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Code Issues 14 Pull requests 2 Packages Activity Actions

Follow the datasets BIDS convention for participants/sessions #325

Merged
fraimondo merged 4 commits from fix/bids into main 2024-04-05 15:06:25 +00:00
Conversation 3 Commits 4 Files changed 18 +200 -199
18 changed files with 200 additions and 199 deletions
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1
docs/changes/newsfragments/325.change Normal file
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@ -0,0 +1 @@
Change the subject and session patterns for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` so that they are consistent with their own ``"participants.tsv"`` file by `Fede Raimondo`_

2
junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py
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@ -33,7 +33,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
patterns = { patterns = {
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz" "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
), ),
"space": "IXI549Space", "space": "IXI549Space",
}, },

2
junifer/configs/juseless/datagrabbers/camcan_vbm.py
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@ -36,7 +36,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
replacements = ["subject"] replacements = ["subject"]
patterns = { patterns = {
"VBM_GM": { "VBM_GM": {
"pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz", "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
"space": "IXI549Space", "space": "IXI549Space",
}, },
} }

2
junifer/configs/juseless/datagrabbers/ixi_vbm.py
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@ -45,7 +45,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
patterns = { patterns = {
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz" "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
), ),
"space": "IXI549Space", "space": "IXI549Space",
}, },

12
junifer/configs/juseless/datagrabbers/ucla.py
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@ -72,42 +72,42 @@ class JuselessUCLA(PatternDataGrabber):
patterns = { patterns = {
"BOLD": { "BOLD": {
"pattern": ( "pattern": (
"sub-{subject}/func/sub-{subject}_task-{task}_bold_space-" "{subject}/func/{subject}_task-{task}_bold_space-"
"MNI152NLin2009cAsym_preproc.nii.gz" "MNI152NLin2009cAsym_preproc.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"BOLD_confounds": { "BOLD_confounds": {
"pattern": ( "pattern": (
"sub-{subject}/func/sub-{subject}_" "{subject}/func/{subject}_"
"task-{task}_bold_confounds.tsv" "task-{task}_bold_confounds.tsv"
), ),
"space": "fmriprep", "space": "fmriprep",
}, },
"T1w": { "T1w": {
"pattern": ( "pattern": (
"sub-{subject}/anat/sub-{subject}_" "{subject}/anat/{subject}_"
"T1w_space-MNI152NLin2009cAsym_preproc.nii.gz" "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_CSF": { "VBM_CSF": {
"pattern": ( "pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space-" "{subject}/anat/{subject}_T1w_space-"
"MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz" "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space-" "{subject}/anat/{subject}_T1w_space-"
"MNI152NLin2009cAsym_class-GM_probtissue.nii.gz" "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_WM": { "VBM_WM": {
"pattern": ( "pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space" "{subject}/anat/{subject}_T1w_space"
"-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz" "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",

2
junifer/configs/juseless/datagrabbers/ukb_vbm.py
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@ -34,7 +34,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
replacements = ["subject", "session"] replacements = ["subject", "session"]
patterns = { patterns = {
"VBM_GM": { "VBM_GM": {
"pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz", "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
"space": "IXI549Space", "space": "IXI549Space",
}, },
} }

4
junifer/data/tests/test_masks.py
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@ -96,14 +96,14 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
""" """
with DMCC13Benchmark( with DMCC13Benchmark(
types=["BOLD"], types=["BOLD"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=True, native_t1w=True,
) as dg: ) as dg:
element_data = DefaultDataReader().fit_transform( element_data = DefaultDataReader().fit_transform(
dg[("f1031ax", "wave1bas", "Rest", "AP", "1")] dg[("sub-f1031ax", "ses-wave1bas", "Rest", "AP", "1")]
) )
mask = compute_brain_mask( mask = compute_brain_mask(
target_data=element_data["BOLD"], target_data=element_data["BOLD"],

