1', 'https://github.com/OpenNeuroDatasets/ds003097.git', '/tmp/tmpuuwkuaq4'] with status 0
[DEBUG  ] Git clone completed
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'checkout', 'HEAD', '.datalad/config'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4)
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/tmp/tmpuuwkuaq4/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/tmp/tmpuuwkuaq4/.datalad/config'] with status 0
2024-11-05 11:23:37,338 - JUNIFER - DEBUG - Got remote dataset ID = aefe5438-e93b-11ea-ad4c-8e2245da6db7
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0
[DEBUG  ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] with status 0
[DEBUG  ] Determined class of decorated function: <class 'datalad.core.local.status.Status'>
[DEBUG  ] Resolved dataset to report status: /home/fraimondo/test_datasets/aomic_id1000
[DEBUG  ] Querying AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).diffstatus() for paths: None
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...)
[DEBUG  ] Query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory']
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Done query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory']
[DEBUG  ] Done AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...)
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '-z', '-m', '-d'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...)
[DEBUG  ] Query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Done query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG  ] Done AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...)
nothing to save, working tree clean
2024-11-05 11:30:56,369 - JUNIFER - DEBUG - Dataset is clean
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'symbolic-ref', 'HEAD'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
2024-11-05 11:30:56,483 - JUNIFER - INFO - Getting element sub-0001
2024-11-05 11:30:56,484 - JUNIFER - DEBUG - Named element: {'subject': 'sub-0001'}
2024-11-05 11:30:56,484 - JUNIFER - INFO - Resolving path from pattern for BOLD
2024-11-05 11:30:56,486 - JUNIFER - INFO - Resolving path from pattern for BOLD.mask
2024-11-05 11:30:56,487 - JUNIFER - INFO - Resolving path from pattern for BOLD.confounds
2024-11-05 11:30:56,487 - JUNIFER - INFO - Resolving path from pattern for T1w
2024-11-05 11:30:56,488 - JUNIFER - INFO - Resolving path from pattern for T1w.mask
2024-11-05 11:30:56,489 - JUNIFER - INFO - Resolving path from pattern for Warp
2024-11-05 11:30:56,489 - JUNIFER - DEBUG - Getting 6 files using datalad:
2024-11-05 11:30:56,489 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
2024-11-05 11:30:56,490 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv
2024-11-05 11:30:56,490 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
2024-11-05 11:30:56,490 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz
2024-11-05 11:30:56,490 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz
2024-11-05 11:30:56,491 - JUNIFER - DEBUG - 	: /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
[DEBUG  ] Determined class of decorated function: <class 'datalad.distribution.get.Get'>
[DEBUG  ] Resolved dataset to get content of <<[PosixPath('/h++872 chars++5')]>>: /home/fraimondo/test_datasets/aomic_id1000
[DEBUG  ] Determined class of decorated function: <class 'datalad.local.subdatasets.Subdatasets'>
[DEBUG  ] Resolved dataset to report on subdataset(s): /home/fraimondo/test_datasets/aomic_id1000
[DEBUG  ] Query subdatasets of Dataset(/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Determine what files match the query to work with
[DEBUG  ] Run ['git', 'annex', 'version', '--raw'] (protocol_class=StdOutErrCapture) (cwd=None)
[DEBUG  ] Finished ['git', 'annex', 'version', '--raw'] with status 0
[DEBUG  ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', '-c', 'annex.merge-annex-branches=false', 'annex', 'find', '--not', '--in', '.', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv'] (protocol_class=AnnexJsonProtocol) (cwd=/home/fraimondo/test_datasets/aomic_id1000)
[DEBUG  ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', '-c', 'annex.merge-annex-branches=false', 'annex', 'find', '--not', '--in', '.', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv'] with status 0
[DEBUG  ] No files found needing fetching.
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz)]
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5)]
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz)]
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz)]
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz)]
[DEBUG  ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv)]
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv was already present
2024-11-05 11:30:56,561 - JUNIFER - DEBUG - Get done
2024-11-05 11:30:56,900 - JUNIFER - INFO - Registering DefaultDataReader in datareader
2024-11-05 11:30:56,900 - JUNIFER - INFO - Reading BOLD.mask from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
2024-11-05 11:30:56,900 - JUNIFER - INFO - BOLD.mask is of type NIFTI
2024-11-05 11:30:56,900 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {}
2024-11-05 11:30:56,902 - JUNIFER - INFO - Reading BOLD.confounds from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv
2024-11-05 11:30:56,902 - JUNIFER - INFO - BOLD.confounds is of type TSV
2024-11-05 11:30:56,902 - JUNIFER - DEBUG - Calling <function read_csv at 0x150404975a80> with {'sep': '\t'}
2024-11-05 11:30:56,916 - JUNIFER - INFO - Reading BOLD from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
2024-11-05 11:30:56,916 - JUNIFER - INFO - BOLD is of type NIFTI
2024-11-05 11:30:56,916 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {}
2024-11-05 11:30:56,918 - JUNIFER - INFO - Reading T1w.mask from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz
2024-11-05 11:30:56,918 - JUNIFER - INFO - T1w.mask is of type NIFTI
2024-11-05 11:30:56,918 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {}
2024-11-05 11:30:56,920 - JUNIFER - INFO - Reading T1w from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz
2024-11-05 11:30:56,920 - JUNIFER - INFO - T1w is of type NIFTI
2024-11-05 11:30:56,920 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {}
2024-11-05 11:31:01,281 - JUNIFER - INFO - Registering fMRIPrepConfoundRemover in preprocessing
2024-11-05 11:31:01,282 - JUNIFER - INFO - Preprocessing BOLD
2024-11-05 11:31:01,282 - JUNIFER - DEBUG - Extra data type for preprocess: dict_keys(['T1w', 'Warp'])
2024-11-05 11:31:03,638 - JUNIFER - INFO - No `t_r` specified, using t_r from NIfTI header
2024-11-05 11:31:03,638 - JUNIFER - INFO - Read t_r from NIfTI header: 2.200000047683716
2024-11-05 11:31:03,639 - JUNIFER - DEBUG - Masking with ['inherit']
2024-11-05 11:31:03,639 - JUNIFER - DEBUG - Setting up temporary directory under /home/fraimondo/dev/scratch/test_junifer_native/temp
2024-11-05 11:31:03,640 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv -> Overall
2024-11-05 11:31:03,641 - JUNIFER - DEBUG - Setting up element directory under /home/fraimondo/dev/scratch/test_junifer_native/temp
2024-11-05 11:31:03,642 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta -> Element
2024-11-05 11:31:03,642 - JUNIFER - DEBUG - Setting `BOLD.mask`
2024-11-05 11:31:03,642 - JUNIFER - INFO - Cleaning image using nilearn
2024-11-05 11:31:03,643 - JUNIFER - DEBUG - 	detrend: True
2024-11-05 11:31:03,643 - JUNIFER - DEBUG - 	standardize: True
2024-11-05 11:31:03,643 - JUNIFER - DEBUG - 	low_pass: None
2024-11-05 11:31:03,643 - JUNIFER - DEBUG - 	high_pass: None
2024-11-05 11:31:05,236 - JUNIFER - DEBUG - Adding BOLD to output
2024-11-05 11:31:05,644 - JUNIFER - INFO - Registering SpaceWarper in preprocessing
2024-11-05 11:31:35,855 - JUNIFER - WARNING - /home/fraimondo/dev/tbox/junifer/junifer/pipeline/utils.py:248: RuntimeWarning: ANTs is installed but some of the required commands were not found. These are the results: {'ResampleImage': 'not found', 'antsApplyTransforms': 'not found'}
  warn_with_log(
2024-11-05 11:31:35,855 - JUNIFER - INFO - Preprocessing BOLD
2024-11-05 11:31:35,855 - JUNIFER - DEBUG - Extra data type for preprocess: dict_keys(['T1w', 'Warp'])
2024-11-05 11:31:35,855 - JUNIFER - INFO - Warping to T1w space using SpaceWarper
2024-11-05 11:31:35,855 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:31:35,857 - JUNIFER - DEBUG - Using ANTs for space warping
2024-11-05 11:31:35,858 - JUNIFER - INFO - ResampleImage command to be executed:
"sub-0001_desc-preproc_T1w.nii.gz"
ResampleImage 3 /home/fraimondo/test_datasets/aomic_id1000/sub-0001_desc-preproc_T1w.nii.gz /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3
2024-11-05 11:31:48,572 - JUNIFER - INFO - ResampleImage command succeeded with the following output:
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_desc-preproc_T1w.nii.gz is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a prefix
Singularity args: --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/91/63/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2
Corrected args for ANTS: ResampleImage 3 /data/mount_1/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz /data/mount_2/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/91/63/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif ResampleImage 3 /data/mount_1/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz /data/mount_2/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3

