------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025932/ses-2/sub-0025932_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 46s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 5s 36s Correct center-of-mass 3s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 86s SPM preprocessing 1 (estimate 2): 75s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 18s Update Skull-Stripping 41s Update probability maps 8s 84s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 26s Fast Optimized Shooting registration 33s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.05) 14s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 26s Intensity transformation 0s SANLM denoising after LAS (medium) 40s 108s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 15s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 23s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 66s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0873 0.0000 0.0873 | 32.0000 2 | 2.50 | 0.0836 0.0015 0.0851 | 29.4886 3 | 2.50 | 0.0824 0.0023 0.0847 | 26.9772 4 | 2.50 | 0.0818 0.0026 0.0845 | 24.6107 5 | 2.50 | 0.0814 0.0029 0.0842 | 22.6548 6 | 2.50 | 0.0810 0.0030 0.0839 | 20.6989 7 | 2.50 | 0.0805 0.0031 0.0837 | 18.9688 8 | 2.50 | 0.0801 0.0033 0.0834 | 17.4455 9 | 2.50 | 0.0797 0.0034 0.0831 | 15.9223 10 | 2.50 | 0.0792 0.0035 0.0828 | 14.6627 11 | 2.50 | 0.0788 0.0037 0.0824 | 13.4764 12 | 2.50 | 0.0783 0.0038 0.0821 | 12.3015 13 | 2.50 | 0.0778 0.0039 0.0817 | 11.3776 14 | 2.50 | 0.0774 0.0040 0.0814 | 10.4537 15 | 2.25 | 0.0777 0.0041 0.0818 | 9.5920 16 | 2.25 | 0.0743 0.0058 0.0801 | 8.8725 29 | 2.00 | 0.0753 0.0026 0.0779 | 3.3283 30 | 2.00 | 0.0684 0.0054 0.0738 | 3.1221 31 | 2.00 | 0.0659 0.0065 0.0724 | 2.9160 43 | 1.75 | 0.0646 0.0038 0.0684 | 1.5785 44 | 1.75 | 0.0602 0.0061 0.0663 | 1.5194 45 | 1.75 | 0.0587 0.0069 0.0655 | 1.4626 57 | 1.50 | 0.0571 0.0051 0.0622 | 1.0900 58 | 1.50 | 0.0540 0.0071 0.0611 | 1.0730 59 | 1.50 | 0.0529 0.0077 0.0607 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 171s Prepare output 11s 182s Jacobian determinant (RMS): 0.013 0.049 0.074 0.101 0.125 | 0.131460 Template Matching: 0.087 0.223 0.198 0.176 0.159 | 0.158805 Write result maps: 35s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 30s CSF distance: 16s PBT2x thickness: 44s 96s Create initial surface 86s Topology correction: 94s Surface refinement: 76s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 78s Spherical registration 300s rh: Thickness estimation (0.50 mm): WM distance: 34s CSF distance: 14s PBT2x thickness: 43s 97s Create initial surface 86s Topology correction: 93s Surface refinement: 107s Reduction of surface collisions with optimization: 69s Spherical mapping with areal smoothing 81s Spherical registration 300s Final surface processing results: Average thickness (FS): 2.5239  0.6208 mm Surface intensity / position RMSE: 0.0683 / 0.0681 Euler number / defect number / defect size: 24.0 / 11.5 / 0.73% Display thickness: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/surf/lh.thickness.sub-0025932_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/surf/rh.thickness.sub-0025932_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/sub-0025932_ses-2_run-1_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1730s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 30s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 22s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 13s ROI estimation of 'mori' atlas 19s ROI estimation of 'anatomy3' atlas 28s ROI estimation of 'julichbrain' atlas 38s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s Write results 14s 435s Quality check: 14s Print 'Graphics' figure to: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/report/catreport_sub-0025932_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 52 minute(s) and 13 second(s). Image Quality Rating (IQR): 80.22% (B-) GM volume (GMV): 49.73% (701.26 / 1410.04 ml) GM thickness (GMT): 2.52  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/report Labels are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/label ------------------------------------------------------------------------