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ds004173-catqc/logs/10071049.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_1233889/ds (dataset)
install(ok): /var/lib/condor/execute/dir_1233889/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_1233889/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 00:40:57 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:40:57 - 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_1233889/ds/sub-613957/sub-613957_acq-headmotion2_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-613957/sub-613957_acq-headmotion2_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 64s
Affine preprocessing (APP)
Initialize 8s
Estimate background 9s
Initial correction 7s
Refine background 4s
Final correction 5s
Final scaling 7s
47s
Correct center-of-mass 5s
Affine registration 14s
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): 76s
SPM preprocessing 2 (write)
Write Segmentation 21s
Update Segmentation 15s
Update Skull-Stripping 41s
Update probability maps 9s
85s
Global intensity correction 16s
SANLM denoising after intensity normalization (medium) 17s
Fast Optimized Shooting registration 7s
101s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.49) 13s
Estimate local tissue thresholds (WM) 17s
Estimate local tissue thresholds (GM) 17s
Intensity transformation 0s
SANLM denoising after LAS (medium) 29s
85s
ROI segmentation (partitioning)
Atlas -> subject space 8s
Major structures 16s
Ventricle detection 14s
Blood vessel detection 8s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 58s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 3s
111s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 29s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.05]
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
11s
Write result maps 2s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 5s
ROI estimation of 'cobra' atlas 17s
ROI estimation of 'neuromorphometrics' atlas 64s
ROI estimation of 'lpba40' atlas 18s
ROI estimation of 'hammers' atlas 45s
ROI estimation of 'thalamus' atlas 4s
ROI estimation of 'suit' atlas 10s
ROI estimation of 'ibsr' atlas 17s
ROI estimation of 'aal3' atlas 28s
ROI estimation of 'mori' atlas 41s
ROI estimation of 'anatomy3' atlas 44s
ROI estimation of 'julichbrain' atlas 45s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 6s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 74s
Write results 75s
529s
Quality check 13s
/var/lib/condor/execute/dir_1233889/ds/sub-613957/report/catreport_sub-613957_acq-headmotion2_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 26 minute(s) and 52 second(s).
Image Quality Rating (IQR): 78.93% (C+)
GM volume (GMV): 40.19% (543.15 / 1351.42 ml)
Segmentations are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/mri
Reports are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/report
Labels are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/label
------------------------------------------------------------------------
22-Oct-2025 01:07:51 - Done 'CAT12: Segmentation'
22-Oct-2025 01:07:51 - Done
Bye for now...
get(ok): sourcedata/raw/sub-613957/anat/sub-613957_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_1233889/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_1233889/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-613957/label/catROI_sub-613957_acq-headmotion2_T1w.mat (file)
add(ok): sub-613957/label/catROI_sub-613957_acq-headmotion2_T1w.xml (file)
add(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/m0wp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/mwp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/p0sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/wp0sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/report/cat_sub-613957_acq-headmotion2_T1w.mat (file)
add(ok): sub-613957/report/cat_sub-613957_acq-headmotion2_T1w.xml (file)
add(ok): sub-613957/report/catlog_sub-613957_acq-headmotion2_T1w.txt (file)
add(ok): sub-613957/report/catreport_sub-613957_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 01:08:35 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 01:08:36 - 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_1233889/ds/sub-613957/sub-613957_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-613957/sub-613957_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 63s
Affine preprocessing (APP)
Initialize 8s
Estimate background 8s
Initial correction 7s
Refine background 4s
Final correction 5s
Final scaling 7s
44s
Correct center-of-mass 5s
Affine registration 10s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
75s
SPM preprocessing 1 (estimate 2): 64s
SPM preprocessing 2 (write)
Write Segmentation 21s
Update Segmentation 15s
Update Skull-Stripping 41s
Update probability maps 8s
85s
Global intensity correction 16s
SANLM denoising after intensity normalization (medium) 16s
Fast Optimized Shooting registration 8s
102s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 3s
Prepare partitions 3s
Prepare segments (LASmod = 1.23) 13s
Estimate local tissue thresholds (WM) 19s
Estimate local tissue thresholds (GM) 22s
Intensity transformation 0s
SANLM denoising after LAS (medium) 26s
90s
ROI segmentation (partitioning)
Atlas -> subject space 8s
Major structures 15s
Ventricle detection 14s
Blood vessel detection 8s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.22) 56s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 4s
Final corrections 3s
109s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.07) 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) 4s
Level 1 cleanup (brain masking) 3s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 3s
12s
11s
Write result maps 2s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 4s
ROI estimation of 'cobra' atlas 10s
ROI estimation of 'neuromorphometrics' atlas 36s
ROI estimation of 'lpba40' atlas 10s
ROI estimation of 'hammers' atlas 26s
ROI estimation of 'thalamus' atlas 2s
ROI estimation of 'suit' atlas 6s
ROI estimation of 'ibsr' atlas 10s
ROI estimation of 'aal3' atlas 15s
ROI estimation of 'mori' atlas 21s
ROI estimation of 'anatomy3' atlas 37s
ROI estimation of 'julichbrain' atlas 35s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 6s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s
Write results 79s
392s
Quality check 13s
/var/lib/condor/execute/dir_1233889/ds/sub-613957/report/catreport_sub-613957_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 24 minute(s) and 54 second(s).