2024-11-05 11:31:48,573 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /home/fraimondo/test_datasets/aomic_id1000/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/output.nii.gz
2024-11-05 11:37:08,157 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/output.nii.gz is a prefix
Singularity args: --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/wV/mx/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_4
Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /data/mount_1/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/output.nii.gz
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/wV/mx/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /data/mount_1/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/output.nii.gz

2024-11-05 11:37:08,161 - JUNIFER - DEBUG - Adding BOLD to output
2024-11-05 11:37:08,203 - JUNIFER - INFO - Registering SphereAggregation in marker
2024-11-05 11:37:08,205 - JUNIFER - INFO - Registering ALFFSpheres in marker
2024-11-05 11:37:08,206 - JUNIFER - INFO - Computing BOLD
2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Extra data type for feature extraction: dict_keys(['T1w', 'Warp'])
2024-11-05 11:37:08,206 - JUNIFER - INFO - Calculating ALFF / fALFF for spheres
2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Calculating ALFF and fALFF
2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Creating cache for ALFF computation via AFNI
2024-11-05 11:37:08,207 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv
2024-11-05 11:37:11,937 - JUNIFER - INFO - 3dRSFC command to be executed:
3dRSFC -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff -input /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend
2024-11-05 11:37:41,528 - JUNIFER - INFO - 3dRSFC command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff is a prefix
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/input.nii is a file
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2
Corrected args for AFNI: 3dRSFC -prefix /data/mount_1/alff_falff -input /data/mount_2/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend
Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dRSFC -prefix /data/mount_1/alff_falff -input /data/mount_2/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend
++ 3dRSFC (from 3dBandpass by RW Cox): version THETA: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit]
++ Authored by: PA Taylor
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /data/mount_2/input.nii to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as /data/mount_2/input.nii,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
     3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/data/mount_2/input.nii is 6.023141 degrees from plumb.
++ Data length = 290  FFT length = 290
 + bandpass: ntime=290 nFFT=290 dt=2.2 dFreq=0.0015674 Nyquist=0.227273 passband indexes=6..51
++ Loading input dataset time series
++ No mask ==> processing all 382925 voxels
++ Bandpassing data time series
 +   -- remove mean
 +   -- FFTs
++ Creating output dataset in memory, then writing it
++ Output dataset /data/mount_1/alff_falff_LFF+orig.BRIK
++ Bandpassing data time series
 +   -- remove mean
++ Creating output dataset 2 in memory
++ Starting the (f)ALaFFel calcs

2024-11-05 11:37:41,528 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:37:41,529 - JUNIFER - INFO - 3dAFNItoNIFTI command to be executed:
3dAFNItoNIFTI -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/alff_0.01_0.08_None_output.nii /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_ALFF+orig.BRIK
2024-11-05 11:37:50,929 - JUNIFER - INFO - 3dAFNItoNIFTI command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/alff_0.01_0.08_None_output.nii is a prefix
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_ALFF+orig.BRIK is a file
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2
Corrected args for AFNI: 3dAFNItoNIFTI -prefix /data/mount_1/alff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_ALFF+orig.BRIK
Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dAFNItoNIFTI -prefix /data/mount_1/alff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_ALFF+orig.BRIK
++ 3dAFNItoNIFTI: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit]
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as /data/mount_2/alff_falff_ALFF+orig.BRIK,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
     3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/data/mount_2/alff_falff_ALFF+orig.BRIK is 6.023141 degrees from plumb.

