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ds004173-catqc/logs/10070969.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_205040/ds (dataset)
install(ok): /var/lib/condor/execute/dir_205040/ds/sourcedata/raw (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_205040/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 00:38:56 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:38:56 - 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_205040/ds/sub-136038/sub-136038_acq-headmotion1_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-136038/sub-136038_acq-headmotion1_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 38s
Affine preprocessing (APP)
Initialize 5s
Estimate background 5s
Initial correction 4s
Refine background 3s
Final correction 3s
Final scaling 4s
29s
Correct center-of-mass 7s
Affine registration 6s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
49s
SPM preprocessing 1 (estimate 2): 43s
SPM preprocessing 2 (write)
Write Segmentation 14s
Update Segmentation 10s
Update Skull-Stripping 28s
Update probability maps 6s
58s
Global intensity correction 12s
SANLM denoising after intensity normalization (medium) 10s
Fast Optimized Shooting registration 3s
69s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 2s
Prepare partitions 1s
Prepare segments (LASmod = 1.00) 8s
Estimate local tissue thresholds (WM) 13s
Estimate local tissue thresholds (GM) 14s
Intensity transformation 0s
SANLM denoising after LAS (medium) 18s
59s
ROI segmentation (partitioning)
Atlas -> subject space 5s
Major structures 10s
Ventricle detection 6s
Blood vessel detection 5s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 37s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 2s
Final corrections 2s
68s
Apply enhanced blood vessel correction 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.07) 20s
AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.06]
Final cleanup (gcutstr=0.25)
Level 1 cleanup (ROI estimation) 3s
Level 1 cleanup (brain masking) 2s
Level 2 cleanup (CSF correction) 1s
Level 3 cleanup (CSF/WM PVE) 2s
7s
2s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 5s
ROI estimation of 'neuromorphometrics' atlas 20s
ROI estimation of 'lpba40' atlas 6s
ROI estimation of 'hammers' atlas 14s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 5s
ROI estimation of 'aal3' atlas 7s
ROI estimation of 'mori' atlas 9s
ROI estimation of 'anatomy3' atlas 13s
ROI estimation of 'julichbrain' atlas 18s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 7s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 14s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 35s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 44s
Write results 45s
207s
Quality check 8s
/var/lib/condor/execute/dir_205040/ds/sub-136038/report/catreport_sub-136038_acq-headmotion1_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 14 minute(s) and 26 second(s).
Image Quality Rating (IQR): 86.12% (B)
GM volume (GMV): 43.81% (494.06 / 1127.84 ml)
Segmentations are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/mri
Reports are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/report
Labels are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/label
------------------------------------------------------------------------
22-Oct-2025 00:53:24 - Done 'CAT12: Segmentation'
22-Oct-2025 00:53:24 - Done
Bye for now...
get(ok): sourcedata/raw/sub-136038/anat/sub-136038_acq-headmotion1_T1w.nii.gz (file) [from s3-PUBLIC...]
install(ok): code/cat12 (dataset) [Installed subdataset in order to get /var/lib/condor/execute/dir_205040/ds/code/cat12]
get(ok): code/cat12/cat12.9_r2665.simg (file) [from inm7-storage...]
run(ok): /var/lib/condor/execute/dir_205040/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-136038/label/catROI_sub-136038_acq-headmotion1_T1w.mat (file)
add(ok): sub-136038/label/catROI_sub-136038_acq-headmotion1_T1w.xml (file)
add(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/m0wp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/mwp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/p0sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/wp0sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/report/cat_sub-136038_acq-headmotion1_T1w.mat (file)
add(ok): sub-136038/report/cat_sub-136038_acq-headmotion1_T1w.xml (file)
add(ok): sub-136038/report/catlog_sub-136038_acq-headmotion1_T1w.txt (file)
add(ok): sub-136038/report/catreport_sub-136038_acq-headmotion1_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 00:53:57 - Running job #1
------------------------------------------------------------------------
22-Oct-2025 00:53:57 - 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_205040/ds/sub-136038/sub-136038_acq-standard_T1w.nii
------------------------------------------------------------------------
CAT12.9 r2665: 1/1: ./ds/sub-136038/sub-136038_acq-standard_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium) 37s
Affine preprocessing (APP)
Initialize 5s
Estimate background 5s
Initial correction 4s
Refine background 3s
Final correction 3s
Final scaling 3s
28s
Correct center-of-mass 4s
Affine registration 5s
SPM preprocessing 1 (estimate 1 - TPM registration): Fontconfig error: Cannot load default config file
Fontconfig error: Cannot load default config file
6s
Use initial fine affine registration. 44s
SPM preprocessing 1 (estimate 2): 35s
SPM preprocessing 2 (write)
Write Segmentation 14s
Update Segmentation 10s
Update Skull-Stripping 29s
Update probability maps 6s
59s
Global intensity correction 12s
SANLM denoising after intensity normalization (medium) 11s
Fast Optimized Shooting registration 2s
68s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 2s
Prepare partitions 1s
Prepare segments (LASmod = 1.00) 8s
Estimate local tissue thresholds (WM) 13s
Estimate local tissue thresholds (GM) 15s
Intensity transformation 0s
SANLM denoising after LAS (medium) 17s
59s
ROI segmentation (partitioning)
Atlas -> subject space 5s
Major structures 10s
Ventricle detection 8s
Blood vessel detection 5s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 36s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 2s
Final corrections 2s
69s
No enhanced blood vessel correction is required 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 21s
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) 2s
Level 2 cleanup (CSF correction) 1s
Level 3 cleanup (CSF/WM PVE) 2s
8s
2s
Write result maps 1s
ROI estimation in native space
ROI estimation of 'thalamic_nuclei' atlas 2s
ROI estimation of 'cobra' atlas 5s
ROI estimation of 'neuromorphometrics' atlas 20s
ROI estimation of 'lpba40' atlas 6s
ROI estimation of 'hammers' atlas 14s
ROI estimation of 'thalamus' atlas 1s
ROI estimation of 'suit' atlas 3s
ROI estimation of 'ibsr' atlas 5s
ROI estimation of 'aal3' atlas 8s
ROI estimation of 'mori' atlas 10s
ROI estimation of 'anatomy3' atlas 14s
ROI estimation of 'julichbrain' atlas 19s
ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s
ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s
ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s
ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 37s
ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 47s
Write results 48s
219s
Quality check 8s
/var/lib/condor/execute/dir_205040/ds/sub-136038/report/catreport_sub-136038_acq-standard_T1w.pdf
------------------------------------------------------------------------
CAT preprocessing takes 13 minute(s) and 56 second(s).