48
junifer/datagrabber/aomic/id1000.py
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@ -43,8 +43,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
patterns = { patterns = {
"BOLD": { "BOLD": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-moviewatching_" "{subject}_task-moviewatching_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -52,16 +52,16 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
}, },
"BOLD_confounds": { "BOLD_confounds": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-moviewatching_" "{subject}_task-moviewatching_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
), ),
"format": "fmriprep", "format": "fmriprep",
}, },
"BOLD_mask": { "BOLD_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-moviewatching_" "{subject}_task-moviewatching_"
"space-MNI152NLin2009cAsym_" "space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz" "desc-brain_mask.nii.gz"
), ),
@ -69,8 +69,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
}, },
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -78,40 +78,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz" "desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_CSF": { "VBM_CSF": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_WM": { "VBM_WM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"DWI": { "DWI": {
"pattern": ( "pattern": (
"derivatives/dwipreproc/sub-{subject}/dwi/" "derivatives/dwipreproc/{subject}/dwi/"
"sub-{subject}_desc-preproc_dwi.nii.gz" "{subject}_desc-preproc_dwi.nii.gz"
), ),
}, },
} }
@ -123,23 +123,23 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
{ {
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz" "{subject}_desc-preproc_T1w.nii.gz"
), ),
"space": "native", "space": "native",
"mask_item": "T1w_mask", "mask_item": "T1w_mask",
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz" "{subject}_desc-brain_mask.nii.gz"
), ),
"space": "native", "space": "native",
}, },
"Warp": { "Warp": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_" "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5" "mode-image_xfm.h5"
), ),
"src": "MNI152NLin2009cAsym", "src": "MNI152NLin2009cAsym",

50
junifer/datagrabber/aomic/piop1.py
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@ -79,8 +79,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
patterns = { patterns = {
"BOLD": { "BOLD": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -88,24 +88,24 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
}, },
"BOLD_confounds": { "BOLD_confounds": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
), ),
"format": "fmriprep", "format": "fmriprep",
}, },
"BOLD_mask": { "BOLD_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz" "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -113,40 +113,40 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz" "desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_CSF": { "VBM_CSF": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_WM": { "VBM_WM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"DWI": { "DWI": {
"pattern": ( "pattern": (
"derivatives/dwipreproc/sub-{subject}/dwi/" "derivatives/dwipreproc/{subject}/dwi/"
"sub-{subject}_desc-preproc_dwi.nii.gz" "{subject}_desc-preproc_dwi.nii.gz"
), ),
}, },
} }
@ -158,23 +158,23 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
{ {
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz" "{subject}_desc-preproc_T1w.nii.gz"
), ),
"space": "native", "space": "native",
"mask_item": "T1w_mask", "mask_item": "T1w_mask",
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz" "{subject}_desc-brain_mask.nii.gz"
), ),
"space": "native", "space": "native",
}, },
"Warp": { "Warp": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_" "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5" "mode-image_xfm.h5"
), ),
"src": "MNI152NLin2009cAsym", "src": "MNI152NLin2009cAsym",
@ -242,7 +242,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
The list of subjects in the dataset. The list of subjects in the dataset.
""" """
subjects = [f"{x:04d}" for x in range(1, 217)] subjects = [f"sub-{x:04d}" for x in range(1, 217)]
elems = [] elems = []
for subject, task in product(subjects, self.tasks): for subject, task in product(subjects, self.tasks):
elems.append((subject, task)) elems.append((subject, task))

