------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_12363/ds/sub-015/sub-015_ses-t2_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 9s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 2s Final correction 4s Final scaling 4s 30s Correct center-of-mass 7s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 53s SPM preprocessing 1 (estimate 2): 61s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 14s Update Skull-Stripping 31s Update probability maps 7s 64s Global intensity correction: 12s SANLM denoising after intensity normalization (medium): 5s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.19) 11s Estimate local tissue thresholds (WM) 13s Estimate local tissue thresholds (GM) 16s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 60s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 2s Ventricle detection 9s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 19s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 50s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] 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 9s 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 | 0.0796 0.0012 0.0808 | 29.4886 3 | 2.50 | 0.0788 0.0019 0.0807 | 26.9772 4 | 2.50 | 0.0784 0.0021 0.0805 | 24.6107 5 | 2.50 | 0.0780 0.0023 0.0803 | 22.6548 6 | 2.50 | 0.0777 0.0024 0.0801 | 20.6989 7 | 2.50 | 0.0774 0.0025 0.0799 | 18.9688 8 | 2.50 | 0.0771 0.0026 0.0797 | 17.4455 9 | 2.50 | 0.0768 0.0027 0.0795 | 15.9223 10 | 2.50 | 0.0764 0.0028 0.0793 | 14.6627 11 | 2.50 | 0.0761 0.0029 0.0790 | 13.4764 12 | 2.50 | 0.0757 0.0030 0.0787 | 12.3015 13 | 2.50 | 0.0753 0.0031 0.0785 | 11.3776 14 | 2.50 | 0.0750 0.0032 0.0782 | 10.4537 15 | 2.25 | 0.0739 0.0033 0.0772 | 9.5920 16 | 2.25 | 0.0709 0.0048 0.0756 | 8.8725 29 | 2.00 | 0.0715 0.0022 0.0736 | 3.3283 30 | 2.00 | 0.0652 0.0046 0.0698 | 3.1221 31 | 2.00 | 0.0629 0.0057 0.0686 | 2.9160 43 | 1.75 | 0.0614 0.0033 0.0647 | 1.5785 44 | 1.75 | 0.0573 0.0054 0.0627 | 1.5194 45 | 1.75 | 0.0559 0.0061 0.0620 | 1.4626 57 | 1.50 | 0.0542 0.0045 0.0587 | 1.0900 58 | 1.50 | 0.0514 0.0063 0.0577 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 119s Prepare output 8s 127s Jacobian determinant (RMS): 0.012 0.043 0.065 0.092 0.115 | 0.120079 Template Matching: 0.082 0.213 0.189 0.168 0.154 | 0.154316 Write result maps: 18s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 26s CSF distance: 10s PBT2x thickness: 29s 69s Create initial surface 60s Topology correction: 56s Surface refinement: 49s Reduction of surface collisions with optimization: 39s Spherical mapping with areal smoothing 52s Spherical registration 246s rh: Thickness estimation (0.50 mm): WM distance: 25s CSF distance: 10s PBT2x thickness: 29s 69s Create initial surface 60s Topology correction: 55s Surface refinement: 63s Reduction of surface collisions with optimization: 38s Spherical mapping with areal smoothing 52s Spherical registration 249s Final surface processing results: Average thickness (FS): 2.3551  0.6046 mm Surface intensity / position RMSE: 0.0628 / 0.0651 Euler number / defect number / defect size: 14.0 / 11.5 / 0.46% Display thickness: /var/lib/condor/execute/dir_12363/ds/sub-015/surf/lh.thickness.sub-015_ses-t2_T1w Display thickness: /var/lib/condor/execute/dir_12363/ds/sub-015/surf/rh.thickness.sub-015_ses-t2_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_12363/ds/sub-015/sub-015_ses-t2_T1w.nii Surface ROI estimation: 6s Surface and thickness estimation takes: 1222s 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 9s ROI estimation of 'mori' atlas 14s ROI estimation of 'anatomy3' atlas 20s ROI estimation of 'julichbrain' atlas 26s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s Write results 64s 260s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_12363/ds/sub-015/report/catreport_sub-015_ses-t2_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 35 minute(s) and 13 second(s). Image Quality Rating (IQR): 84.33% (B) GM volume (GMV): 43.50% (530.78 / 1220.19 ml) GM thickness (GMT): 2.36  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/mri Reports are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/report Labels are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/label ------------------------------------------------------------------------