install(ok): /var/lib/condor/execute/dir_1300134/ds (dataset)
install(ok): /var/lib/condor/execute/dir_1300134/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_1300134/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 00:39:22 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:39:22 - 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_1300134/ds/sub-105822/sub-105822_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-105822/sub-105822_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 52s
Affine preprocessing (APP)
Initialize 7s
Estimate background 6s
Initial correction 6s
Refine background 3s
Final correction 5s
Final scaling 5s
39s
Correct center-of-mass 4s
Affine registration 10s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
66s
SPM preprocessing 1 (estimate 2): 84s
SPM preprocessing 2 (write)
Write Segmentation 19s
Update Segmentation 13s
Update Skull-Stripping 38s
Update probability maps 9s
79s
Global intensity correction 15s
SANLM denoising after intensity normalization (medium) 14s
Fast Optimized Shooting registration 6s
95s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.09) 12s
Estimate local tissue thresholds (WM) 18s
Estimate local tissue thresholds (GM) 20s
Intensity transformation 0s
SANLM denoising after LAS (medium) 25s
84s
ROI segmentation (partitioning)
Atlas -> subject space 7s
Major structures 14s
Ventricle detection 13s
Blood vessel detection 7s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.21) 59s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 2s
107s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.07) 26s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.06]
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
10s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 3s
ROI estimation of 'cobra' atlas 10s
ROI estimation of 'neuromorphometrics' atlas 41s
ROI estimation of 'lpba40' atlas 12s
ROI estimation of 'hammers' atlas 28s
ROI estimation of 'thalamus' atlas 2s
ROI estimation of 'suit' atlas 6s
ROI estimation of 'ibsr' atlas 11s
ROI estimation of 'aal3' atlas 21s
ROI estimation of 'mori' atlas 31s
ROI estimation of 'anatomy3' atlas 45s
ROI estimation of 'julichbrain' atlas 59s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 8s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 75s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 104s
Write results 106s
522s
Quality check 14s
/var/lib/condor/execute/dir_1300134/ds/sub-105822/report/catreport_sub-105822_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 25 minute(s) and 31 second(s).
Image Quality Rating (IQR): 83.81% (B)
GM volume (GMV): 42.24% (550.30 / 1302.82 ml)
Segmentations are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/mri
Reports are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/report
Labels are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/label
------------------------------------------------------------------------
22-Oct-2025 01:04:56 - Done 'CAT12: Segmentation'
22-Oct-2025 01:04:56 - Done
Bye for now...
get(ok): sourcedata/raw/sub-105822/anat/sub-105822_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_1300134/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_1300134/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-105822/label/catROI_sub-105822_acq-headmotion2_T1w.mat (file)
add(ok): sub-105822/label/catROI_sub-105822_acq-headmotion2_T1w.xml (file)
add(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/m0wp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/mwp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/p0sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/wp0sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/report/cat_sub-105822_acq-headmotion2_T1w.mat (file)
add(ok): sub-105822/report/cat_sub-105822_acq-headmotion2_T1w.xml (file)
add(ok): sub-105822/report/catlog_sub-105822_acq-headmotion2_T1w.txt (file)
add(ok): sub-105822/report/catreport_sub-105822_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 01:05:40 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 01:05:40 - 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_1300134/ds/sub-105822/sub-105822_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-105822/sub-105822_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 50s
Affine preprocessing (APP)
Initialize 7s
Estimate background 6s
Initial correction 6s
Refine background 3s
Final correction 5s
Final scaling 5s
37s
Correct center-of-mass 5s
Affine registration 7s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
69s
SPM preprocessing 1 (estimate 2): 52s
SPM preprocessing 2 (write)
Write Segmentation 18s
Update Segmentation 13s
Update Skull-Stripping 39s
Update probability maps 8s
78s
Global intensity correction 15s
SANLM denoising after intensity normalization (medium) 15s
Fast Optimized Shooting registration 3s
91s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.00) 12s
Estimate local tissue thresholds (WM) 18s
Estimate local tissue thresholds (GM) 21s
Intensity transformation 0s
SANLM denoising after LAS (medium) 24s
84s
ROI segmentation (partitioning)
Atlas -> subject space 7s
Major structures 15s
Ventricle detection 13s
Blood vessel detection 8s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.22) 52s
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) 27s
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
11s
3s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 9s
ROI estimation of 'neuromorphometrics' atlas 32s
ROI estimation of 'lpba40' atlas 9s
ROI estimation of 'hammers' atlas 22s
ROI estimation of 'thalamus' atlas 2s
ROI estimation of 'suit' atlas 6s
ROI estimation of 'ibsr' atlas 10s
ROI estimation of 'aal3' atlas 17s
ROI estimation of 'mori' atlas 23s
ROI estimation of 'anatomy3' atlas 33s
ROI estimation of 'julichbrain' atlas 47s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 6s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 75s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
Write results 113s
461s
Quality check 14s
/var/lib/condor/execute/dir_1300134/ds/sub-105822/report/catreport_sub-105822_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 22 minute(s) and 57 second(s).