50
junifer/datagrabber/aomic/piop2.py
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@ -76,8 +76,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
patterns = { patterns = {
"BOLD": { "BOLD": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -85,24 +85,24 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
}, },
"BOLD_confounds": { "BOLD_confounds": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
), ),
"format": "fmriprep", "format": "fmriprep",
}, },
"BOLD_mask": { "BOLD_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/func/" "derivatives/fmriprep/{subject}/func/"
"sub-{subject}_task-{task}_" "{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz" "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
@ -110,40 +110,40 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_" "{subject}_space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz" "desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_CSF": { "VBM_CSF": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_WM": { "VBM_WM": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-" "{subject}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"DWI": { "DWI": {
"pattern": ( "pattern": (
"derivatives/dwipreproc/sub-{subject}/dwi/" "derivatives/dwipreproc/{subject}/dwi/"
"sub-{subject}_desc-preproc_dwi.nii.gz" "{subject}_desc-preproc_dwi.nii.gz"
), ),
}, },
} }
@ -155,23 +155,23 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
{ {
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz" "{subject}_desc-preproc_T1w.nii.gz"
), ),
"space": "native", "space": "native",
"mask_item": "T1w_mask", "mask_item": "T1w_mask",
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz" "{subject}_desc-brain_mask.nii.gz"
), ),
"space": "native", "space": "native",
}, },
"Warp": { "Warp": {
"pattern": ( "pattern": (
"derivatives/fmriprep/sub-{subject}/anat/" "derivatives/fmriprep/{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_" "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5" "mode-image_xfm.h5"
), ),
"src": "MNI152NLin2009cAsym", "src": "MNI152NLin2009cAsym",
@ -208,7 +208,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
imposing constraints based on specified tasks. imposing constraints based on specified tasks.
""" """
subjects = [f"{x:04d}" for x in range(1, 227)] subjects = [f"sub-{x:04d}" for x in range(1, 227)]
elems = [] elems = []
for subject, task in product(subjects, self.tasks): for subject, task in product(subjects, self.tasks):
elems.append((subject, task)) elems.append((subject, task))

14
junifer/datagrabber/aomic/tests/test_id1000.py
View file

@ -34,7 +34,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["BOLD"]["path"].name out["BOLD"]["path"].name
== f"sub-{test_element}_task-moviewatching_" == f"{test_element}_task-moviewatching_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
) )
@ -46,7 +46,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["BOLD_confounds"]["path"].name out["BOLD_confounds"]["path"].name
== f"sub-{test_element}_task-moviewatching_" == f"{test_element}_task-moviewatching_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
) )
@ -61,7 +61,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["T1w"]["path"].name out["T1w"]["path"].name
== f"sub-{test_element}_space-MNI152NLin2009cAsym_" == f"{test_element}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
) )
@ -76,7 +76,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["VBM_CSF"]["path"].name out["VBM_CSF"]["path"].name
== f"sub-{test_element}_space-MNI152NLin2009cAsym_label-" == f"{test_element}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
) )
@ -88,7 +88,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["VBM_GM"]["path"].name out["VBM_GM"]["path"].name
== f"sub-{test_element}_space-MNI152NLin2009cAsym_label-" == f"{test_element}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
) )
@ -100,7 +100,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["VBM_WM"]["path"].name out["VBM_WM"]["path"].name
== f"sub-{test_element}_space-MNI152NLin2009cAsym_label-" == f"{test_element}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
) )
@ -112,7 +112,7 @@ def test_DataladAOMICID1000() -> None:
assert ( assert (
out["DWI"]["path"].name out["DWI"]["path"].name
== f"sub-{test_element}_desc-preproc_dwi.nii.gz" == f"{test_element}_desc-preproc_dwi.nii.gz"
) )
assert out["DWI"]["path"].exists() assert out["DWI"]["path"].exists()

14
junifer/datagrabber/aomic/tests/test_piop1.py
View file

@ -56,7 +56,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
acq = task_acqs[task] acq = task_acqs[task]
new_task = f"{task}_acq-{acq}" new_task = f"{task}_acq-{acq}"
assert ( assert (
out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_" out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
) )
@ -67,7 +67,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
assert "BOLD_confounds" in out assert "BOLD_confounds" in out
assert ( assert (
out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_" out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
) )
@ -81,7 +81,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
assert "T1w" in out assert "T1w" in out
assert ( assert (
out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_" out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
) )
@ -96,7 +96,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_CSF"]["path"].name out["VBM_CSF"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
) )
@ -108,7 +108,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_GM"]["path"].name out["VBM_GM"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
) )
@ -120,7 +120,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_WM"]["path"].name out["VBM_WM"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
) )
@ -130,7 +130,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
# asserts type "DWI" # asserts type "DWI"
assert "DWI" in out assert "DWI" in out
assert out["DWI"]["path"].name == f"sub-{sub}_desc-preproc_dwi.nii.gz" assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
assert out["DWI"]["path"].exists() assert out["DWI"]["path"].exists()
assert out["DWI"]["path"].is_file() assert out["DWI"]["path"].is_file()

