------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025977/ses-2/sub-0025977_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 55s APP: Rough bias correction: Initialize 7s Estimate background 6s Initial correction 7s Refine background 3s Final correction 6s Final scaling 5s 42s Correct center-of-mass 3s Affine registration 11s SPM preprocessing 1 (estimate 1 - TPM registration): 92s SPM preprocessing 1 (estimate 2): 110s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 22s Update Skull-Stripping 49s Update probability maps 10s 103s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 30s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 3s Prepare segments (LASmod = 1.00) 16s Estimate local tissue thresholds (WM) 24s Estimate local tissue thresholds (GM) 36s Intensity transformation 0s SANLM denoising after LAS (medium) 52s 138s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 15s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 5s 77s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s 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 | 0.0814 0.0000 0.0814 | 32.0000 2 | 2.50 | 0.0787 0.0012 0.0799 | 29.4886 3 | 2.50 | 0.0779 0.0018 0.0797 | 26.9772 4 | 2.50 | 0.0775 0.0021 0.0796 | 24.6107 5 | 2.50 | 0.0772 0.0022 0.0794 | 22.6548 6 | 2.50 | 0.0769 0.0023 0.0792 | 20.6989 7 | 2.50 | 0.0766 0.0024 0.0790 | 18.9688 8 | 2.50 | 0.0762 0.0026 0.0788 | 17.4455 9 | 2.50 | 0.0759 0.0026 0.0786 | 15.9223 10 | 2.50 | 0.0756 0.0028 0.0784 | 14.6627 11 | 2.50 | 0.0753 0.0028 0.0781 | 13.4764 12 | 2.50 | 0.0750 0.0029 0.0779 | 12.3015 13 | 2.50 | 0.0746 0.0030 0.0776 | 11.3776 14 | 2.50 | 0.0743 0.0031 0.0774 | 10.4537 15 | 2.25 | 0.0733 0.0032 0.0765 | 9.5920 16 | 2.25 | 0.0704 0.0046 0.0750 | 8.8725 29 | 2.00 | 0.0715 0.0021 0.0736 | 3.3283 30 | 2.00 | 0.0654 0.0045 0.0698 | 3.1221 31 | 2.00 | 0.0632 0.0054 0.0687 | 2.9160 43 | 1.75 | 0.0622 0.0032 0.0654 | 1.5785 44 | 1.75 | 0.0581 0.0053 0.0634 | 1.5194 45 | 1.75 | 0.0567 0.0061 0.0627 | 1.4626 57 | 1.50 | 0.0552 0.0044 0.0596 | 1.0900 58 | 1.50 | 0.0523 0.0063 0.0586 | 1.0730 59 | 1.50 | 0.0513 0.0069 0.0582 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 206s Prepare output 14s 220s Jacobian determinant (RMS): 0.011 0.040 0.059 0.081 0.103 | 0.109847 Template Matching: 0.081 0.211 0.190 0.170 0.154 | 0.153896 Write result maps: 47s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 39s CSF distance: 21s PBT2x thickness: 58s 125s Create initial surface 102s Topology correction: 114s Surface refinement: 119s Reduction of surface collisions with optimization: 85s Spherical mapping with areal smoothing 107s Spherical registration 363s rh: Thickness estimation (0.50 mm): WM distance: 33s CSF distance: 19s PBT2x thickness: 56s 115s Create initial surface 101s Topology correction: 112s Surface refinement: 91s Reduction of surface collisions with optimization: 79s Spherical mapping with areal smoothing 105s Spherical registration 336s Final surface processing results: Average thickness (FS): 2.5806  0.6359 mm Surface intensity / position RMSE: 0.0710 / 0.0748 Euler number / defect number / defect size: 20.0 / 17.0 / 0.78% Display thickness: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/surf/lh.thickness.sub-0025977_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/surf/rh.thickness.sub-0025977_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/sub-0025977_ses-2_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2075s ROI estimation in native space: ROI estimation of 'cobra' atlas 14s ROI estimation of 'neuromorphometrics' atlas 52s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 35s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 20s ROI estimation of 'mori' atlas 33s ROI estimation of 'anatomy3' atlas 46s ROI estimation of 'julichbrain' atlas 60s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 54s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 109s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 150s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s Write results 16s 646s Quality check: 16s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/report/catreport_sub-0025977_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 64 minute(s) and 55 second(s). Image Quality Rating (IQR): 83.75% (B) GM volume (GMV): 50.97% (699.63 / 1372.65 ml) GM thickness (GMT): 2.58  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/report Labels are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/label ------------------------------------------------------------------------