Image Quality Rating (IQR): 87.81% (B+)
GM volume (GMV): 41.92% (568.15 / 1355.19 ml)
Segmentations are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/mri
Reports are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/report
Labels are saved in /var/lib/condor/execute/dir_1300134/ds/sub-105822/label
------------------------------------------------------------------------
22-Oct-2025 01:28:40 - Done 'CAT12: Segmentation'
22-Oct-2025 01:28:40 - Done
Bye for now...
get(ok): sourcedata/raw/sub-105822/anat/sub-105822_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-105822/label/catROI_sub-105822_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-105822/mri/m0wp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-105822/mri/mwp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-105822/mri/p0sub-105822_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-105822/mri/wp0sub-105822_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-105822/report/cat_sub-105822_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-105822/report/catreport_sub-105822_acq-headmotion2_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_1300134/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-105822/label/catROI_sub-105822_acq-standard_T1w.mat (file)
add(ok): sub-105822/label/catROI_sub-105822_acq-standard_T1w.xml (file)
add(ok): sub-105822/mri/it_sub-105822_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/it_sub-105822_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/m0wp1sub-105822_acq-standard_T1w.nii.gz (file)
add(ok): sub-105822/mri/mwp1sub-105822_acq-standard_T1w.nii.gz (file)
add(ok): sub-105822/mri/p0sub-105822_acq-standard_T1w.nii.gz (file)
add(ok): sub-105822/mri/t_sub-105822_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/t_sub-105822_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/wp0sub-105822_acq-standard_T1w.nii.gz (file)
add(ok): sub-105822/report/cat_sub-105822_acq-standard_T1w.mat (file)
add(ok): sub-105822/report/cat_sub-105822_acq-standard_T1w.xml (file)
add(ok): sub-105822/report/catlog_sub-105822_acq-standard_T1w.txt (file)
add(ok): sub-105822/report/catreport_sub-105822_acq-standard_T1w.pdf (file)
add(ok): sub-105822/label/catROI_sub-105822_acq-headmotion2_T1w.mat (file)
add(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/m0wp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/mwp1sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/p0sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-105822/mri/wp0sub-105822_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-105822/report/cat_sub-105822_acq-headmotion2_T1w.mat (file)
add(ok): sub-105822/report/catreport_sub-105822_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-105822/label/catROI_sub-105822_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/label/catROI_sub-105822_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/it_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/it_sub-105822_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/it_sub-105822_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/m0wp1sub-105822_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/m0wp1sub-105822_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/mwp1sub-105822_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/mwp1sub-105822_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/p0sub-105822_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/p0sub-105822_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/t_sub-105822_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/t_sub-105822_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/t_sub-105822_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/wp0sub-105822_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/mri/wp0sub-105822_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-105822/report/cat_sub-105822_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/report/cat_sub-105822_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-105822/report/catreport_sub-105822_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-105822/report/catreport_sub-105822_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000869 seconds
flock: executing git
SUCCESS