14
junifer/datagrabber/aomic/tests/test_piop2.py
View file

@ -50,7 +50,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
new_task = f"{task}_acq-seq" new_task = f"{task}_acq-seq"
assert ( assert (
out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_" out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
) )
@ -61,7 +61,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
assert "BOLD_confounds" in out assert "BOLD_confounds" in out
assert ( assert (
out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_" out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
) )
@ -75,7 +75,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
assert "T1w" in out assert "T1w" in out
assert ( assert (
out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_" out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz" "desc-preproc_T1w.nii.gz"
) )
@ -90,7 +90,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_CSF"]["path"].name out["VBM_CSF"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz" "CSF_probseg.nii.gz"
) )
@ -102,7 +102,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_GM"]["path"].name out["VBM_GM"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz" "GM_probseg.nii.gz"
) )
@ -114,7 +114,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
assert ( assert (
out["VBM_WM"]["path"].name out["VBM_WM"]["path"].name
== f"sub-{sub}_space-MNI152NLin2009cAsym_label-" == f"{sub}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz" "WM_probseg.nii.gz"
) )
@ -124,7 +124,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
# asserts type "DWI" # asserts type "DWI"
assert "DWI" in out assert "DWI" in out
assert out["DWI"]["path"].name == f"sub-{sub}_desc-preproc_dwi.nii.gz" assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
assert out["DWI"]["path"].exists() assert out["DWI"]["path"].exists()
assert out["DWI"]["path"].is_file() assert out["DWI"]["path"].is_file()

