------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 58s APP: Rough bias correction: Initialize 7s Estimate background 7s Initial correction 7s Refine background 3s Final correction 6s Final scaling 5s 43s Correct center-of-mass 5s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 83s SPM preprocessing 1 (estimate 2): 81s SPM preprocessing 2 (write): Write Segmentation 22s Update Segmentation 22s Update Skull-Stripping 47s Update probability maps 10s 101s Global intensity correction: 18s SANLM denoising after intensity normalization (medium): 31s Fast Optimized Shooting registration 39s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 4s Prepare segments (LASmod = 1.12) 17s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 49s 138s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 19s Blood vessel detection 12s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 83s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50): Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii" 1 | 2.50 | 0.0823 0.0000 0.0823 | 32.0000 2 | 2.50 | 0.0802 0.0010 0.0812 | 29.4886 3 | 2.50 | 0.0796 0.0015 0.0812 | 26.9772 4 | 2.50 | 0.0793 0.0017 0.0810 | 24.6107 5 | 2.50 | 0.0791 0.0018 0.0809 | 22.6548 6 | 2.50 | 0.0789 0.0019 0.0808 | 20.6989 7 | 2.50 | 0.0786 0.0020 0.0806 | 18.9688 8 | 2.50 | 0.0784 0.0021 0.0805 | 17.4455 9 | 2.50 | 0.0782 0.0021 0.0803 | 15.9223 10 | 2.50 | 0.0779 0.0022 0.0802 | 14.6627 11 | 2.50 | 0.0777 0.0023 0.0800 | 13.4764 12 | 2.50 | 0.0774 0.0024 0.0798 | 12.3015 13 | 2.50 | 0.0771 0.0025 0.0796 | 11.3776 14 | 2.50 | 0.0769 0.0025 0.0794 | 10.4537 15 | 2.25 | 0.0763 0.0026 0.0788 | 9.5920 16 | 2.25 | 0.0735 0.0039 0.0774 | 8.8725 29 | 2.00 | 0.0750 0.0018 0.0767 | 3.3283 30 | 2.00 | 0.0692 0.0041 0.0733 | 3.1221 31 | 2.00 | 0.0673 0.0050 0.0723 | 2.9160 43 | 1.75 | 0.0664 0.0029 0.0693 | 1.5785 44 | 1.75 | 0.0621 0.0051 0.0673 | 1.5194 45 | 1.75 | 0.0607 0.0059 0.0666 | 1.4626 57 | 1.50 | 0.0594 0.0043 0.0636 | 1.0900 58 | 1.50 | 0.0562 0.0064 0.0625 | 1.0730 59 | 1.50 | 0.0551 0.0070 0.0621 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 205s Prepare output 14s 219s Jacobian determinant (RMS): 0.010 0.036 0.054 0.078 0.102 | 0.108453 Template Matching: 0.082 0.221 0.202 0.182 0.165 | 0.165227 Write result maps: 45s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 21s PBT2x thickness: 60s 127s Create initial surface 105s Topology correction: 124s Surface refinement: 132s Reduction of surface collisions with optimization: 88s Spherical mapping with areal smoothing 111s Spherical registration 317s rh: Thickness estimation (0.50 mm): WM distance: 40s CSF distance: 20s PBT2x thickness: 60s 127s Create initial surface 102s Topology correction: 128s Surface refinement: 137s Reduction of surface collisions with optimization: 87s Spherical mapping with areal smoothing 109s Spherical registration 351s Final surface processing results: Average thickness (FS): 2.4779  0.6458 mm Surface intensity / position RMSE: 0.0749 / 0.1057 Euler number / defect number / defect size: 22.0 / 13.0 / 1.65% Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/lh.thickness.sub-0025625_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/rh.thickness.sub-0025625_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2170s ROI estimation in native space: ROI estimation of 'cobra' atlas 13s ROI estimation of 'neuromorphometrics' atlas 45s ROI estimation of 'lpba40' atlas 13s ROI estimation of 'hammers' atlas 31s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 20s ROI estimation of 'mori' atlas 27s ROI estimation of 'anatomy3' atlas 40s ROI estimation of 'julichbrain' atlas 52s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s Write results 10s 510s Quality check: 14s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report/catreport_sub-0025625_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 63 minute(s) and 16 second(s). Image Quality Rating (IQR): 83.02% (B-) GM volume (GMV): 49.74% (741.37 / 1490.36 ml) GM thickness (GMT): 2.48  0.65 mm Segmentations are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report Labels are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/label ------------------------------------------------------------------------