Image Quality Rating (IQR): 87.39% (B+)
GM volume (GMV): 40.92% (538.80 / 1316.59 ml)
Segmentations are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/mri
Reports are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/report
Labels are saved in /var/lib/condor/execute/dir_1233889/ds/sub-613957/label
------------------------------------------------------------------------
22-Oct-2025 01:33:32 - Done 'CAT12: Segmentation'
22-Oct-2025 01:33:32 - Done
Bye for now...
get(ok): sourcedata/raw/sub-613957/anat/sub-613957_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-613957/label/catROI_sub-613957_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-613957/mri/m0wp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-613957/mri/mwp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-613957/mri/p0sub-613957_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
unlock(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
unlock(ok): sub-613957/mri/wp0sub-613957_acq-headmotion2_T1w.nii.gz (file)
unlock(ok): sub-613957/report/cat_sub-613957_acq-headmotion2_T1w.mat (file)
unlock(ok): sub-613957/report/catreport_sub-613957_acq-headmotion2_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_1233889/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-613957/label/catROI_sub-613957_acq-standard_T1w.mat (file)
add(ok): sub-613957/label/catROI_sub-613957_acq-standard_T1w.xml (file)
add(ok): sub-613957/mri/it_sub-613957_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/it_sub-613957_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/m0wp1sub-613957_acq-standard_T1w.nii.gz (file)
add(ok): sub-613957/mri/mwp1sub-613957_acq-standard_T1w.nii.gz (file)
add(ok): sub-613957/mri/p0sub-613957_acq-standard_T1w.nii.gz (file)
add(ok): sub-613957/mri/t_sub-613957_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/t_sub-613957_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/wp0sub-613957_acq-standard_T1w.nii.gz (file)
add(ok): sub-613957/report/cat_sub-613957_acq-standard_T1w.mat (file)
add(ok): sub-613957/report/cat_sub-613957_acq-standard_T1w.xml (file)
add(ok): sub-613957/report/catlog_sub-613957_acq-standard_T1w.txt (file)
add(ok): sub-613957/report/catreport_sub-613957_acq-standard_T1w.pdf (file)
add(ok): sub-613957/label/catROI_sub-613957_acq-headmotion2_T1w.mat (file)
add(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/m0wp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/mwp1sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/p0sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file)
add(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file)
add(ok): sub-613957/mri/wp0sub-613957_acq-headmotion2_T1w.nii.gz (file)
add(ok): sub-613957/report/cat_sub-613957_acq-headmotion2_T1w.mat (file)
add(ok): sub-613957/report/catreport_sub-613957_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-613957/label/catROI_sub-613957_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/label/catROI_sub-613957_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/it_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/it_sub-613957_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/it_sub-613957_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/m0wp1sub-613957_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/m0wp1sub-613957_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/mwp1sub-613957_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/mwp1sub-613957_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/p0sub-613957_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/p0sub-613957_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/t_sub-613957_acq-headmotion2_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/t_sub-613957_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/t_sub-613957_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/wp0sub-613957_acq-headmotion2_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/mri/wp0sub-613957_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-613957/report/cat_sub-613957_acq-headmotion2_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/report/cat_sub-613957_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-613957/report/catreport_sub-613957_acq-headmotion2_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-613957/report/catreport_sub-613957_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.001148 seconds
flock: executing git
SUCCESS
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