------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 30s APP: Rough bias correction: Initialize 4s Estimate background 3s Initial correction 3s Refine background 2s Final correction 3s Final scaling 3s 22s Correct center-of-mass 3s Affine registration 5s SPM preprocessing 1 (estimate 1 - TPM registration): 5s Use initial fine affine registration. 34s SPM preprocessing 1 (estimate 2): 35s SPM preprocessing 2 (write): Write Segmentation 10s Update Segmentation 11s Update Skull-Stripping 24s Update probability maps 5s 51s Global intensity correction: 10s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 20s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 1s Prepare segments (LASmod = 1.00) 7s Estimate local tissue thresholds (WM) 11s Estimate local tissue thresholds (GM) 15s Intensity transformation 0s SANLM denoising after LAS (medium) 27s 65s ROI segmentation (partitioning): Atlas -> subject space 4s Major structures 2s Ventricle detection 5s Blood vessel detection 5s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 11s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 3s 32s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 19s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 2s Level 1 cleanup (brain masking) 1s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 1s 6s 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 | 0.0836 0.0000 0.0836 | 32.0000 2 | 2.50 | 0.0808 0.0012 0.0821 | 29.4886 3 | 2.50 | 0.0800 0.0019 0.0819 | 26.9772 4 | 2.50 | 0.0796 0.0021 0.0817 | 24.6107 5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548 6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989 7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688 8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455 9 | 2.50 | 0.0780 0.0027 0.0807 | 15.9223 10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627 11 | 2.50 | 0.0772 0.0029 0.0802 | 13.4764 12 | 2.50 | 0.0769 0.0030 0.0799 | 12.3015 13 | 2.50 | 0.0765 0.0031 0.0796 | 11.3776 14 | 2.50 | 0.0761 0.0032 0.0793 | 10.4537 15 | 2.25 | 0.0759 0.0033 0.0792 | 9.5920 16 | 2.25 | 0.0727 0.0049 0.0776 | 8.8725 29 | 2.00 | 0.0736 0.0022 0.0758 | 3.3283 30 | 2.00 | 0.0670 0.0048 0.0718 | 3.1221 31 | 2.00 | 0.0647 0.0059 0.0706 | 2.9160 43 | 1.75 | 0.0634 0.0034 0.0668 | 1.5785 44 | 1.75 | 0.0590 0.0057 0.0647 | 1.5194 45 | 1.75 | 0.0576 0.0065 0.0641 | 1.4626 57 | 1.50 | 0.0562 0.0047 0.0609 | 1.0900 58 | 1.50 | 0.0531 0.0067 0.0599 | 1.0730 59 | 1.50 | 0.0521 0.0073 0.0595 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 97s Prepare output 6s 103s Jacobian determinant (RMS): 0.011 0.042 0.063 0.087 0.111 | 0.116150 Template Matching: 0.084 0.218 0.194 0.173 0.156 | 0.156349 Write result maps: 20s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 21s CSF distance: 8s PBT2x thickness: 23s 55s Create initial surface 41s Topology correction: 54s Surface refinement: 50s Reduction of surface collisions with optimization: 34s Spherical mapping with areal smoothing 45s Spherical registration 164s rh: Thickness estimation (0.50 mm): WM distance: 15s CSF distance: 8s PBT2x thickness: 23s 48s Create initial surface 41s Topology correction: 54s Surface refinement: 53s Reduction of surface collisions with optimization: 34s Spherical mapping with areal smoothing 45s Spherical registration 176s Final surface processing results: Average thickness (FS): 2.3834  0.6297 mm Surface intensity / position RMSE: 0.0696 / 0.0742 Euler number / defect number / defect size: 30.0 / 14.5 / 0.84% Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/lh.thickness.sub-0025995_ses-4_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/rh.thickness.sub-0025995_ses-4_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.nii Surface ROI estimation: 5s Surface and thickness estimation takes: 948s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 21s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 15s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 5s ROI estimation of 'aal3' atlas 8s ROI estimation of 'mori' atlas 11s ROI estimation of 'anatomy3' atlas 16s ROI estimation of 'julichbrain' atlas 21s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 34s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s Write results 5s 224s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report/catreport_sub-0025995_ses-4_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 28 minute(s) and 33 second(s). Image Quality Rating (IQR): 81.21% (B-) GM volume (GMV): 45.87% (597.31 / 1302.25 ml) GM thickness (GMT): 2.38  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/mri Reports are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report Labels are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/label ------------------------------------------------------------------------