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ds004173-catqc/logs/10071043.out
Felix Hoffstaedter b5c00fc272 add logs
2025-10-23 16:31:13 +02:00

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install(ok): /var/lib/condor/execute/dir_922600/ds (dataset)
install(ok): /var/lib/condor/execute/dir_922600/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_922600/ds/sourcedata/raw]
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/R2023b/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/opengl/lib/glnxa64
SPM25, version 25.01.02 (standalone)
MATLAB, version 23.2.0.2859533 (R2023b) Update 10
___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( Statistical Parametric Mapping
(___/(__) (_/\/\_) SPM25 - https://www.fil.ion.ucl.ac.uk/spm/
Item opts: No field(s) named
ngaus
warpreg
bias
acc
redspmres
Item registration: No field(s) named
T1
brainmask
cat12atlas
darteltpm
shootingtpm
regstr
Item atlas: No field(s) named
warped
dartel
------------------------------------------------------------------------
22-Oct-2025 00:40:08 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:40:08 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
<a href = "https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf">https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf</a>
--------------------------------------------
--------------------------------------------
No commercial use of SUIT cerebellar atlas!
Creative Commons Attribution-NonCommercial 3.0 Unported License does not allow commercial use.
--------------------------------------------
Uncompress /var/lib/condor/execute/dir_922600/ds/sub-424015/sub-424015_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-424015/sub-424015_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 60s
Affine preprocessing (APP)
Initialize 7s
Estimate background 7s
Initial correction 7s
Refine background 3s
Final correction 5s
Final scaling 7s
42s
Correct center-of-mass 4s
Affine registration 9s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
81s
SPM preprocessing 1 (estimate 2): 51s
SPM preprocessing 2 (write)
Write Segmentation 20s
Update Segmentation 15s
Update Skull-Stripping 43s
Update probability maps 8s
85s
Global intensity correction 15s
SANLM denoising after intensity normalization (medium) 18s
Fast Optimized Shooting registration 6s
96s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 3s
Prepare segments (LASmod = 1.06) 15s
Estimate local tissue thresholds (WM) 19s
Estimate local tissue thresholds (GM) 23s
Intensity transformation 0s
SANLM denoising after LAS (medium) 28s
95s
ROI segmentation (partitioning)
Atlas -> subject space 8s
Major structures 18s
Ventricle detection 16s
Blood vessel detection 10s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 71s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 5s
Final corrections 3s
132s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 29s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 5s
Level 1 cleanup (brain masking) 4s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 3s
13s
6s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 4s
ROI estimation of 'cobra' atlas 13s
ROI estimation of 'neuromorphometrics' atlas 52s
ROI estimation of 'lpba40' atlas 16s
ROI estimation of 'hammers' atlas 38s
ROI estimation of 'thalamus' atlas 3s
ROI estimation of 'suit' atlas 9s
ROI estimation of 'ibsr' atlas 15s
ROI estimation of 'aal3' atlas 23s
ROI estimation of 'mori' atlas 35s
ROI estimation of 'anatomy3' atlas 51s
ROI estimation of 'julichbrain' atlas 62s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 9s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s
Write results 71s
530s
Quality check 14s
/var/lib/condor/execute/dir_922600/ds/sub-424015/report/catreport_sub-424015_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 25 minute(s) and 8 second(s).
Image Quality Rating (IQR): 87.64% (B+)
GM volume (GMV): 42.40% (673.15 / 1587.54 ml)
Segmentations are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/mri
Reports are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/report
Labels are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/label
------------------------------------------------------------------------
22-Oct-2025 01:05:18 - Done 'CAT12: Segmentation'
22-Oct-2025 01:05:18 - Done
Bye for now...
get(ok): sourcedata/raw/sub-424015/anat/sub-424015_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
install(ok): code/cat12 (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_922600/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_922600/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-424015/label/catROI_sub-424015_acq-standard_T1w.mat (file)
add(ok): sub-424015/label/catROI_sub-424015_acq-standard_T1w.xml (file)
add(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/m0wp1sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/mwp1sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/p0sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/wp0sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/report/cat_sub-424015_acq-standard_T1w.mat (file)
add(ok): sub-424015/report/cat_sub-424015_acq-standard_T1w.xml (file)
add(ok): sub-424015/report/catlog_sub-424015_acq-standard_T1w.txt (file)
add(ok): sub-424015/report/catreport_sub-424015_acq-standard_T1w.pdf (file)
save(ok): . (dataset)
action summary:
add (ok: 14)
get (notneeded: 2, ok: 2)
install (ok: 1)
run (ok: 1)
save (ok: 1)
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/R2023b/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/opengl/lib/glnxa64
SPM25, version 25.01.02 (standalone)
MATLAB, version 23.2.0.2859533 (R2023b) Update 10
___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( Statistical Parametric Mapping
(___/(__) (_/\/\_) SPM25 - https://www.fil.ion.ucl.ac.uk/spm/
Item opts: No field(s) named
ngaus
warpreg
bias
acc
redspmres
Item registration: No field(s) named
T1
brainmask
cat12atlas
darteltpm
shootingtpm
regstr
Item atlas: No field(s) named
warped
dartel
------------------------------------------------------------------------
22-Oct-2025 01:06:00 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 01:06:00 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
<a href = "https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf">https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf</a>
--------------------------------------------
--------------------------------------------
No commercial use of SUIT cerebellar atlas!