90
junifer/datagrabber/dmcc13_benchmark.py
View file

@ -29,8 +29,8 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
"VBM_WM"} or a list of the options, optional "VBM_WM"} or a list of the options, optional
DMCC data types. If None, all available data types are selected. DMCC data types. If None, all available data types are selected.
(default None). (default None).
sessions: {"wave1bas", "wave1pro", "wave1rea"} or list of the options, \ sessions: {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"} or list of \
optional the options, optional
DMCC sessions. If None, all available sessions are selected DMCC sessions. If None, all available sessions are selected
(default None). (default None).
tasks: {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} or \ tasks: {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} or \
@ -68,9 +68,9 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
) -> None: ) -> None:
# Declare all sessions # Declare all sessions
all_sessions = [ all_sessions = [
"wave1bas", "ses-wave1bas",
"wave1pro", "ses-wave1pro",
"wave1rea", "ses-wave1rea",
] ]
# Set default sessions # Set default sessions
if sessions is None: if sessions is None:
@ -141,8 +141,8 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
patterns = { patterns = {
"BOLD": { "BOLD": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/" "derivatives/fmriprep-1.3.2/{subject}/{session}/"
"func/sub-{subject}_ses-{session}_task-{task}_acq-mb4" "func/{subject}_{session}_task-{task}_acq-mb4"
"{phase_encoding}_run-{run}_" "{phase_encoding}_run-{run}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
), ),
@ -151,16 +151,16 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
}, },
"BOLD_confounds": { "BOLD_confounds": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/" "derivatives/fmriprep-1.3.2/{subject}/{session}/"
"func/sub-{subject}_ses-{session}_task-{task}_acq-mb4" "func/{subject}_{session}_task-{task}_acq-mb4"
"{phase_encoding}_run-{run}_desc-confounds_regressors.tsv" "{phase_encoding}_run-{run}_desc-confounds_regressors.tsv"
), ),
"format": "fmriprep", "format": "fmriprep",
}, },
"BOLD_mask": { "BOLD_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/" "derivatives/fmriprep-1.3.2/{subject}/{session}/"
"/func/sub-{subject}_ses-{session}_task-{task}_acq-mb4" "/func/{subject}_{session}_task-{task}_acq-mb4"
"{phase_encoding}_run-{run}_" "{phase_encoding}_run-{run}_"
"space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz" "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
), ),
@ -168,37 +168,37 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
}, },
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz" "{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
"mask_item": "T1w_mask", "mask_item": "T1w_mask",
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz" "{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_CSF": { "VBM_CSF": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz" "{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_GM": { "VBM_GM": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz" "{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
"VBM_WM": { "VBM_WM": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz" "{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz"
), ),
"space": "MNI152NLin2009cAsym", "space": "MNI152NLin2009cAsym",
}, },
@ -211,23 +211,23 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
{ {
"T1w": { "T1w": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz" "{subject}_desc-preproc_T1w.nii.gz"
), ),
"space": "native", "space": "native",
"mask_item": "T1w_mask", "mask_item": "T1w_mask",
}, },
"T1w_mask": { "T1w_mask": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz" "{subject}_desc-brain_mask.nii.gz"
), ),
"space": "native", "space": "native",
}, },
"Warp": { "Warp": {
"pattern": ( "pattern": (
"derivatives/fmriprep-1.3.2/sub-{subject}/anat/" "derivatives/fmriprep-1.3.2/{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_" "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5" "mode-image_xfm.h5"
), ),
"src": "MNI152NLin2009cAsym", "src": "MNI152NLin2009cAsym",
@ -268,7 +268,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
---------- ----------
subject : str subject : str
The subject ID. The subject ID.
session : {"wave1bas", "wave1pro", "wave1rea"} session : {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"}
The session to get. The session to get.
task : {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} task : {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"}
The task to get. The task to get.
@ -323,25 +323,25 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
""" """
subjects = [ subjects = [
"f1031ax", "sub-f1031ax",
"f1552xo", "sub-f1552xo",
"f1659oa", "sub-f1659oa",
"f1670rz", "sub-f1670rz",
"f1951tt", "sub-f1951tt",
"f3300jh", "sub-f3300jh",
"f3720ca", "sub-f3720ca",
"f5004cr", "sub-f5004cr",
"f5407sl", "sub-f5407sl",
"f5416zj", "sub-f5416zj",
"f8113do", "sub-f8113do",
"f8570ui", "sub-f8570ui",
"f9057kp", "sub-f9057kp",
] ]
elems = [] elems = []
# For wave1bas session # For wave1bas session
for subject, session, task, phase_encoding in product( for subject, session, task, phase_encoding in product(
subjects, subjects,
["wave1bas"], ["ses-wave1bas"],
self.tasks, self.tasks,
self.phase_encodings, self.phase_encodings,
): ):
@ -350,13 +350,13 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
else: else:
run = "2" run = "2"
# Bypass for f1951tt not having run 2 for Rest # Bypass for f1951tt not having run 2 for Rest
if subject == "f1951tt" and task == "Rest" and run == "2": if subject == "sub-f1951tt" and task == "Rest" and run == "2":
continue continue
elems.append((subject, session, task, phase_encoding, run)) elems.append((subject, session, task, phase_encoding, run))
# For other sessions # For other sessions
for subject, session, task, phase_encoding in product( for subject, session, task, phase_encoding in product(
subjects, subjects,
["wave1pro", "wave1rea"], ["ses-wave1pro", "ses-wave1rea"],
["Rest"], ["Rest"],
self.phase_encodings, self.phase_encodings,
): ):
@ -365,7 +365,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
else: else:
run = "2" run = "2"
# Bypass for f5416zj for not having wave1rea session # Bypass for f5416zj for not having wave1rea session
if subject == "f5416zj" and session == "wave1rea": if subject == "sub-f5416zj" and session == "ses-wave1rea":
continue continue
elems.append((subject, session, task, phase_encoding, run)) elems.append((subject, session, task, phase_encoding, run))