Image Quality Rating (IQR): 87.97% (B+)
GM volume (GMV): 45.22% (533.31 / 1179.44 ml)
Segmentations are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/mri
Reports are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/report
Labels are saved in /var/lib/condor/execute/dir_205040/ds/sub-136038/label
------------------------------------------------------------------------
22-Oct-2025 01:07:55 - Done 'CAT12: Segmentation'
22-Oct-2025 01:07:55 - Done
Bye for now...
get(ok): sourcedata/raw/sub-136038/anat/sub-136038_acq-standard_T1w.nii.gz (file) [from s3-PUBLIC...]
unlock(ok): sub-136038/label/catROI_sub-136038_acq-headmotion1_T1w.mat (file)
unlock(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
unlock(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
unlock(ok): sub-136038/mri/m0wp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
unlock(ok): sub-136038/mri/mwp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
unlock(ok): sub-136038/mri/p0sub-136038_acq-headmotion1_T1w.nii.gz (file)
unlock(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
unlock(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
unlock(ok): sub-136038/mri/wp0sub-136038_acq-headmotion1_T1w.nii.gz (file)
unlock(ok): sub-136038/report/cat_sub-136038_acq-headmotion1_T1w.mat (file)
unlock(ok): sub-136038/report/catreport_sub-136038_acq-headmotion1_T1w.pdf (file)
run(ok): /var/lib/condor/execute/dir_205040/ds (dataset) [singularity exec -B /var/lib/condor/exec...]
add(ok): sub-136038/label/catROI_sub-136038_acq-standard_T1w.mat (file)
add(ok): sub-136038/label/catROI_sub-136038_acq-standard_T1w.xml (file)
add(ok): sub-136038/mri/it_sub-136038_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/it_sub-136038_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/m0wp1sub-136038_acq-standard_T1w.nii.gz (file)
add(ok): sub-136038/mri/mwp1sub-136038_acq-standard_T1w.nii.gz (file)
add(ok): sub-136038/mri/p0sub-136038_acq-standard_T1w.nii.gz (file)
add(ok): sub-136038/mri/t_sub-136038_acq-standard_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/t_sub-136038_acq-standard_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/wp0sub-136038_acq-standard_T1w.nii.gz (file)
add(ok): sub-136038/report/cat_sub-136038_acq-standard_T1w.mat (file)
add(ok): sub-136038/report/cat_sub-136038_acq-standard_T1w.xml (file)
add(ok): sub-136038/report/catlog_sub-136038_acq-standard_T1w.txt (file)
add(ok): sub-136038/report/catreport_sub-136038_acq-standard_T1w.pdf (file)
add(ok): sub-136038/label/catROI_sub-136038_acq-headmotion1_T1w.mat (file)
add(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/m0wp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/mwp1sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/p0sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file)
add(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file)
add(ok): sub-136038/mri/wp0sub-136038_acq-headmotion1_T1w.nii.gz (file)
add(ok): sub-136038/report/cat_sub-136038_acq-headmotion1_T1w.mat (file)
add(ok): sub-136038/report/catreport_sub-136038_acq-headmotion1_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-136038/label/catROI_sub-136038_acq-headmotion1_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/label/catROI_sub-136038_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/it_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/it_sub-136038_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/it_sub-136038_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/m0wp1sub-136038_acq-headmotion1_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/m0wp1sub-136038_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/mwp1sub-136038_acq-headmotion1_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/mwp1sub-136038_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/p0sub-136038_acq-headmotion1_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/p0sub-136038_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/t_sub-136038_acq-headmotion1_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/t_sub-136038_acq-standard_T1w_affine_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/t_sub-136038_acq-standard_T1w_rigid_reorient.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/wp0sub-136038_acq-headmotion1_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/mri/wp0sub-136038_acq-standard_T1w.nii.gz (file) [to catqc_out-storage...]
copy(ok): sub-136038/report/cat_sub-136038_acq-headmotion1_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/report/cat_sub-136038_acq-standard_T1w.mat (file) [to catqc_out-storage...]
copy(ok): sub-136038/report/catreport_sub-136038_acq-headmotion1_T1w.pdf (file) [to catqc_out-storage...]
copy(ok): sub-136038/report/catreport_sub-136038_acq-standard_T1w.pdf (file) [to catqc_out-storage...]
action summary:
copy (ok: 22)
flock: getting lock took 0.000442 seconds
flock: executing git
SUCCESS
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