2024-11-05 11:37:50,930 - JUNIFER - INFO - 3dAFNItoNIFTI command to be executed:
3dAFNItoNIFTI -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/falff_0.01_0.08_None_output.nii /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_fALFF+orig.BRIK
2024-11-05 11:38:01,573 - JUNIFER - INFO - 3dAFNItoNIFTI command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/falff_0.01_0.08_None_output.nii is a prefix
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_fALFF+orig.BRIK is a file
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2
Corrected args for AFNI: 3dAFNItoNIFTI -prefix /data/mount_1/falff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_fALFF+orig.BRIK
Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dAFNItoNIFTI -prefix /data/mount_1/falff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_fALFF+orig.BRIK
++ 3dAFNItoNIFTI: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit]
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as /data/mount_2/alff_falff_fALFF+orig.BRIK,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
     3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/data/mount_2/alff_falff_fALFF+orig.BRIK is 6.023141 degrees from plumb.

2024-11-05 11:38:01,599 - JUNIFER - DEBUG - Sphere aggregation using mean
2024-11-05 11:38:01,607 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv
2024-11-05 11:38:01,607 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:38:01,610 - JUNIFER - DEBUG - Using ANTs for coordinates transformation
2024-11-05 11:38:01,615 - JUNIFER - INFO - antsApplyTransformsToPoints command to be executed:
antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo/pretransform_coordinates.csv -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3/coordinates_transformed.csv -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5;
2024-11-05 11:38:11,929 - JUNIFER - INFO - antsApplyTransformsToPoints command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo/pretransform_coordinates.csv is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3/coordinates_transformed.csv is a prefix
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3
Corrected args for ANTS: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5

2024-11-05 11:38:11,931 - JUNIFER - DEBUG - Masking with inherit
2024-11-05 11:38:11,932 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv
2024-11-05 11:38:11,932 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:38:11,940 - JUNIFER - DEBUG - Using ANTs for mask warping
2024-11-05 11:38:11,942 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as/prewarp_mask.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju/mask_warped.nii.gz
2024-11-05 11:38:21,697 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as/prewarp_mask.nii.gz is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju/mask_warped.nii.gz is a prefix
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju:/data/mount_4
Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz

2024-11-05 11:38:21,698 - JUNIFER - DEBUG - Masking
2024-11-05 11:38:22,638 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,

2024-11-05 11:38:22,640 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide
  ret = um.true_divide(

2024-11-05 11:38:22,644 - JUNIFER - DEBUG - Sphere aggregation using mean
2024-11-05 11:38:22,646 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv
2024-11-05 11:38:22,647 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:38:22,650 - JUNIFER - DEBUG - Using ANTs for coordinates transformation
2024-11-05 11:38:22,651 - JUNIFER - INFO - antsApplyTransformsToPoints command to be executed:
antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j/pretransform_coordinates.csv -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris/coordinates_transformed.csv -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5;
2024-11-05 11:38:33,675 - JUNIFER - INFO - antsApplyTransformsToPoints command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j/pretransform_coordinates.csv is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris/coordinates_transformed.csv is a prefix
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3
Corrected args for ANTS: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5

2024-11-05 11:38:33,677 - JUNIFER - DEBUG - Masking with inherit
2024-11-05 11:38:33,677 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv
2024-11-05 11:38:33,679 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta
2024-11-05 11:38:33,686 - JUNIFER - DEBUG - Using ANTs for mask warping
2024-11-05 11:38:33,687 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o/prewarp_mask.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg/mask_warped.nii.gz
2024-11-05 11:38:43,446 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o/prewarp_mask.nii.gz is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file
/home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file
/home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg/mask_warped.nii.gz is a prefix
Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg:/data/mount_4
Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz
Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz

2024-11-05 11:38:43,449 - JUNIFER - DEBUG - Masking
2024-11-05 11:38:44,396 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,

2024-11-05 11:38:44,397 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide
  ret = um.true_divide(

2024-11-05 11:38:44,401 - JUNIFER - INFO - No storage specified, returning dictionary
2024-11-05 11:38:44,402 - JUNIFER - INFO - No storage specified, returning dictionary
2024-11-05 11:38:44,404 - JUNIFER - DEBUG - Cleaning up dataset
2024-11-05 11:38:44,405 - JUNIFER - DEBUG - Dropping files that were downloaded
2024-11-05 11:38:44,405 - JUNIFER - DEBUG - Dataset state restored
2024-11-05 11:38:44,574 - JUNIFER - DEBUG - Clearing cache for ALFF computation via AFNI

Anything else?

