Felix Hoffstaedter
49a1686fa7
=== Do not change lines below ===
{
"chain": [],
"cmd": "singularity exec -B {pwd} --cleanenv code/cat12/cat12.9_r2665.simg sh -e -u -x -c '\n mkdir -p {outputs[0]} || true && cp {inputs[0]} {outputs[0]} && /singularity -b /batch/CATpreprocessing4qc+ROIs.m {outputs[0]}/*.nii.gz && rm -f {outputs[0]}/*.nii* {outputs[0]}/report/*.jpg && gzip {outputs[0]}/*/*.nii '",
"dsid": "a4334989-99d1-47ac-9d97-91726e2296e4",
"exit": 0,
"extra_inputs": [
"code/cat12/cat12.9_r2665.simg"
],
"inputs": [
"sourcedata/raw/sub-03/anat/sub-03_T1w.nii.gz"
],
"outputs": [
"sub-03"
],
"pwd": "."
}
^^^ Do not change lines above ^^^
91 lines
6.1 KiB
Text
91 lines
6.1 KiB
Text
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------------------------------------------------------------------------
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CAT12.9 r2665: 1/1: ./condor/execute/dir_3982995/ds/sub-03/sub-03_T1w.n
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------------------------------------------------------------------------
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SANLM denoising (medium) 51s
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Internal resampling (1.00x1.33x1.33mm > 1.00x1.00x1.00mm) 1s
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Affine preprocessing (APP)
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Initialize 8s
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Estimate background 9s
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Initial correction 6s
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Refine background 4s
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Final correction 5s
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Final scaling 6s
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45s
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Correct center-of-mass 4s
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Affine registration 8s
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SPM preprocessing 1 (estimate 1 - TPM registration): 87s
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SPM preprocessing 1 (estimate 2): 73s
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SPM preprocessing 2 (write)
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Write Segmentation 19s
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Update Segmentation 17s
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Update Skull-Stripping 44s
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Update probability maps 8s
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88s
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Global intensity correction 16s
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SANLM denoising after intensity normalization (medium) 21s
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Fast Optimized Shooting registration 3s
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119s
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Local adaptive segmentation (LASstr=0.50)
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Prepare maps 5s
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Prepare partitions 2s
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Prepare segments (LASmod = 1.01) 16s
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Estimate local tissue thresholds (WM) 20s
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Estimate local tissue thresholds (GM) 24s
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Intensity transformation 0s
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SANLM denoising after LAS (medium) 38s
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107s
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ROI segmentation (partitioning)
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Atlas -> subject space 10s
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Major structures 21s
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Ventricle detection 19s
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Blood vessel detection 10s
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WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 90s
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Manual stroke lesion detection 0s
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Closing of deep structures 2s
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Side alignment 5s
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Final corrections 3s
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160s
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Apply enhanced blood vessel correction 1s
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Amap using initial SPM12 segmentations (MRF filter strength 0.06) 31s
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AMAP peaks: [CSF,GM,WM] = [0.36±0.05,0.68±0.08,0.98±0.05]
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Final cleanup (gcutstr=0.25)
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Level 1 cleanup (ROI estimation) 5s
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Level 1 cleanup (brain masking) 4s
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Level 2 cleanup (CSF correction) 2s
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Level 3 cleanup (CSF/WM PVE) 3s
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13s
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5s
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Write result maps 2s
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ROI estimation in native space
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ROI estimation of 'thalamic_nuclei' atlas 3s
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ROI estimation of 'cobra' atlas 13s
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ROI estimation of 'neuromorphometrics' atlas 47s
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ROI estimation of 'lpba40' atlas 13s
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ROI estimation of 'hammers' atlas 33s
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ROI estimation of 'thalamus' atlas 2s
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ROI estimation of 'suit' atlas 7s
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ROI estimation of 'ibsr' atlas 11s
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ROI estimation of 'aal3' atlas 19s
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ROI estimation of 'mori' atlas 16s
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ROI estimation of 'anatomy3' atlas 24s
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ROI estimation of 'julichbrain' atlas 31s
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ROI estimation of 'Tian_Subcortex_S4_7T' atlas 7s
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ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
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ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
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ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
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ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s
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Write results 86s
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441s
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Quality check 12s
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/var/lib/condor/execute/dir_3982995/ds/sub-03/report/catreport_sub-03_T1w.pdf
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------------------------------------------------------------------------
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CAT preprocessing takes 26 minute(s) and 25 second(s).
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Image Quality Rating (IQR): 82.55% (B-)
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GM volume (GMV): 51.02% (753.07 / 1476.16 ml)
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Segmentations are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/mri
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Reports are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/report
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Labels are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/label
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------------------------------------------------------------------------
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