install(ok): /var/lib/condor/execute/dir_3197381/ds (dataset)
install(ok): /var/lib/condor/execute/dir_3197381/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_3197381/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 00:41:06 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:41:06 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf
--------------------------------------------
--------------------------------------------
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_3197381/ds/sub-279373/sub-279373_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-279373/sub-279373_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 81s
Affine preprocessing (APP)
Initialize 9s
Estimate background 10s
Initial correction 8s
Refine background 5s
Final correction 7s
Final scaling 8s
53s
Correct center-of-mass 6s
Affine registration 14s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
100s
SPM preprocessing 1 (estimate 2): 85s
SPM preprocessing 2 (write)
Write Segmentation 25s
Update Segmentation 17s
Update Skull-Stripping 48s
Update probability maps 11s
101s
Global intensity correction 18s
SANLM denoising after intensity normalization (medium) 18s
Fast Optimized Shooting registration 12s
120s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 4s
Prepare segments (LASmod = 1.42) 16s
Estimate local tissue thresholds (WM) 19s
Estimate local tissue thresholds (GM) 19s
Intensity transformation 0s
SANLM denoising after LAS (medium) 34s
100s
ROI segmentation (partitioning)
Atlas -> subject space 9s
Major structures 20s
Ventricle detection 16s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 93s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 5s
Final corrections 3s
156s
Apply enhanced blood vessel correction 2s
Amap using initial SPM12 segmentations (MRF filter strength 0.07) 34s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.690.08,0.970.06]
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
14s
7s
Write result maps 2s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 6s
ROI estimation of 'cobra' atlas 19s
ROI estimation of 'neuromorphometrics' atlas 69s
ROI estimation of 'lpba40' atlas 20s
ROI estimation of 'hammers' atlas 49s
ROI estimation of 'thalamus' atlas 4s
ROI estimation of 'suit' atlas 11s
ROI estimation of 'ibsr' atlas 18s
ROI estimation of 'aal3' atlas 29s
ROI estimation of 'mori' atlas 43s
ROI estimation of 'anatomy3' atlas 63s
ROI estimation of 'julichbrain' atlas 85s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 12s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 34s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 68s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s
Write results 87s
732s
Quality check 15s
/var/lib/condor/execute/dir_3197381/ds/sub-279373/report/catreport_sub-279373_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 34 minute(s) and 51 second(s).
Image Quality Rating (IQR): 72.86% (C-)
GM volume (GMV): 42.77% (629.44 / 1471.79 ml)
Segmentations are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/mri
Reports are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/report
Labels are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/label
------------------------------------------------------------------------
22-Oct-2025 01:16:00 - Done 'CAT12: Segmentation'
22-Oct-2025 01:16:00 - Done
Bye for now...
get(ok): sourcedata/raw/sub-279373/anat/sub-279373_acq-headmotion2_T1w.nii.gz (file) [from s3-PUBLIC...]
install(ok): code/cat12 (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_3197381/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_3197381/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-279373/label/catROI_sub-279373_acq-headmotion2_T1w.mat (file)
add(ok): sub-279373/label/catROI_sub-279373_acq-headmotion2_T1w.xml (file)
add(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/m0wp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/mwp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/p0sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/wp0sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/report/cat_sub-279373_acq-headmotion2_T1w.mat (file)
add(ok): sub-279373/report/cat_sub-279373_acq-headmotion2_T1w.xml (file)
add(ok): sub-279373/report/catlog_sub-279373_acq-headmotion2_T1w.txt (file)
add(ok): sub-279373/report/catreport_sub-279373_acq-headmotion2_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 01:16:44 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 01:16:44 - Running 'CAT12: Segmentation'
--------------------------------------------
No commercial use of LPBA40 atlas!