Creative Commons Attribution-NonCommercial 3.0 Unported License does not allow commercial use.
--------------------------------------------
Uncompress /var/lib/condor/execute/dir_922600/ds/sub-424015/sub-424015_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-424015/sub-424015_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 61s
Affine preprocessing (APP)
Initialize 7s
Estimate background 7s
Initial correction 7s
Refine background 3s
Final correction 6s
Final scaling 6s
41s
Correct center-of-mass 4s
Affine registration 9s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
76s
SPM preprocessing 1 (estimate 2): 50s
SPM preprocessing 2 (write)
Write Segmentation 19s
Update Segmentation 15s
Update Skull-Stripping 42s
Update probability maps 8s
85s
Global intensity correction 15s
SANLM denoising after intensity normalization (medium) 18s
Fast Optimized Shooting registration 6s
98s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 2s
Prepare segments (LASmod = 1.04) 14s
Estimate local tissue thresholds (WM) 19s
Estimate local tissue thresholds (GM) 23s
Intensity transformation 0s
SANLM denoising after LAS (medium) 27s
92s
ROI segmentation (partitioning)
Atlas -> subject space 8s
Major structures 17s
Ventricle detection 15s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 71s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 4s
Final corrections 3s
129s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 31s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 4s
Level 1 cleanup (brain masking) 3s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 3s
12s
10s
Write result maps 2s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 4s
ROI estimation of 'cobra' atlas 13s
ROI estimation of 'neuromorphometrics' atlas 50s
ROI estimation of 'lpba40' atlas 15s
ROI estimation of 'hammers' atlas 32s
ROI estimation of 'thalamus' atlas 2s
ROI estimation of 'suit' atlas 6s
ROI estimation of 'ibsr' atlas 13s
ROI estimation of 'aal3' atlas 19s
ROI estimation of 'mori' atlas 25s
ROI estimation of 'anatomy3' atlas 29s
ROI estimation of 'julichbrain' atlas 41s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 5s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s
Write results 70s
414s
Quality check 14s
/var/lib/condor/execute/dir_922600/ds/sub-424015/report/catreport_sub-424015_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 24 minute(s) and 1 second(s).
Image Quality Rating (IQR): 85.45% (B)
GM volume (GMV): 41.47% (654.56 / 1578.42 ml)
Segmentations are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/mri
Reports are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/report
Labels are saved in /var/lib/condor/execute/dir_922600/ds/sub-424015/label
------------------------------------------------------------------------
22-Oct-2025 01:30:03 - Done 'CAT12: Segmentation'
22-Oct-2025 01:30:03 - Done
Bye for now...
get(ok): sourcedata/raw/sub-424015/anat/sub-424015_acq-headmotion2_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-424015/label/catROI_sub-424015_acq-standard_T1w.mat (file)
unlock(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
unlock(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
unlock(ok): sub-424015/mri/m0wp1sub-424015_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-424015/mri/mwp1sub-424015_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-424015/mri/p0sub-424015_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
unlock(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
unlock(ok): sub-424015/mri/wp0sub-424015_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-424015/report/cat_sub-424015_acq-standard_T1w.mat (file)
unlock(ok): sub-424015/report/catreport_sub-424015_acq-standard_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_922600/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-424015/label/catROI_sub-424015_acq-headmotion2_T1w.mat (file)
add(ok): sub-424015/label/catROI_sub-424015_acq-headmotion2_T1w.xml (file)
add(ok): sub-424015/mri/it_sub-424015_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/it_sub-424015_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/m0wp1sub-424015_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-424015/mri/mwp1sub-424015_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-424015/mri/p0sub-424015_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-424015/mri/t_sub-424015_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/t_sub-424015_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/wp0sub-424015_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-424015/report/cat_sub-424015_acq-headmotion2_T1w.mat (file)
add(ok): sub-424015/report/cat_sub-424015_acq-headmotion2_T1w.xml (file)
add(ok): sub-424015/report/catlog_sub-424015_acq-headmotion2_T1w.txt (file)
add(ok): sub-424015/report/catreport_sub-424015_acq-headmotion2_T1w.pdf (file)
add(ok): sub-424015/label/catROI_sub-424015_acq-standard_T1w.mat (file)
add(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/m0wp1sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/mwp1sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/p0sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-424015/mri/wp0sub-424015_acq-standard_T1w.nii.gz (file)
add(ok): sub-424015/report/cat_sub-424015_acq-standard_T1w.mat (file)
add(ok): sub-424015/report/catreport_sub-424015_acq-standard_T1w.pdf (file)
save(ok): . (dataset)
action summary:
add (ok: 25)
get (notneeded: 4, ok: 1)
run (ok: 1)
save (ok: 1)
unlock (ok: 11)
copy(ok): sub-424015/label/catROI_sub-424015_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/label/catROI_sub-424015_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/it_sub-424015_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/it_sub-424015_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/it_sub-424015_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/m0wp1sub-424015_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/m0wp1sub-424015_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/mwp1sub-424015_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/mwp1sub-424015_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/p0sub-424015_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/p0sub-424015_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/t_sub-424015_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/t_sub-424015_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/t_sub-424015_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/wp0sub-424015_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/mri/wp0sub-424015_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-424015/report/cat_sub-424015_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/report/cat_sub-424015_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-424015/report/catreport_sub-424015_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-424015/report/catreport_sub-424015_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.001124 seconds
flock: executing git
SUCCESS
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