install(ok): /var/lib/condor/execute/dir_3197559/ds (dataset)
install(ok): /var/lib/condor/execute/dir_3197559/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_3197559/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 00:41:07 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:41:07 - 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_3197559/ds/sub-694330/sub-694330_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-694330/sub-694330_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 60s
Affine preprocessing (APP)
Initialize 9s
Estimate background 8s
Initial correction 7s
Refine background 4s
Final correction 6s
Final scaling 6s
46s
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): 71s
SPM preprocessing 2 (write)
Write Segmentation 23s
Update Segmentation 16s
Update Skull-Stripping 47s
Update probability maps 10s
96s
Global intensity correction 18s
SANLM denoising after intensity normalization (medium) 18s
Fast Optimized Shooting registration 11s
120s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 4s
Prepare segments (LASmod = 1.18) 16s
Estimate local tissue thresholds (WM) 21s
Estimate local tissue thresholds (GM) 24s
Intensity transformation 0s
SANLM denoising after LAS (medium) 29s
101s
ROI segmentation (partitioning)
Atlas -> subject space 9s
Major structures 17s
Ventricle detection 15s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.36) 65s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 5s
Final corrections 3s
125s
Apply enhanced blood vessel correction 2s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 34s
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) 4s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 3s
13s
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 66s
ROI estimation of 'lpba40' atlas 20s
ROI estimation of 'hammers' atlas 48s
ROI estimation of 'thalamus' atlas 3s
ROI estimation of 'suit' atlas 11s
ROI estimation of 'ibsr' atlas 18s
ROI estimation of 'aal3' atlas 29s
ROI estimation of 'mori' atlas 42s
ROI estimation of 'anatomy3' atlas 61s
ROI estimation of 'julichbrain' atlas 82s
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 66s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 134s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 169s
Write results 171s
817s
Quality check 13s
/var/lib/condor/execute/dir_3197559/ds/sub-694330/report/catreport_sub-694330_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 32 minute(s) and 28 second(s).
Image Quality Rating (IQR): 87.64% (B+)
GM volume (GMV): 39.63% (524.60 / 1323.88 ml)
Segmentations are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/mri
Reports are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/report
Labels are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/label
------------------------------------------------------------------------
22-Oct-2025 01:13:38 - Done 'CAT12: Segmentation'
22-Oct-2025 01:13:38 - Done
Bye for now...
get(ok): sourcedata/raw/sub-694330/anat/sub-694330_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_3197559/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_3197559/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-694330/label/catROI_sub-694330_acq-standard_T1w.mat (file)
add(ok): sub-694330/label/catROI_sub-694330_acq-standard_T1w.xml (file)
add(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/m0wp1sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/mwp1sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/p0sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/wp0sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/report/cat_sub-694330_acq-standard_T1w.mat (file)
add(ok): sub-694330/report/cat_sub-694330_acq-standard_T1w.xml (file)
add(ok): sub-694330/report/catlog_sub-694330_acq-standard_T1w.txt (file)
add(ok): sub-694330/report/catreport_sub-694330_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 01:14:23 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 01:14:23 - 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_3197559/ds/sub-694330/sub-694330_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-694330/sub-694330_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 61s
Affine preprocessing (APP)
Initialize 8s
Estimate background 8s
Initial correction 7s
Refine background 4s
Final correction 6s
Final scaling 6s
46s
Correct center-of-mass 5s
Affine registration 9s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
85s
SPM preprocessing 1 (estimate 2): 69s
SPM preprocessing 2 (write)
Write Segmentation 24s
Update Segmentation 16s
Update Skull-Stripping 47s
Update probability maps 9s
96s
Global intensity correction 18s
SANLM denoising after intensity normalization (medium) 17s
Fast Optimized Shooting registration 11s
117s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 4s
Prepare segments (LASmod = 1.18) 14s
Estimate local tissue thresholds (WM) 21s
Estimate local tissue thresholds (GM) 24s
Intensity transformation 0s
SANLM denoising after LAS (medium) 28s
99s
ROI segmentation (partitioning)
Atlas -> subject space 9s
Major structures 17s
Ventricle detection 16s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.35) 60s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 4s
Final corrections 3s
120s
Apply enhanced blood vessel correction 2s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 34s
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) 4s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 3s
13s
10s
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 61s
ROI estimation of 'lpba40' atlas 19s
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 62s
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 67s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 118s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 125s
Write results 127s
756s
Quality check 14s
/var/lib/condor/execute/dir_3197559/ds/sub-694330/report/catreport_sub-694330_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 31 minute(s) and 20 second(s).
Image Quality Rating (IQR): 87.69% (B+)
GM volume (GMV): 39.91% (525.50 / 1316.64 ml)
Segmentations are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/mri
Reports are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/report
Labels are saved in /var/lib/condor/execute/dir_3197559/ds/sub-694330/label
------------------------------------------------------------------------
22-Oct-2025 01:45:46 - Done 'CAT12: Segmentation'
22-Oct-2025 01:45:46 - Done
Bye for now...
get(ok): sourcedata/raw/sub-694330/anat/sub-694330_acq-headmotion2_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-694330/label/catROI_sub-694330_acq-standard_T1w.mat (file)
unlock(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
unlock(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
unlock(ok): sub-694330/mri/m0wp1sub-694330_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-694330/mri/mwp1sub-694330_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-694330/mri/p0sub-694330_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
unlock(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
unlock(ok): sub-694330/mri/wp0sub-694330_acq-standard_T1w.nii.gz (file)
unlock(ok): sub-694330/report/cat_sub-694330_acq-standard_T1w.mat (file)
unlock(ok): sub-694330/report/catreport_sub-694330_acq-standard_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_3197559/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-694330/label/catROI_sub-694330_acq-headmotion2_T1w.mat (file)
add(ok): sub-694330/label/catROI_sub-694330_acq-headmotion2_T1w.xml (file)
add(ok): sub-694330/mri/it_sub-694330_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/it_sub-694330_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/m0wp1sub-694330_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-694330/mri/mwp1sub-694330_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-694330/mri/p0sub-694330_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-694330/mri/t_sub-694330_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/t_sub-694330_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/wp0sub-694330_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-694330/report/cat_sub-694330_acq-headmotion2_T1w.mat (file)
add(ok): sub-694330/report/cat_sub-694330_acq-headmotion2_T1w.xml (file)
add(ok): sub-694330/report/catlog_sub-694330_acq-headmotion2_T1w.txt (file)
add(ok): sub-694330/report/catreport_sub-694330_acq-headmotion2_T1w.pdf (file)
add(ok): sub-694330/label/catROI_sub-694330_acq-standard_T1w.mat (file)
add(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/m0wp1sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/mwp1sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/p0sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-694330/mri/wp0sub-694330_acq-standard_T1w.nii.gz (file)
add(ok): sub-694330/report/cat_sub-694330_acq-standard_T1w.mat (file)
add(ok): sub-694330/report/catreport_sub-694330_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-694330/label/catROI_sub-694330_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/label/catROI_sub-694330_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/it_sub-694330_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/it_sub-694330_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/it_sub-694330_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/m0wp1sub-694330_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/m0wp1sub-694330_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/mwp1sub-694330_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/mwp1sub-694330_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/p0sub-694330_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/p0sub-694330_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/t_sub-694330_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/t_sub-694330_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/t_sub-694330_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/wp0sub-694330_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/mri/wp0sub-694330_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-694330/report/cat_sub-694330_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/report/cat_sub-694330_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-694330/report/catreport_sub-694330_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-694330/report/catreport_sub-694330_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000732 seconds
flock: executing git
SUCCESS