------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_12661/ds/sub-040/sub-040_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 25s APP: Rough bias correction: Initialize 6s Estimate background 8s Initial correction 6s Refine background 3s Final correction 5s Final scaling 7s 41s Correct center-of-mass 4s Affine registration 16s SPM preprocessing 1 (estimate 1 - TPM registration): 69s SPM preprocessing 1 (estimate 2): 65s SPM preprocessing 2 (write): Write Segmentation 16s Update Segmentation 18s Update Skull-Stripping 39s Update probability maps 8s 81s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 21s Fast Optimized Shooting registration 31s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.22) 14s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 30s 91s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 14s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 26s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 69s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 12s 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 | 0.0868 0.0000 0.0868 | 32.0000 2 | 2.50 | 0.0836 0.0014 0.0850 | 29.4886 3 | 2.50 | 0.0826 0.0021 0.0847 | 26.9772 4 | 2.50 | 0.0822 0.0023 0.0845 | 24.6107 5 | 2.50 | 0.0818 0.0025 0.0843 | 22.6548 6 | 2.50 | 0.0815 0.0026 0.0841 | 20.6989 7 | 2.50 | 0.0812 0.0027 0.0839 | 18.9688 8 | 2.50 | 0.0808 0.0028 0.0837 | 17.4455 9 | 2.50 | 0.0805 0.0029 0.0834 | 15.9223 10 | 2.50 | 0.0801 0.0030 0.0831 | 14.6627 11 | 2.50 | 0.0797 0.0031 0.0829 | 13.4764 12 | 2.50 | 0.0794 0.0032 0.0826 | 12.3015 13 | 2.50 | 0.0790 0.0033 0.0823 | 11.3776 14 | 2.50 | 0.0786 0.0034 0.0820 | 10.4537 15 | 2.25 | 0.0789 0.0035 0.0823 | 9.5920 16 | 2.25 | 0.0755 0.0051 0.0806 | 8.8725 17 | 2.25 | 0.0741 0.0057 0.0798 | 8.1530 29 | 2.00 | 0.0761 0.0026 0.0787 | 3.3283 30 | 2.00 | 0.0700 0.0052 0.0752 | 3.1221 31 | 2.00 | 0.0680 0.0062 0.0741 | 2.9160 43 | 1.75 | 0.0670 0.0035 0.0706 | 1.5785 44 | 1.75 | 0.0624 0.0060 0.0684 | 1.5194 45 | 1.75 | 0.0609 0.0068 0.0677 | 1.4626 57 | 1.50 | 0.0595 0.0050 0.0645 | 1.0900 58 | 1.50 | 0.0561 0.0072 0.0633 | 1.0730 59 | 1.50 | 0.0550 0.0079 0.0629 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 170s Prepare output 10s 180s Jacobian determinant (RMS): 0.012 0.043 0.066 0.093 0.119 | 0.126772 Template Matching: 0.087 0.222 0.204 0.183 0.165 | 0.164995 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 57s CSF distance: 15s PBT2x thickness: 42s 120s Create initial surface 81s Topology correction: 92s Surface refinement: 97s Reduction of surface collisions with optimization: 68s Spherical mapping with areal smoothing 77s Spherical registration 269s rh: Thickness estimation (0.50 mm): WM distance: 37s CSF distance: 15s PBT2x thickness: 42s 100s Create initial surface 82s Topology correction: 90s Surface refinement: 87s Reduction of surface collisions with optimization: 65s Spherical mapping with areal smoothing 78s Spherical registration 304s Final surface processing results: Average thickness (FS): 2.4192  0.6304 mm Surface intensity / position RMSE: 0.0618 / 0.0641 Euler number / defect number / defect size: 10.0 / 8.5 / 0.64% Display thickness: /var/lib/condor/execute/dir_12661/ds/sub-040/surf/lh.thickness.sub-040_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_12661/ds/sub-040/surf/rh.thickness.sub-040_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_12661/ds/sub-040/sub-040_ses-t0_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 1701s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 36s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 27s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 19s ROI estimation of 'mori' atlas 29s ROI estimation of 'anatomy3' atlas 43s ROI estimation of 'julichbrain' atlas 64s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 77s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s Write results 114s 503s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_12661/ds/sub-040/report/catreport_sub-040_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 51 minute(s) and 26 second(s). Image Quality Rating (IQR): 83.78% (B) GM volume (GMV): 42.99% (638.68 / 1485.52 ml) GM thickness (GMT): 2.42  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/mri Reports are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/report Labels are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/label ------------------------------------------------------------------------