66
junifer/datagrabber/tests/test_dmcc13_benchmark.py
View file

@ -17,34 +17,34 @@ URI = "https://gin.g-node.org/synchon/datalad-example-dmcc13-benchmark"
"sessions, tasks, phase_encodings, runs, native_t1w", "sessions, tasks, phase_encodings, runs, native_t1w",
[ [
(None, None, None, None, False), (None, None, None, None, False),
("wave1bas", "Rest", "AP", "1", False), ("ses-wave1bas", "Rest", "AP", "1", False),
("wave1bas", "Axcpt", "AP", "1", False), ("ses-wave1bas", "Axcpt", "AP", "1", False),
("wave1bas", "Cuedts", "AP", "1", False), ("ses-wave1bas", "Cuedts", "AP", "1", False),
("wave1bas", "Stern", "AP", "1", False), ("ses-wave1bas", "Stern", "AP", "1", False),
("wave1bas", "Stroop", "AP", "1", False), ("ses-wave1bas", "Stroop", "AP", "1", False),
("wave1bas", "Rest", "PA", "2", False), ("ses-wave1bas", "Rest", "PA", "2", False),
("wave1bas", "Axcpt", "PA", "2", False), ("ses-wave1bas", "Axcpt", "PA", "2", False),
("wave1bas", "Cuedts", "PA", "2", False), ("ses-wave1bas", "Cuedts", "PA", "2", False),
("wave1bas", "Stern", "PA", "2", False), ("ses-wave1bas", "Stern", "PA", "2", False),
("wave1bas", "Stroop", "PA", "2", False), ("ses-wave1bas", "Stroop", "PA", "2", False),
("wave1bas", "Rest", "AP", "1", True), ("ses-wave1bas", "Rest", "AP", "1", True),
("wave1bas", "Axcpt", "AP", "1", True), ("ses-wave1bas", "Axcpt", "AP", "1", True),
("wave1bas", "Cuedts", "AP", "1", True), ("ses-wave1bas", "Cuedts", "AP", "1", True),
("wave1bas", "Stern", "AP", "1", True), ("ses-wave1bas", "Stern", "AP", "1", True),
("wave1bas", "Stroop", "AP", "1", True), ("ses-wave1bas", "Stroop", "AP", "1", True),
("wave1bas", "Rest", "PA", "2", True), ("ses-wave1bas", "Rest", "PA", "2", True),
("wave1bas", "Axcpt", "PA", "2", True), ("ses-wave1bas", "Axcpt", "PA", "2", True),
("wave1bas", "Cuedts", "PA", "2", True), ("ses-wave1bas", "Cuedts", "PA", "2", True),
("wave1bas", "Stern", "PA", "2", True), ("ses-wave1bas", "Stern", "PA", "2", True),
("wave1bas", "Stroop", "PA", "2", True), ("ses-wave1bas", "Stroop", "PA", "2", True),
("wave1pro", "Rest", "AP", "1", False), ("ses-wave1pro", "Rest", "AP", "1", False),
("wave1pro", "Rest", "PA", "2", False), ("ses-wave1pro", "Rest", "PA", "2", False),
("wave1pro", "Rest", "AP", "1", True), ("ses-wave1pro", "Rest", "AP", "1", True),
("wave1pro", "Rest", "PA", "2", True), ("ses-wave1pro", "Rest", "PA", "2", True),
("wave1rea", "Rest", "AP", "1", False), ("ses-wave1rea", "Rest", "AP", "1", False),
("wave1rea", "Rest", "PA", "2", False), ("ses-wave1rea", "Rest", "PA", "2", False),
("wave1rea", "Rest", "AP", "1", True), ("ses-wave1rea", "Rest", "AP", "1", True),
("wave1rea", "Rest", "PA", "2", True), ("ses-wave1rea", "Rest", "PA", "2", True),
], ],
) )
def test_DMCC13Benchmark( def test_DMCC13Benchmark(
@ -88,7 +88,7 @@ def test_DMCC13Benchmark(
# Get test element's access values # Get test element's access values
_, ses, task, phase, run = test_element _, ses, task, phase, run = test_element
# Access data # Access data
out = dg[("01", ses, task, phase, run)] out = dg[("sub-01", ses, task, phase, run)]
# Available data types # Available data types
data_types = [ data_types = [
@ -108,15 +108,15 @@ def test_DMCC13Benchmark(
# Data type file name formats # Data type file name formats
data_file_names = [ data_file_names = [
( (
f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_" f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz" "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
), ),
( (
f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_" f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
"desc-confounds_regressors.tsv" "desc-confounds_regressors.tsv"
), ),
( (
f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_" f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
"space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz" "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
), ),
"sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz", "sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz",
@ -199,7 +199,7 @@ def test_DMCC13Benchmark_partial_data_access(
# Get test element's access values # Get test element's access values
_, ses, task, phase, run = test_element _, ses, task, phase, run = test_element
# Access data # Access data
out = dg[("01", ses, task, phase, run)] out = dg[("sub-01", ses, task, phase, run)]
# Assert data type # Assert data type
if isinstance(types, list): if isinstance(types, list):
for type_ in types: for type_ in types:

