------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025985/ses-2/sub-0025985_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 37s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 4s Refine background 2s Final correction 4s Final scaling 3s 29s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 58s SPM preprocessing 1 (estimate 2): 66s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 15s Update Skull-Stripping 33s Update probability maps 7s 67s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 17s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 10s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 20s Intensity transformation 0s SANLM denoising after LAS (medium) 36s 87s ROI segmentation (partitioning): Atlas -> subject space 5s Major structures 2s Ventricle detection 9s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 16s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 4s 46s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 24s 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 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 | 0.0883 0.0000 0.0883 | 32.0000 2 | 2.50 | 0.0849 0.0014 0.0863 | 29.4886 3 | 2.50 | 0.0839 0.0022 0.0860 | 26.9772 4 | 2.50 | 0.0833 0.0025 0.0858 | 24.6107 5 | 2.50 | 0.0829 0.0027 0.0856 | 22.6548 6 | 2.50 | 0.0826 0.0028 0.0854 | 20.6989 7 | 2.50 | 0.0822 0.0029 0.0851 | 18.9688 8 | 2.50 | 0.0818 0.0031 0.0849 | 17.4455 9 | 2.50 | 0.0814 0.0032 0.0846 | 15.9223 10 | 2.50 | 0.0810 0.0033 0.0843 | 14.6627 11 | 2.50 | 0.0806 0.0034 0.0840 | 13.4764 12 | 2.50 | 0.0802 0.0035 0.0837 | 12.3015 13 | 2.50 | 0.0798 0.0036 0.0834 | 11.3776 14 | 2.50 | 0.0794 0.0037 0.0831 | 10.4537 15 | 2.25 | 0.0797 0.0038 0.0835 | 9.5920 16 | 2.25 | 0.0762 0.0055 0.0818 | 8.8725 17 | 2.25 | 0.0748 0.0062 0.0810 | 8.1530 29 | 2.00 | 0.0767 0.0028 0.0795 | 3.3283 30 | 2.00 | 0.0700 0.0056 0.0756 | 3.1221 31 | 2.00 | 0.0676 0.0067 0.0743 | 2.9160 43 | 1.75 | 0.0662 0.0039 0.0701 | 1.5785 44 | 1.75 | 0.0616 0.0063 0.0679 | 1.5194 45 | 1.75 | 0.0600 0.0071 0.0671 | 1.4626 57 | 1.50 | 0.0584 0.0052 0.0637 | 1.0900 58 | 1.50 | 0.0553 0.0073 0.0626 | 1.0730 59 | 1.50 | 0.0543 0.0079 0.0621 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 136s Prepare output 8s 144s Jacobian determinant (RMS): 0.012 0.045 0.068 0.094 0.125 | 0.124004 Template Matching: 0.088 0.224 0.203 0.180 0.163 | 0.162802 Write result maps: 26s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 21s CSF distance: 10s PBT2x thickness: 30s 65s Create initial surface 58s Topology correction: 58s Surface refinement: 69s Reduction of surface collisions with optimization: 42s Spherical mapping with areal smoothing 56s Spherical registration 255s rh: Thickness estimation (0.50 mm): WM distance: 20s CSF distance: 10s PBT2x thickness: 30s 64s Create initial surface 58s Topology correction: 58s Surface refinement: 53s Reduction of surface collisions with optimization: 44s Spherical mapping with areal smoothing 56s Spherical registration 233s Final surface processing results: Average thickness (FS): 2.3929  0.6276 mm Surface intensity / position RMSE: 0.0625 / 0.0656 Euler number / defect number / defect size: 22.0 / 12.0 / 0.69% Display thickness: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/surf/lh.thickness.sub-0025985_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/surf/rh.thickness.sub-0025985_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/sub-0025985_ses-2_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1238s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 30s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 301s Quality check: 9s Print 'Graphics' figure to: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/report/catreport_sub-0025985_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 38 minute(s) and 2 second(s). Image Quality Rating (IQR): 82.30% (B-) GM volume (GMV): 45.85% (559.53 / 1220.48 ml) GM thickness (GMT): 2.39  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/report Labels are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/label ------------------------------------------------------------------------