No response

### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior When computing any marker on coordinates in native space, the coordinates in native space do not match the corresponding landmark in MNI space. These are two examples in which the left (MNI space) do not match the right (T1w space). In this first example, the coordinates are off-brain: ![Screenshot 2024-11-06 at 10 04 17 (2)](https://github.com/user-attachments/assets/e3a9c589-4b65-4400-ad82-0df1ecdec433) In this second example, the coordinates are in the brain, but not in the same landmark: ![Screenshot 2024-11-06 at 10 06 17 (2)](https://github.com/user-attachments/assets/74a3ab21-c27c-42f8-b3c2-d7a5c1c97c81) ### Expected Behavior I expect that the coordinates point to the right landmark. ### Steps To Reproduce 1. With latest junifer (main branch) 2. Modify the `WorkdirManager` code so that temporary directories are not cleaned. 3. Compute (f)ALFF on Aomic's `sub-0001` using `"Power2011"` using this script: ``` # %% import pickle from junifer.datagrabber.aomic import DataladAOMICID1000 from junifer.utils import configure_logging from junifer.pipeline import WorkDirManager configure_logging(level="DEBUG") WorkDirManager( workdir="/home/fraimondo/dev/scratch/test_junifer_native/temp", cleanup=False, ) element = "sub-0001" # %% Load data dg = DataladAOMICID1000( native_t1w=True, datadir="/home/fraimondo/test_datasets/aomic_id1000/", types=["BOLD", "T1w", "Warp"] ) with dg: data = dg[element] # %% Read data from junifer.datareader import DefaultDataReader reader = DefaultDataReader() data = reader.fit_transform(data) pickle.dump(data, open(f"aomic_{element}_read.pkl", "wb")) # # %% Preprocess from junifer.preprocess import fMRIPrepConfoundRemover confound = fMRIPrepConfoundRemover( detrend=True, standardize=True, strategy={ "motion": "full", "wm_csf": "full", "global_signal": "full", }, # masks=["inherit", "compute_epi_mask", {"threshold": 0}], masks=["inherit"], ) data = confound.fit_transform(data) pickle.dump(data, open(f"aomic_{element}_deconfounded.pkl", "wb")) # %% Warp from junifer.preprocess import SpaceWarper warper = SpaceWarper(reference="T1w", on="BOLD", using="ants") data = warper.fit_transform(data) pickle.dump(data, open(f"aomic_{element}_warped.pkl", "wb")) # %% Compute marker # data = pickle.load(open(f"aomic_{element}_warped.pkl", "rb")) from junifer.markers import ALFFSpheres marker = ALFFSpheres( coords="Power2011", radius=5, allow_overlap=True, using="afni", agg_method="mean", highpass=0.01, lowpass=0.08, masks="inherit", ) out = marker.fit_transform(data) pickle.dump(out, open(f"aomic_{element}_out.pkl", "wb")) ``` 4. Check the output and temporary directory and find the pretransformed and transformed coordinates. Visualize them in the MNI and T1w images. ### Environment ```markdown junifer: version: 0.0.6.dev176 python: version: 3.12.6 implementation: CPython dependencies: click: 8.1.7 numpy: 1.26.4 scipy: 1.14.1 datalad: 1.1.3 pandas: 2.2.2 nibabel: 5.2.1 ruamel.yaml: 0.17.40 looseversion: None system: platform: Linux-6.6.13+bpo-amd64-x86_64-with-glibc2.36 environment: PATH: /data/group/appliedml/tools/ants_2.5.0/binaries:/home/fraimondo/miniconda3/envs/junifer/bin:/home/fraimondo/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/games ``` ### Relevant log output ```shell [WARNING] Requested extension 'next' is not available 2024-11-05 11:23:10,090 - JUNIFER - INFO - ===== Lib Versions ===== 2024-11-05 11:23:10,090 - JUNIFER - INFO - numpy: 1.26.4 2024-11-05 11:23:10,090 - JUNIFER - INFO - junifer: 0.0.6.dev176 2024-11-05 11:23:10,090 - JUNIFER - INFO - ======================== 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - Initializing PatternDataladDataGrabber 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - types = ['BOLD', 'T1w', 'Warp'] 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - datadir = /home/fraimondo/test_datasets/aomic_id1000/ 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - uri = https://github.com/OpenNeuroDatasets/ds003097.git 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - patterns = {'BOLD': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'space': 'MNI152NLin2009cAsym', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'confounds': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_desc-confounds_regressors.tsv', 'format': 'fmriprep'}}, 'T1w': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-preproc_T1w.nii.gz', 'space': 'native', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-brain_mask.nii.gz', 'space': 'native'}}, 'VBM_CSF': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_GM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_WM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'DWI': {'pattern': 'derivatives/dwipreproc/{subject}/dwi/{subject}_desc-preproc_dwi.nii.gz'}, 'FreeSurfer': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]', 'aseg': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]'}, 'norm': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]'}, 'lh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]'}, 'rh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]'}, 'lh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]'}, 'rh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]'}}, 'Warp': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'src': 'MNI152NLin2009cAsym', 'dst': 'native'}} 2024-11-05 11:23:10,090 - JUNIFER - DEBUG - replacements = ['subject'] 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - confounds_format = fmriprep 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for BOLD 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mask` found for BOLD 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD.mask 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for BOLD.mask 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `confounds` found for BOLD 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for BOLD.confounds 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `format` found for BOLD.confounds 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mappings` found for BOLD.confounds 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for T1w 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for T1w 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Optional key: `mask` found for T1w 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for T1w.mask 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `space` found for T1w.mask 2024-11-05 11:23:10,091 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_CSF 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_CSF 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_GM 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_GM 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for VBM_WM 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `space` found for VBM_WM 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for DWI 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `aseg` found for FreeSurfer 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.aseg 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `norm` found for FreeSurfer 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.norm 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `lh_white` found for FreeSurfer 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.lh_white 2024-11-05 11:23:10,092 - JUNIFER - DEBUG - Optional key: `rh_white` found for FreeSurfer 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.rh_white 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Optional key: `lh_pial` found for FreeSurfer 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.lh_pial 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Optional key: `rh_pial` found for FreeSurfer 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for FreeSurfer.rh_pial 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `pattern` found for Warp 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `src` found for Warp 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Mandatory key: `dst` found for Warp 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing BaseDataGrabber 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - _datadir = /home/fraimondo/test_datasets/aomic_id1000 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - types = ['BOLD', 'T1w', 'Warp'] 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing PatternDataGrabber 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - patterns = {'BOLD': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'space': 'MNI152NLin2009cAsym', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'confounds': {'pattern': 'derivatives/fmriprep/{subject}/func/{subject}_task-moviewatching_desc-confounds_regressors.tsv', 'format': 'fmriprep'}}, 'T1w': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-preproc_T1w.nii.gz', 'space': 'native', 'mask': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_desc-brain_mask.nii.gz', 'space': 'native'}}, 'VBM_CSF': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_GM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_WM': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'DWI': {'pattern': 'derivatives/dwipreproc/{subject}/dwi/{subject}_desc-preproc_dwi.nii.gz'}, 'FreeSurfer': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]', 'aseg': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]'}, 'norm': {'pattern': 'derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]'}, 'lh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]'}, 'rh_white': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]'}, 'lh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]'}, 'rh_pial': {'pattern': 'derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]'}}, 'Warp': {'pattern': 'derivatives/fmriprep/{subject}/anat/{subject}_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'src': 'MNI152NLin2009cAsym', 'dst': 'native'}} 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - replacements = ['subject'] 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - confounds_format = fmriprep 2024-11-05 11:23:10,093 - JUNIFER - DEBUG - Initializing DataladDataGrabber 2024-11-05 11:23:10,094 - JUNIFER - DEBUG - uri = https://github.com/OpenNeuroDatasets/ds003097.git 2024-11-05 11:23:10,094 - JUNIFER - DEBUG - _rootdir = . [DEBUG ] Run ['git', 'version'] (protocol_class=StdOutErrCapture) (cwd=None) [DEBUG ] Finished ['git', 'version'] with status 0 [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0 [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] with status 0 2024-11-05 11:23:10,106 - JUNIFER - DEBUG - Dataset already installed 2024-11-05 11:23:10,106 - JUNIFER - DEBUG - Querying https://github.com/OpenNeuroDatasets/ds003097.git for dataset ID [DEBUG ] Git clone from https://github.com/OpenNeuroDatasets/ds003097.git to /tmp/tmpuuwkuaq4 [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'clone', '--progress', '-n', '--depth=1', 'https://github.com/OpenNeuroDatasets/ds003097.git', '/tmp/tmpuuwkuaq4'] (protocol_class=GitProgress) (cwd=None) [DEBUG ] Non-progress stderr: b"Cloning into '/tmp/tmpuuwkuaq4'...\n" [DEBUG ] Non-progress stderr: b'remote: Total 362591 (delta 6578), reused 362588 (delta 6578), pack-reused 0 (from 0) \n' [DEBUG ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'clone', '--progress', '-n', '--depth=1', 'https://github.com/OpenNeuroDatasets/ds003097.git', '/tmp/tmpuuwkuaq4'] with status 0 [DEBUG ] Git clone completed [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0 [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'checkout', 'HEAD', '.datalad/config'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4) [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/tmp/tmpuuwkuaq4/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/tmp/tmpuuwkuaq4) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/tmp/tmpuuwkuaq4/.datalad/config'] with status 0 2024-11-05 11:23:37,338 - JUNIFER - DEBUG - Got remote dataset ID = aefe5438-e93b-11ea-ad4c-8e2245da6db7 [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0 [DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] (protocol_class=StdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin', '--file', '/home/fraimondo/test_datasets/aomic_id1000/.datalad/config'] with status 0 [DEBUG ] Determined class of decorated function: <class 'datalad.core.local.status.Status'> [DEBUG ] Resolved dataset to report status: /home/fraimondo/test_datasets/aomic_id1000 [DEBUG ] Querying AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).diffstatus() for paths: None [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...) [DEBUG ] Query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory'] [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Done query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory'] [DEBUG ] Done AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...) [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '-z', '-m', '-d'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...) [DEBUG ] Query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l'] [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Done query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l'] [DEBUG ] Done AnnexRepo(/home/fraimondo/test_datasets/aomic_id1000).get_content_info(...) nothing to save, working tree clean 2024-11-05 11:30:56,369 - JUNIFER - DEBUG - Dataset is clean [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'symbolic-ref', 'HEAD'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/fraimondo/test_datasets/aomic_id1000) 2024-11-05 11:30:56,483 - JUNIFER - INFO - Getting element sub-0001 2024-11-05 11:30:56,484 - JUNIFER - DEBUG - Named element: {'subject': 'sub-0001'} 2024-11-05 11:30:56,484 - JUNIFER - INFO - Resolving path from pattern for BOLD 2024-11-05 11:30:56,486 - JUNIFER - INFO - Resolving path from pattern for BOLD.mask 2024-11-05 11:30:56,487 - JUNIFER - INFO - Resolving path from pattern for BOLD.confounds 2024-11-05 11:30:56,487 - JUNIFER - INFO - Resolving path from pattern for T1w 2024-11-05 11:30:56,488 - JUNIFER - INFO - Resolving path from pattern for T1w.mask 2024-11-05 11:30:56,489 - JUNIFER - INFO - Resolving path from pattern for Warp 2024-11-05 11:30:56,489 - JUNIFER - DEBUG - Getting 6 files using datalad: 2024-11-05 11:30:56,489 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz 2024-11-05 11:30:56,490 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv 2024-11-05 11:30:56,490 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz 2024-11-05 11:30:56,490 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz 2024-11-05 11:30:56,490 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz 2024-11-05 11:30:56,491 - JUNIFER - DEBUG - : /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 [DEBUG ] Determined class of decorated function: <class 'datalad.distribution.get.Get'> [DEBUG ] Resolved dataset to get content of <<[PosixPath('/h++872 chars++5')]>>: /home/fraimondo/test_datasets/aomic_id1000 [DEBUG ] Determined class of decorated function: <class 'datalad.local.subdatasets.Subdatasets'> [DEBUG ] Resolved dataset to report on subdataset(s): /home/fraimondo/test_datasets/aomic_id1000 [DEBUG ] Query subdatasets of Dataset(/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Determine what files match the query to work with [DEBUG ] Run ['git', 'annex', 'version', '--raw'] (protocol_class=StdOutErrCapture) (cwd=None) [DEBUG ] Finished ['git', 'annex', 'version', '--raw'] with status 0 [DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', '-c', 'annex.merge-annex-branches=false', 'annex', 'find', '--not', '--in', '.', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv'] (protocol_class=AnnexJsonProtocol) (cwd=/home/fraimondo/test_datasets/aomic_id1000) [DEBUG ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', '-c', 'annex.merge-annex-branches=false', 'annex', 'find', '--not', '--in', '.', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz', 'derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv'] with status 0 [DEBUG ] No files found needing fetching. [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz)] [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5)] [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz)] [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz)] [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz)] [DEBUG ] already present [get(/home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv)] 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - File /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv was already present 2024-11-05 11:30:56,561 - JUNIFER - DEBUG - Get done 2024-11-05 11:30:56,900 - JUNIFER - INFO - Registering DefaultDataReader in datareader 2024-11-05 11:30:56,900 - JUNIFER - INFO - Reading BOLD.mask from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz 2024-11-05 11:30:56,900 - JUNIFER - INFO - BOLD.mask is of type NIFTI 2024-11-05 11:30:56,900 