------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_4169/ds/sub-030/sub-030_ses-t1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 9s APP: Rough bias correction: Initialize 4s Estimate background 4s Initial correction 4s Refine background 2s Final correction 4s Final scaling 4s 27s Correct center-of-mass 3s Affine registration 6s SPM preprocessing 1 (estimate 1 - TPM registration): 50s SPM preprocessing 1 (estimate 2): 47s SPM preprocessing 2 (write): Write Segmentation 11s Update Segmentation 13s Update Skull-Stripping 29s Update probability maps 6s 59s Global intensity correction: 10s SANLM denoising after intensity normalization (medium): 6s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.05) 9s Estimate local tissue thresholds (WM) 11s Estimate local tissue thresholds (GM) 15s Intensity transformation 0s SANLM denoising after LAS (medium) 11s 53s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 2s Ventricle detection 8s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 18s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 3s 47s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 19s 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 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 | 0.0832 0.0000 0.0832 | 32.0000 2 | 2.50 | 0.0805 0.0012 0.0817 | 29.4886 3 | 2.50 | 0.0796 0.0019 0.0815 | 26.9772 4 | 2.50 | 0.0792 0.0021 0.0813 | 24.6107 5 | 2.50 | 0.0789 0.0023 0.0812 | 22.6548 6 | 2.50 | 0.0786 0.0024 0.0810 | 20.6989 7 | 2.50 | 0.0782 0.0025 0.0808 | 18.9688 8 | 2.50 | 0.0779 0.0027 0.0806 | 17.4455 9 | 2.50 | 0.0776 0.0028 0.0803 | 15.9223 10 | 2.50 | 0.0772 0.0029 0.0801 | 14.6627 11 | 2.50 | 0.0768 0.0030 0.0798 | 13.4764 12 | 2.50 | 0.0765 0.0031 0.0796 | 12.3015 13 | 2.50 | 0.0761 0.0032 0.0793 | 11.3776 14 | 2.50 | 0.0757 0.0033 0.0790 | 10.4537 15 | 2.25 | 0.0746 0.0034 0.0780 | 9.5920 16 | 2.25 | 0.0715 0.0050 0.0765 | 8.8725 29 | 2.00 | 0.0721 0.0023 0.0743 | 3.3283 30 | 2.00 | 0.0657 0.0048 0.0705 | 3.1221 31 | 2.00 | 0.0635 0.0058 0.0693 | 2.9160 43 | 1.75 | 0.0621 0.0034 0.0656 | 1.5785 44 | 1.75 | 0.0581 0.0055 0.0636 | 1.5194 45 | 1.75 | 0.0567 0.0063 0.0630 | 1.4626 57 | 1.50 | 0.0550 0.0046 0.0596 | 1.0900 58 | 1.50 | 0.0522 0.0064 0.0587 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 110s Prepare output 7s 117s Jacobian determinant (RMS): 0.012 0.046 0.070 0.099 0.122 | 0.127636 Template Matching: 0.083 0.215 0.191 0.170 0.157 | 0.156711 Write result maps: 18s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 31s CSF distance: 11s PBT2x thickness: 32s 78s Create initial surface 54s Topology correction: 58s Surface refinement: 51s Reduction of surface collisions with optimization: 39s Spherical mapping with areal smoothing 52s Spherical registration 175s rh: Thickness estimation (0.50 mm): WM distance: 39s CSF distance: 10s PBT2x thickness: 31s 84s Create initial surface 50s Topology correction: 60s Surface refinement: 66s Reduction of surface collisions with optimization: 38s Spherical mapping with areal smoothing 53s Spherical registration 166s Final surface processing results: Average thickness (FS): 2.4931  0.6336 mm Surface intensity / position RMSE: 0.0658 / 0.0667 Euler number / defect number / defect size: 28.0 / 19.0 / 0.86% Display thickness: /var/lib/condor/execute/dir_4169/ds/sub-030/surf/lh.thickness.sub-030_ses-t1_T1w Display thickness: /var/lib/condor/execute/dir_4169/ds/sub-030/surf/rh.thickness.sub-030_ses-t1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_4169/ds/sub-030/sub-030_ses-t1_T1w.nii Surface ROI estimation: 5s Surface and thickness estimation takes: 1084s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 33s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 24s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 13s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 29s ROI estimation of 'julichbrain' atlas 39s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 97s Write results 98s 381s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_4169/ds/sub-030/report/catreport_sub-030_ses-t1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 33 minute(s) and 56 second(s). Image Quality Rating (IQR): 83.80% (B) GM volume (GMV): 46.32% (646.71 / 1396.33 ml) GM thickness (GMT): 2.49  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_4169/ds/sub-030/mri Reports are saved in /var/lib/condor/execute/dir_4169/ds/sub-030/report Labels are saved in /var/lib/condor/execute/dir_4169/ds/sub-030/label ------------------------------------------------------------------------