4
junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py
View file

@ -35,7 +35,7 @@ def test_AntsApplyTransformsWarper_preprocess() -> None:
"""Test AntsApplyTransformsWarper preprocess.""" """Test AntsApplyTransformsWarper preprocess."""
with DMCC13Benchmark( with DMCC13Benchmark(
types=["BOLD", "T1w", "Warp"], types=["BOLD", "T1w", "Warp"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
@ -43,7 +43,7 @@ def test_AntsApplyTransformsWarper_preprocess() -> None:
) as dg: ) as dg:
# Read data # Read data
element_data = DefaultDataReader().fit_transform( element_data = DefaultDataReader().fit_transform(
dg[("f9057kp", "wave1bas", "Rest", "AP", "1")] dg[("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1")]
) )
# Preprocess data # Preprocess data
data_type, data = _AntsApplyTransformsWarper( data_type, data = _AntsApplyTransformsWarper(

12
junifer/preprocess/tests/test_bold_warper.py
View file

@ -43,13 +43,13 @@ def test_BOLDWarper_get_output_type() -> None:
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["BOLD", "T1w", "Warp"], types=["BOLD", "T1w", "Warp"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=True, native_t1w=True,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
], ],
[ [
DataladHCP1200( DataladHCP1200(
@ -99,25 +99,25 @@ def test_BOLDWarper_preprocess_to_native(
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["BOLD"], types=["BOLD"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=False, native_t1w=False,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
"MNI152NLin2009aAsym", "MNI152NLin2009aAsym",
], ],
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["BOLD"], types=["BOLD"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=False, native_t1w=False,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
"MNI152NLin6Asym", "MNI152NLin6Asym",
], ],
], ],

12
junifer/preprocess/warping/tests/test_space_warper.py
View file

@ -70,13 +70,13 @@ def test_SpaceWarper_errors(
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["BOLD", "T1w", "Warp"], types=["BOLD", "T1w", "Warp"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=True, native_t1w=True,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
"ants", "ants",
], ],
[ [
@ -135,25 +135,25 @@ def test_SpaceWarper_native(
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["T1w"], types=["T1w"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=False, native_t1w=False,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
"MNI152NLin2009aAsym", "MNI152NLin2009aAsym",
], ],
[ [
DMCC13Benchmark( DMCC13Benchmark(
types=["T1w"], types=["T1w"],
sessions=["wave1bas"], sessions=["ses-wave1bas"],
tasks=["Rest"], tasks=["Rest"],
phase_encodings=["AP"], phase_encodings=["AP"],
runs=["1"], runs=["1"],
native_t1w=False, native_t1w=False,
), ),
("f9057kp", "wave1bas", "Rest", "AP", "1"), ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
"MNI152NLin6Asym", "MNI152NLin6Asym",
], ],
], ],