------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025955/ses-1/sub-0025955_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 36s Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 4s Final scaling 5s 36s Correct center-of-mass 4s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 73s SPM preprocessing 1 (estimate 2): 71s SPM preprocessing 2 (write): Write Segmentation 16s Update Segmentation 18s Update Skull-Stripping 41s Update probability maps 8s 84s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 28s Fast Optimized Shooting registration 31s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 105s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 13s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 23s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 65s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05] 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 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 | 0.0854 0.0000 0.0854 | 32.0000 2 | 2.50 | 0.0825 0.0012 0.0837 | 29.4886 3 | 2.50 | 0.0816 0.0019 0.0835 | 26.9772 4 | 2.50 | 0.0811 0.0022 0.0833 | 24.6107 5 | 2.50 | 0.0808 0.0024 0.0831 | 22.6548 6 | 2.50 | 0.0805 0.0025 0.0829 | 20.6989 7 | 2.50 | 0.0801 0.0026 0.0827 | 18.9688 8 | 2.50 | 0.0798 0.0027 0.0825 | 17.4455 9 | 2.50 | 0.0795 0.0028 0.0823 | 15.9223 10 | 2.50 | 0.0791 0.0030 0.0820 | 14.6627 11 | 2.50 | 0.0787 0.0031 0.0818 | 13.4764 12 | 2.50 | 0.0784 0.0031 0.0815 | 12.3015 13 | 2.50 | 0.0780 0.0033 0.0812 | 11.3776 14 | 2.50 | 0.0776 0.0033 0.0810 | 10.4537 15 | 2.25 | 0.0776 0.0034 0.0810 | 9.5920 16 | 2.25 | 0.0744 0.0050 0.0795 | 8.8725 29 | 2.00 | 0.0758 0.0023 0.0781 | 3.3283 30 | 2.00 | 0.0694 0.0049 0.0742 | 3.1221 31 | 2.00 | 0.0671 0.0059 0.0730 | 2.9160 43 | 1.75 | 0.0661 0.0034 0.0695 | 1.5785 44 | 1.75 | 0.0617 0.0058 0.0674 | 1.5194 45 | 1.75 | 0.0602 0.0066 0.0668 | 1.4626 57 | 1.50 | 0.0588 0.0048 0.0636 | 1.0900 58 | 1.50 | 0.0556 0.0069 0.0625 | 1.0730 59 | 1.50 | 0.0545 0.0075 0.0621 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 169s Prepare output 10s 179s Jacobian determinant (RMS): 0.012 0.046 0.069 0.098 0.124 | 0.130830 Template Matching: 0.085 0.223 0.201 0.181 0.164 | 0.163567 Write result maps: 55s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 15s PBT2x thickness: 46s 96s Create initial surface 87s Topology correction: 98s Surface refinement: 85s Reduction of surface collisions with optimization: 73s Spherical mapping with areal smoothing 83s Spherical registration 294s rh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 15s PBT2x thickness: 45s 93s Create initial surface 83s Topology correction: 99s Surface refinement: 82s Reduction of surface collisions with optimization: 75s Spherical mapping with areal smoothing 84s Spherical registration 301s Final surface processing results: Average thickness (FS): 2.5218  0.5981 mm Surface intensity / position RMSE: 0.0688 / 0.0706 Euler number / defect number / defect size: 22.0 / 12.0 / 0.65% Display thickness: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/surf/lh.thickness.sub-0025955_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/surf/rh.thickness.sub-0025955_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/sub-0025955_ses-1_run-1_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 1731s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 29s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 20s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 12s ROI estimation of 'mori' atlas 19s ROI estimation of 'anatomy3' atlas 28s ROI estimation of 'julichbrain' atlas 43s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s Write results 11s 413s Quality check: 12s Print 'Graphics' figure to: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/report/catreport_sub-0025955_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 51 minute(s) and 21 second(s). Image Quality Rating (IQR): 80.85% (B-) GM volume (GMV): 51.92% (745.36 / 1435.49 ml) GM thickness (GMT): 2.52  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/report Labels are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/label ------------------------------------------------------------------------