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {} 2024-11-05 11:30:56,902 - JUNIFER - INFO - Reading BOLD.confounds from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_desc-confounds_regressors.tsv 2024-11-05 11:30:56,902 - JUNIFER - INFO - BOLD.confounds is of type TSV 2024-11-05 11:30:56,902 - JUNIFER - DEBUG - Calling <function read_csv at 0x150404975a80> with {'sep': '\t'} 2024-11-05 11:30:56,916 - JUNIFER - INFO - Reading BOLD from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/func/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz 2024-11-05 11:30:56,916 - JUNIFER - INFO - BOLD is of type NIFTI 2024-11-05 11:30:56,916 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {} 2024-11-05 11:30:56,918 - JUNIFER - INFO - Reading T1w.mask from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-brain_mask.nii.gz 2024-11-05 11:30:56,918 - JUNIFER - INFO - T1w.mask is of type NIFTI 2024-11-05 11:30:56,918 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {} 2024-11-05 11:30:56,920 - JUNIFER - INFO - Reading T1w from /home/fraimondo/test_datasets/aomic_id1000/derivatives/fmriprep/sub-0001/anat/sub-0001_desc-preproc_T1w.nii.gz 2024-11-05 11:30:56,920 - JUNIFER - INFO - T1w is of type NIFTI 2024-11-05 11:30:56,920 - JUNIFER - DEBUG - Calling <function load at 0x1504037cc540> with {} 2024-11-05 11:31:01,281 - JUNIFER - INFO - Registering fMRIPrepConfoundRemover in preprocessing 2024-11-05 11:31:01,282 - JUNIFER - INFO - Preprocessing BOLD 2024-11-05 11:31:01,282 - JUNIFER - DEBUG - Extra data type for preprocess: dict_keys(['T1w', 'Warp']) 2024-11-05 11:31:03,638 - JUNIFER - INFO - No `t_r` specified, using t_r from NIfTI header 2024-11-05 11:31:03,638 - JUNIFER - INFO - Read t_r from NIfTI header: 2.200000047683716 2024-11-05 11:31:03,639 - JUNIFER - DEBUG - Masking with ['inherit'] 2024-11-05 11:31:03,639 - JUNIFER - DEBUG - Setting up temporary directory under /home/fraimondo/dev/scratch/test_junifer_native/temp 2024-11-05 11:31:03,640 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv -> Overall 2024-11-05 11:31:03,641 - JUNIFER - DEBUG - Setting up element directory under /home/fraimondo/dev/scratch/test_junifer_native/temp 2024-11-05 11:31:03,642 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta -> Element 2024-11-05 11:31:03,642 - JUNIFER - DEBUG - Setting `BOLD.mask` 2024-11-05 11:31:03,642 - JUNIFER - INFO - Cleaning image using nilearn 2024-11-05 11:31:03,643 - JUNIFER - DEBUG - detrend: True 2024-11-05 11:31:03,643 - JUNIFER - DEBUG - standardize: True 2024-11-05 11:31:03,643 - JUNIFER - DEBUG - low_pass: None 2024-11-05 11:31:03,643 - JUNIFER - DEBUG - high_pass: None 2024-11-05 11:31:05,236 - JUNIFER - DEBUG - Adding BOLD to output 2024-11-05 11:31:05,644 - JUNIFER - INFO - Registering SpaceWarper in preprocessing 2024-11-05 11:31:35,855 - JUNIFER - WARNING - /home/fraimondo/dev/tbox/junifer/junifer/pipeline/utils.py:248: RuntimeWarning: ANTs is installed but some of the required commands were not found. These are the results: {'ResampleImage': 'not found', 'antsApplyTransforms': 'not found'} warn_with_log( 2024-11-05 11:31:35,855 - JUNIFER - INFO - Preprocessing BOLD 2024-11-05 11:31:35,855 - JUNIFER - DEBUG - Extra data type for preprocess: dict_keys(['T1w', 'Warp']) 2024-11-05 11:31:35,855 - JUNIFER - INFO - Warping to T1w space using SpaceWarper 2024-11-05 11:31:35,855 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:31:35,857 - JUNIFER - DEBUG - Using ANTs for space warping 2024-11-05 11:31:35,858 - JUNIFER - INFO - ResampleImage command to be executed: "sub-0001_desc-preproc_T1w.nii.gz" ResampleImage 3 /home/fraimondo/test_datasets/aomic_id1000/sub-0001_desc-preproc_T1w.nii.gz /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3 2024-11-05 11:31:48,572 - JUNIFER - INFO - ResampleImage command succeeded with the following output: /home/fraimondo/test_datasets/aomic_id1000/sub-0001_desc-preproc_T1w.nii.gz is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a prefix Singularity args: --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/91/63/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 Corrected args for ANTS: ResampleImage 3 /data/mount_1/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz /data/mount_2/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3 Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/91/63/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif ResampleImage 3 /data/mount_1/MD5E-s31808414--24945231a2d73d0d08c4e402abd2f866.nii.gz /data/mount_2/resampled_reference.nii.gz 3.0x3.0x3.0 0 3 3 2024-11-05 11:31:48,573 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /home/fraimondo/test_datasets/aomic_id1000/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/output.nii.gz 2024-11-05 11:37:08,157 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: /home/fraimondo/test_datasets/aomic_id1000/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/output.nii.gz is a prefix Singularity args: --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/wV/mx/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_4 Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /data/mount_1/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/output.nii.gz Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/wV/mx/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n LanczosWindowedSinc -i /data/mount_1/sub-0001_task-moviewatching_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/output.nii.gz 2024-11-05 11:37:08,161 - JUNIFER - DEBUG - Adding BOLD to output 2024-11-05 11:37:08,203 - JUNIFER - INFO - Registering SphereAggregation in marker 2024-11-05 11:37:08,205 - JUNIFER - INFO - Registering ALFFSpheres in marker 2024-11-05 11:37:08,206 - JUNIFER - INFO - Computing BOLD 2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Extra data type for feature extraction: dict_keys(['T1w', 'Warp']) 2024-11-05 11:37:08,206 - JUNIFER - INFO - Calculating ALFF / fALFF for spheres 2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Calculating ALFF and fALFF 2024-11-05 11:37:08,206 - JUNIFER - DEBUG - Creating cache for ALFF computation via AFNI 2024-11-05 11:37:08,207 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv 2024-11-05 11:37:11,937 - JUNIFER - INFO - 3dRSFC command to be executed: 3dRSFC -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff -input /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend 2024-11-05 11:37:41,528 - JUNIFER - INFO - 3dRSFC command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff is a prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/input.nii is a file Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 Corrected args for AFNI: 3dRSFC -prefix /data/mount_1/alff_falff -input /data/mount_2/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dRSFC -prefix /data/mount_1/alff_falff -input /data/mount_2/input.nii -band 0.01 0.08 -no_rsfa -nosat -nodetrend ++ 3dRSFC (from 3dBandpass by RW Cox): version THETA: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit] ++ Authored by: PA Taylor ** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /data/mount_2/input.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /data/mount_2/input.nii, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:/data/mount_2/input.nii is 6.023141 degrees from plumb. ++ Data length = 290 FFT length = 290 + bandpass: ntime=290 nFFT=290 dt=2.2 dFreq=0.0015674 Nyquist=0.227273 passband indexes=6..51 ++ Loading input dataset time series ++ No mask ==> processing all 382925 voxels ++ Bandpassing data time series + -- remove mean + -- FFTs ++ Creating output dataset in memory, then writing it ++ Output dataset /data/mount_1/alff_falff_LFF+orig.BRIK ++ Bandpassing data time series + -- remove mean ++ Creating output dataset 2 in memory ++ Starting the (f)ALaFFel calcs 2024-11-05 11:37:41,528 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:37:41,529 - JUNIFER - INFO - 3dAFNItoNIFTI command to be executed: 3dAFNItoNIFTI -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/alff_0.01_0.08_None_output.nii /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_ALFF+orig.BRIK 2024-11-05 11:37:50,929 - JUNIFER - INFO - 3dAFNItoNIFTI command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/alff_0.01_0.08_None_output.nii is a prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_ALFF+orig.BRIK is a file Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 Corrected args for AFNI: 3dAFNItoNIFTI -prefix /data/mount_1/alff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_ALFF+orig.BRIK Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dAFNItoNIFTI -prefix /data/mount_1/alff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_ALFF+orig.BRIK ++ 3dAFNItoNIFTI: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /data/mount_2/alff_falff_ALFF+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:/data/mount_2/alff_falff_ALFF+orig.BRIK is 6.023141 degrees from plumb. 