Permission is granted to use this atlas without charge for non-commercial research purposes only:
https://www.loni.usc.edu/docs/atlases_methods/Human_Atlas_Methods.pdf
--------------------------------------------
--------------------------------------------
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_3197381/ds/sub-279373/sub-279373_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-279373/sub-279373_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 75s
Affine preprocessing (APP)
Initialize 9s
Estimate background 8s
Initial correction 8s
Refine background 4s
Final correction 6s
Final scaling 8s
49s
Correct center-of-mass 6s
Affine registration 9s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
88s
SPM preprocessing 1 (estimate 2): 72s
SPM preprocessing 2 (write)
Write Segmentation 24s
Update Segmentation 17s
Update Skull-Stripping 49s
Update probability maps 10s
100s
Global intensity correction 18s
SANLM denoising after intensity normalization (medium) 19s
Fast Optimized Shooting registration 3s
110s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 2s
Prepare segments (LASmod = 1.00) 16s
Estimate local tissue thresholds (WM) 22s
Estimate local tissue thresholds (GM) 26s
Intensity transformation 0s
SANLM denoising after LAS (medium) 32s
106s
ROI segmentation (partitioning)
Atlas -> subject space 9s
Major structures 19s
Ventricle detection 15s
Blood vessel detection 11s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.29) 87s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 5s
Final corrections 3s
151s
No enhanced blood vessel correction is required 2s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 38s
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
15s
7s
Write result maps 2s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 4s
ROI estimation of 'cobra' atlas 16s
ROI estimation of 'neuromorphometrics' atlas 69s
ROI estimation of 'lpba40' atlas 20s
ROI estimation of 'hammers' atlas 48s
ROI estimation of 'thalamus' atlas 4s
ROI estimation of 'suit' atlas 11s
ROI estimation of 'ibsr' atlas 18s
ROI estimation of 'aal3' atlas 29s
ROI estimation of 'mori' atlas 43s
ROI estimation of 'anatomy3' atlas 63s
ROI estimation of 'julichbrain' atlas 83s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 12s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 35s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 62s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 86s
Write results 87s
698s
Quality check 14s
/var/lib/condor/execute/dir_3197381/ds/sub-279373/report/catreport_sub-279373_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 31 minute(s) and 59 second(s).
Image Quality Rating (IQR): 87.80% (B+)
GM volume (GMV): 41.19% (638.55 / 1550.25 ml)
Segmentations are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/mri
Reports are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/report
Labels are saved in /var/lib/condor/execute/dir_3197381/ds/sub-279373/label
------------------------------------------------------------------------
22-Oct-2025 01:48:45 - Done 'CAT12: Segmentation'
22-Oct-2025 01:48:45 - Done
Bye for now...
get(ok): sourcedata/raw/sub-279373/anat/sub-279373_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-279373/label/catROI_sub-279373_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-279373/mri/m0wp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-279373/mri/mwp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-279373/mri/p0sub-279373_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-279373/mri/wp0sub-279373_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-279373/report/cat_sub-279373_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-279373/report/catreport_sub-279373_acq-headmotion2_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_3197381/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-279373/label/catROI_sub-279373_acq-standard_T1w.mat (file)
add(ok): sub-279373/label/catROI_sub-279373_acq-standard_T1w.xml (file)
add(ok): sub-279373/mri/it_sub-279373_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/it_sub-279373_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/m0wp1sub-279373_acq-standard_T1w.nii.gz (file)
add(ok): sub-279373/mri/mwp1sub-279373_acq-standard_T1w.nii.gz (file)
add(ok): sub-279373/mri/p0sub-279373_acq-standard_T1w.nii.gz (file)
add(ok): sub-279373/mri/t_sub-279373_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/t_sub-279373_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/wp0sub-279373_acq-standard_T1w.nii.gz (file)
add(ok): sub-279373/report/cat_sub-279373_acq-standard_T1w.mat (file)
add(ok): sub-279373/report/cat_sub-279373_acq-standard_T1w.xml (file)
add(ok): sub-279373/report/catlog_sub-279373_acq-standard_T1w.txt (file)
add(ok): sub-279373/report/catreport_sub-279373_acq-standard_T1w.pdf (file)
add(ok): sub-279373/label/catROI_sub-279373_acq-headmotion2_T1w.mat (file)
add(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/m0wp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/mwp1sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/p0sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-279373/mri/wp0sub-279373_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-279373/report/cat_sub-279373_acq-headmotion2_T1w.mat (file)
add(ok): sub-279373/report/catreport_sub-279373_acq-headmotion2_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-279373/label/catROI_sub-279373_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/label/catROI_sub-279373_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/it_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/it_sub-279373_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/it_sub-279373_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/m0wp1sub-279373_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/m0wp1sub-279373_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/mwp1sub-279373_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/mwp1sub-279373_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/p0sub-279373_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/p0sub-279373_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/t_sub-279373_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/t_sub-279373_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/t_sub-279373_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/wp0sub-279373_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/mri/wp0sub-279373_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-279373/report/cat_sub-279373_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/report/cat_sub-279373_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-279373/report/catreport_sub-279373_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-279373/report/catreport_sub-279373_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000305 seconds
flock: executing git
SUCCESS