install(ok): /var/lib/condor/execute/dir_136591/ds (dataset)
install(ok): /var/lib/condor/execute/dir_136591/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_136591/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 00:38:52 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:38:52 - 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_136591/ds/sub-185823/sub-185823_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-185823/sub-185823_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 43s
Affine preprocessing (APP)
Initialize 6s
Estimate background 6s
Initial correction 5s
Refine background 3s
Final correction 4s
Final scaling 5s
34s
Correct center-of-mass 3s
Affine registration 8s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
60s
SPM preprocessing 1 (estimate 2): 45s
SPM preprocessing 2 (write)
Write Segmentation 16s
Update Segmentation 12s
Update Skull-Stripping 33s
Update probability maps 7s
68s
Global intensity correction 12s
SANLM denoising after intensity normalization (medium) 14s
Fast Optimized Shooting registration 2s
76s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.00) 11s
Estimate local tissue thresholds (WM) 16s
Estimate local tissue thresholds (GM) 19s
Intensity transformation 0s
SANLM denoising after LAS (medium) 22s
76s
ROI segmentation (partitioning)
Atlas -> subject space 6s
Major structures 14s
Ventricle detection 10s
Blood vessel detection 7s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 45s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 3s
Final corrections 2s
89s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 25s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 3s
Level 1 cleanup (brain masking) 3s
Level 2 cleanup (CSF correction) 1s
Level 3 cleanup (CSF/WM PVE) 2s
10s
2s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 6s
ROI estimation of 'neuromorphometrics' atlas 23s
ROI estimation of 'lpba40' atlas 7s
ROI estimation of 'hammers' atlas 16s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 6s
ROI estimation of 'aal3' atlas 9s
ROI estimation of 'mori' atlas 11s
ROI estimation of 'anatomy3' atlas 17s
ROI estimation of 'julichbrain' atlas 22s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 54s
Write results 55s
249s
Quality check 11s
/var/lib/condor/execute/dir_136591/ds/sub-185823/report/catreport_sub-185823_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 16 minute(s) and 42 second(s).
Image Quality Rating (IQR): 84.48% (B)
GM volume (GMV): 45.40% (670.45 / 1476.74 ml)
Segmentations are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/mri
Reports are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/report
Labels are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/label
------------------------------------------------------------------------
22-Oct-2025 00:55:36 - Done 'CAT12: Segmentation'
22-Oct-2025 00:55:36 - Done
Bye for now...
get(ok): sourcedata/raw/sub-185823/anat/sub-185823_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_136591/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_136591/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-185823/label/catROI_sub-185823_acq-headmotion2_T1w.mat (file)
add(ok): sub-185823/label/catROI_sub-185823_acq-headmotion2_T1w.xml (file)
add(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/m0wp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/mwp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/p0sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/wp0sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/report/cat_sub-185823_acq-headmotion2_T1w.mat (file)
add(ok): sub-185823/report/cat_sub-185823_acq-headmotion2_T1w.xml (file)
add(ok): sub-185823/report/catlog_sub-185823_acq-headmotion2_T1w.txt (file)
add(ok): sub-185823/report/catreport_sub-185823_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 00:56:09 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:56:09 - 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_136591/ds/sub-185823/sub-185823_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-185823/sub-185823_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 42s
Affine preprocessing (APP)
Initialize 6s
Estimate background 5s
Initial correction 5s
Refine background 3s
Final correction 4s
Final scaling 4s
32s
Correct center-of-mass 4s
Affine registration 7s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
59s
SPM preprocessing 1 (estimate 2): 38s
SPM preprocessing 2 (write)
Write Segmentation 16s
Update Segmentation 12s
Update Skull-Stripping 34s
Update probability maps 7s
68s
Global intensity correction 12s
SANLM denoising after intensity normalization (medium) 16s
Fast Optimized Shooting registration 8s
82s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.12) 12s
Estimate local tissue thresholds (WM) 16s
Estimate local tissue thresholds (GM) 19s
Intensity transformation 0s
SANLM denoising after LAS (medium) 21s
76s
ROI segmentation (partitioning)
Atlas -> subject space 6s
Major structures 14s
Ventricle detection 12s
Blood vessel detection 7s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 54s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 2s
101s
No enhanced blood vessel correction is required 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 25s
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) 1s
Level 3 cleanup (CSF/WM PVE) 2s
10s
8s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 6s
ROI estimation of 'neuromorphometrics' atlas 22s
ROI estimation of 'lpba40' atlas 6s
ROI estimation of 'hammers' atlas 15s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 5s
ROI estimation of 'aal3' atlas 9s
ROI estimation of 'mori' atlas 11s
ROI estimation of 'anatomy3' atlas 16s
ROI estimation of 'julichbrain' atlas 21s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 39s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 52s
Write results 53s
238s
Quality check 11s
/var/lib/condor/execute/dir_136591/ds/sub-185823/report/catreport_sub-185823_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 16 minute(s) and 42 second(s).