2024-11-05 11:37:50,930 - JUNIFER - INFO - 3dAFNItoNIFTI command to be executed: 3dAFNItoNIFTI -prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/falff_0.01_0.08_None_output.nii /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_fALFF+orig.BRIK 2024-11-05 11:38:01,573 - JUNIFER - INFO - 3dAFNItoNIFTI command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w/falff_0.01_0.08_None_output.nii is a prefix /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e/alff_falff_fALFF+orig.BRIK is a file Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 Corrected args for AFNI: 3dAFNItoNIFTI -prefix /data/mount_1/falff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_fALFF+orig.BRIK Running command: /data/group/appliedml/tools/afni_24.1.19/singularity_cmd exec --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/afni_alff_falffspjg0j9w:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/afni_alff+falff9nbdly1e:/data/mount_2 /data/group/appliedml/tools/afni_24.1.19/afni_make_build_AFNI_24.1.19.sif 3dAFNItoNIFTI -prefix /data/mount_1/falff_0.01_0.08_None_output.nii /data/mount_2/alff_falff_fALFF+orig.BRIK ++ 3dAFNItoNIFTI: AFNI version=AFNI_24.1.19 (Jun 14 2024) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /data/mount_2/alff_falff_fALFF+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:/data/mount_2/alff_falff_fALFF+orig.BRIK is 6.023141 degrees from plumb. 2024-11-05 11:38:01,599 - JUNIFER - DEBUG - Sphere aggregation using mean 2024-11-05 11:38:01,607 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv 2024-11-05 11:38:01,607 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:38:01,610 - JUNIFER - DEBUG - Using ANTs for coordinates transformation 2024-11-05 11:38:01,615 - JUNIFER - INFO - antsApplyTransformsToPoints command to be executed: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo/pretransform_coordinates.csv -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3/coordinates_transformed.csv -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5; 2024-11-05 11:38:11,929 - JUNIFER - INFO - antsApplyTransformsToPoints command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo/pretransform_coordinates.csv is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3/coordinates_transformed.csv is a prefix /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 Corrected args for ANTS: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates03pg_fuo:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatestdyr5io3:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 2024-11-05 11:38:11,931 - JUNIFER - DEBUG - Masking with inherit 2024-11-05 11:38:11,932 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv 2024-11-05 11:38:11,932 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:38:11,940 - JUNIFER - DEBUG - Using ANTs for mask warping 2024-11-05 11:38:11,942 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as/prewarp_mask.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju/mask_warped.nii.gz 2024-11-05 11:38:21,697 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as/prewarp_mask.nii.gz is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju/mask_warped.nii.gz is a prefix Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju:/data/mount_4 Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/maskssgpc42as:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/masksh0jb15ju:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz 2024-11-05 11:38:21,698 - JUNIFER - DEBUG - Masking 2024-11-05 11:38:22,638 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, 2024-11-05 11:38:22,640 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide ret = um.true_divide( 2024-11-05 11:38:22,644 - JUNIFER - DEBUG - Sphere aggregation using mean 2024-11-05 11:38:22,646 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv 2024-11-05 11:38:22,647 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:38:22,650 - JUNIFER - DEBUG - Using ANTs for coordinates transformation 2024-11-05 11:38:22,651 - JUNIFER - INFO - antsApplyTransformsToPoints command to be executed: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j/pretransform_coordinates.csv -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris/coordinates_transformed.csv -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5; 2024-11-05 11:38:33,675 - JUNIFER - INFO - antsApplyTransformsToPoints command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j/pretransform_coordinates.csv is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris/coordinates_transformed.csv is a prefix /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 Corrected args for ANTS: antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/coordinates5hfj5d4j:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/coordinatesqemgqris:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransformsToPoints -d 3 -p 1 -f 0 -i /data/mount_1/pretransform_coordinates.csv -o /data/mount_2/coordinates_transformed.csv -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 2024-11-05 11:38:33,677 - JUNIFER - DEBUG - Masking with inherit 2024-11-05 11:38:33,677 - JUNIFER - DEBUG - Creating temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv 2024-11-05 11:38:33,679 - JUNIFER - DEBUG - Creating element temporary directory at /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta 2024-11-05 11:38:33,686 - JUNIFER - DEBUG - Using ANTs for mask warping 2024-11-05 11:38:33,687 - JUNIFER - INFO - antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o/prewarp_mask.nii.gz -r /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz -t /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg/mask_warped.nii.gz 2024-11-05 11:38:43,446 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output: /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o/prewarp_mask.nii.gz is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_/resampled_reference.nii.gz is a file /home/fraimondo/test_datasets/aomic_id1000/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 is a file /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg/mask_warped.nii.gz is a prefix Singularity args: --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg:/data/mount_4 Corrected args for ANTS: antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz Running command: /data/group/appliedml/tools/ants_2.5.0/singularity_cmd exec --cleanenv --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpt2qgzhuv/masksdreztg7o:/data/mount_1 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/ants_warperlzyoyrg_:/data/mount_2 --bind /home/fraimondo/test_datasets/aomic_id1000/.git/annex/objects/Zf/zk/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5:/data/mount_3 --bind /home/fraimondo/dev/scratch/test_junifer_native/temp/tmpqlhylwta/maskso_3or_bg:/data/mount_4 /data/group/appliedml/tools/ants_2.5.0/ants_v2.5.0.sif antsApplyTransforms -d 3 -e 3 -n GenericLabel[NearestNeighbor] -i /data/mount_1/prewarp_mask.nii.gz -r /data/mount_2/resampled_reference.nii.gz -t /data/mount_3/sub-0001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -o /data/mount_4/mask_warped.nii.gz 2024-11-05 11:38:43,449 - JUNIFER - DEBUG - Masking 2024-11-05 11:38:44,396 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, 2024-11-05 11:38:44,397 - JUNIFER - WARNING - /home/fraimondo/miniconda3/envs/junifer/lib/python3.12/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide ret = um.true_divide( 2024-11-05 11:38:44,401 - JUNIFER - INFO - No storage specified, returning dictionary 2024-11-05 11:38:44,402 - JUNIFER - INFO - No storage specified, returning dictionary 2024-11-05 11:38:44,404 - JUNIFER - DEBUG - Cleaning up dataset 2024-11-05 11:38:44,405 - JUNIFER - DEBUG - Dropping files that were downloaded 2024-11-05 11:38:44,405 - JUNIFER - DEBUG - Dataset state restored 2024-11-05 11:38:44,574 - JUNIFER - DEBUG - Clearing cache for ALFF computation via AFNI ``` ### Anything else? _No response_
fraimondo commented 2024-11-06 12:42:43 +00:00 (Migrated from github.com)
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This is due to two key differences between fsl and ANTs:

