------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025326/ses-2/sub-0025326_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 32s APP: Rough bias correction: Initialize 3s Estimate background 4s Initial correction 3s Refine background 2s Final correction 3s Final scaling 3s 21s Correct center-of-mass 2s Affine registration 5s SPM preprocessing 1 (estimate 1 - TPM registration): 50s SPM preprocessing 1 (estimate 2): 40s SPM preprocessing 2 (write): Write Segmentation 10s Update Segmentation 13s Update Skull-Stripping 24s Update probability maps 5s 52s Global intensity correction: 9s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 21s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 1s Prepare segments (LASmod = 1.00) 9s Estimate local tissue thresholds (WM) 11s Estimate local tissue thresholds (GM) 15s Intensity transformation 0s SANLM denoising after LAS (medium) 28s 69s ROI segmentation (partitioning): Atlas -> subject space 4s Major structures 2s Ventricle detection 9s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 13s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 3s 40s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] 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 7s 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 | 0.0841 0.0000 0.0841 | 32.0000 2 | 2.50 | 0.0811 0.0013 0.0824 | 29.4886 3 | 2.50 | 0.0802 0.0020 0.0822 | 26.9772 4 | 2.50 | 0.0798 0.0022 0.0820 | 24.6107 5 | 2.50 | 0.0795 0.0024 0.0818 | 22.6548 6 | 2.50 | 0.0792 0.0025 0.0816 | 20.6989 7 | 2.50 | 0.0788 0.0026 0.0814 | 18.9688 8 | 2.50 | 0.0785 0.0027 0.0812 | 17.4455 9 | 2.50 | 0.0782 0.0028 0.0809 | 15.9223 10 | 2.50 | 0.0778 0.0029 0.0807 | 14.6627 11 | 2.50 | 0.0775 0.0030 0.0805 | 13.4764 12 | 2.50 | 0.0771 0.0031 0.0802 | 12.3015 13 | 2.50 | 0.0767 0.0032 0.0799 | 11.3776 14 | 2.50 | 0.0764 0.0032 0.0796 | 10.4537 15 | 2.25 | 0.0755 0.0033 0.0788 | 9.5920 16 | 2.25 | 0.0721 0.0050 0.0771 | 8.8725 29 | 2.00 | 0.0726 0.0023 0.0748 | 3.3283 30 | 2.00 | 0.0662 0.0048 0.0710 | 3.1221 31 | 2.00 | 0.0640 0.0058 0.0697 | 2.9160 43 | 1.75 | 0.0625 0.0033 0.0658 | 1.5785 44 | 1.75 | 0.0584 0.0054 0.0638 | 1.5194 45 | 1.75 | 0.0570 0.0062 0.0632 | 1.4626 57 | 1.50 | 0.0553 0.0045 0.0598 | 1.0900 58 | 1.50 | 0.0524 0.0063 0.0587 | 1.0730 59 | 1.50 | 0.0515 0.0069 0.0584 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 111s Prepare output 7s 118s Jacobian determinant (RMS): 0.012 0.044 0.065 0.089 0.111 | 0.116807 Template Matching: 0.084 0.216 0.192 0.171 0.154 | 0.154402 Write result maps: 20s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 19s CSF distance: 10s PBT2x thickness: 29s 62s Create initial surface 51s Topology correction: 63s Surface refinement: 56s Reduction of surface collisions with optimization: 46s Spherical mapping with areal smoothing 58s Spherical registration 189s rh: Thickness estimation (0.50 mm): WM distance: 18s CSF distance: 9s PBT2x thickness: 28s 59s Create initial surface 50s Topology correction: 62s Surface refinement: 66s Reduction of surface collisions with optimization: 43s Spherical mapping with areal smoothing 55s Spherical registration 188s Final surface processing results: Average thickness (FS): 2.6367  0.6252 mm Surface intensity / position RMSE: 0.0684 / 0.0654 Euler number / defect number / defect size: 14.0 / 12.5 / 0.28% Display thickness: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/surf/lh.thickness.sub-0025326_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/surf/rh.thickness.sub-0025326_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/sub-0025326_ses-2_run-1_T1w.nii Surface ROI estimation: 6s Surface and thickness estimation takes: 1108s ROI estimation in native space: ROI estimation of 'cobra' atlas 5s ROI estimation of 'neuromorphometrics' atlas 19s ROI estimation of 'lpba40' atlas 5s ROI estimation of 'hammers' atlas 14s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 5s ROI estimation of 'aal3' atlas 8s ROI estimation of 'mori' atlas 12s ROI estimation of 'anatomy3' atlas 17s ROI estimation of 'julichbrain' atlas 24s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 257s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/report/catreport_sub-0025326_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 33 minute(s) and 26 second(s). Image Quality Rating (IQR): 79.98% (C+) GM volume (GMV): 49.52% (708.58 / 1431.03 ml) GM thickness (GMT): 2.64  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/report Labels are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-2/label ------------------------------------------------------------------------