Image Quality Rating (IQR): 87.67% (B+)
GM volume (GMV): 47.11% (704.76 / 1495.95 ml)
Segmentations are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/mri
Reports are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/report
Labels are saved in /var/lib/condor/execute/dir_136591/ds/sub-185823/label
------------------------------------------------------------------------
22-Oct-2025 01:12:53 - Done 'CAT12: Segmentation'
22-Oct-2025 01:12:53 - Done
Bye for now...
get(ok): sourcedata/raw/sub-185823/anat/sub-185823_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-185823/label/catROI_sub-185823_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-185823/mri/m0wp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-185823/mri/mwp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-185823/mri/p0sub-185823_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-185823/mri/wp0sub-185823_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-185823/report/cat_sub-185823_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-185823/report/catreport_sub-185823_acq-headmotion2_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_136591/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-185823/label/catROI_sub-185823_acq-standard_T1w.mat (file)
add(ok): sub-185823/label/catROI_sub-185823_acq-standard_T1w.xml (file)
add(ok): sub-185823/mri/it_sub-185823_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/it_sub-185823_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/m0wp1sub-185823_acq-standard_T1w.nii.gz (file)
add(ok): sub-185823/mri/mwp1sub-185823_acq-standard_T1w.nii.gz (file)
add(ok): sub-185823/mri/p0sub-185823_acq-standard_T1w.nii.gz (file)
add(ok): sub-185823/mri/t_sub-185823_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/t_sub-185823_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/wp0sub-185823_acq-standard_T1w.nii.gz (file)
add(ok): sub-185823/report/cat_sub-185823_acq-standard_T1w.mat (file)
add(ok): sub-185823/report/cat_sub-185823_acq-standard_T1w.xml (file)
add(ok): sub-185823/report/catlog_sub-185823_acq-standard_T1w.txt (file)
add(ok): sub-185823/report/catreport_sub-185823_acq-standard_T1w.pdf (file)
add(ok): sub-185823/label/catROI_sub-185823_acq-headmotion2_T1w.mat (file)
add(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/m0wp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/mwp1sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/p0sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-185823/mri/wp0sub-185823_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-185823/report/cat_sub-185823_acq-headmotion2_T1w.mat (file)
add(ok): sub-185823/report/catreport_sub-185823_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-185823/label/catROI_sub-185823_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/label/catROI_sub-185823_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/it_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/it_sub-185823_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/it_sub-185823_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/m0wp1sub-185823_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/m0wp1sub-185823_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/mwp1sub-185823_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/mwp1sub-185823_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/p0sub-185823_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/p0sub-185823_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/t_sub-185823_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/t_sub-185823_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/t_sub-185823_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/wp0sub-185823_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/mri/wp0sub-185823_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-185823/report/cat_sub-185823_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/report/cat_sub-185823_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-185823/report/catreport_sub-185823_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-185823/report/catreport_sub-185823_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000809 seconds
flock: executing git
SUCCESS