  1. Coordinates in ANTs are in LPS and not RAS
  2. antsApplyTransformsToPoints expects the inverse transform.

Solutions:

  1. Invert the sign of the x and y coordinates before saving the file in the antsApplyTransformsToPoints and do the same after reading the coordinates from the output file.
  2. Select the opposite transformation file.
This is due to two key differences between fsl and ANTs: 1) Coordinates in ANTs are in LPS and not RAS 2) `antsApplyTransformsToPoints` expects the inverse transform. Solutions: 1) Invert the sign of the x and y coordinates before saving the file in the `antsApplyTransformsToPoints` and do the same after reading the coordinates from the output file. 2) Select the opposite transformation file.
codecov[bot] commented 2024-11-13 12:13:50 +00:00 (Migrated from github.com)
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junifer/data/coordinates/_coordinates.py 85.71% <ø> (ø)
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synchon commented 2024-11-13 12:14:21 +00:00 (Migrated from github.com)
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@fraimondo Can you please check if this solves your issue?

@fraimondo Can you please check if this solves your issue?
github-actions[bot] commented 2024-11-13 12:23:10 +00:00 (Migrated from github.com)
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PR Preview Action v1.4.8
Preview removed because the pull request was closed.
2024-11-19 12:38 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.8 :---: Preview removed because the pull request was closed. 2024-11-19 12:38 UTC <!-- Sticky Pull Request Commentpr-preview -->
fraimondo commented 2024-11-18 19:42:57 +00:00 (Migrated from github.com)
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I can confirm that this code now provides the right transform for the two coordinates displayed in the issue.

I can confirm that this code now provides the right transform for the two coordinates displayed in the issue.
fraimondo (Migrated from github.com) requested changes 2024-11-18 19:44:34 +00:00
junifer/data/coordinates/_ants_coordinates_warper.py
@ -57,3 +57,3 @@
pretransform_coordinates_path = (
element_tempdir / "pretransform_coordinates.txt"
element_tempdir / "pretransform_coordinates.csv"
)
fraimondo (Migrated from github.com) commented 2024-11-18 19:44:14 +00:00
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can we just do x[0] *= -1... It's more easy to read than a lambda function to multiply two axis by -1 and another axis by 1.

can we just do `x[0] *= -1`... It's more easy to read than a lambda function to multiply two axis by -1 and another axis by 1.
junifer/data/coordinates/_ants_coordinates_warper.py
fraimondo (Migrated from github.com) commented 2024-11-18 19:44:20 +00:00
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Same as above.

Same as above.
synchon (Migrated from github.com) reviewed 2024-11-19 10:06:24 +00:00
junifer/data/coordinates/_ants_coordinates_warper.py
@ -57,3 +57,3 @@
pretransform_coordinates_path = (
element_tempdir / "pretransform_coordinates.txt"
element_tempdir / "pretransform_coordinates.csv"
)
synchon (Migrated from github.com) commented 2024-11-19 10:06:24 +00:00
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Not sure I follow, could you please show what L63 should be?

Not sure I follow, could you please show what L63 should be?
fraimondo (Migrated from github.com) reviewed 2024-11-19 11:29:55 +00:00
junifer/data/coordinates/_ants_coordinates_warper.py
@ -57,3 +57,3 @@
pretransform_coordinates_path = (
element_tempdir / "pretransform_coordinates.txt"
element_tempdir / "pretransform_coordinates.csv"
)
fraimondo (Migrated from github.com) commented 2024-11-19 11:29:55 +00:00
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before L60

# Convert LPS to RAS
seeds[:, 0] *= -1
seeds[:, 1] *= -1
before L60 ```python # Convert LPS to RAS seeds[:, 0] *= -1 seeds[:, 1] *= -1 ```
fraimondo (Migrated from github.com) approved these changes 2024-11-19 11:58:17 +00:00
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