------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season216_ses-2_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 56s APP: Rough bias correction: Initialize 8s Estimate background 10s Initial correction 12s Refine background 4s Final correction 10s Final scaling 9s 62s Correct center-of-mass 8s Affine registration 19s SPM preprocessing 1 (estimate 1 - TPM registration): 100s SPM preprocessing 1 (estimate 2): 71s SPM preprocessing 2 (write): Write Segmentation 20s Update Segmentation 27s Update Skull-Stripping 55s Update probability maps 11s 112s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 31s Fast Optimized Shooting registration 37s Local adaptive segmentation (LASstr=0.50): Prepare maps 6s Prepare partitions 7s Prepare segments (LASmod = 1.00) 21s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 32s Intensity transformation 0s SANLM denoising after LAS (medium) 51s 144s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 5s Ventricle detection 20s Blood vessel detection 14s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 41s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 6s 103s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 6s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 16s 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 | 0.0833 0.0000 0.0833 | 32.0000 2 | 2.50 | 0.0807 0.0012 0.0819 | 29.4886 3 | 2.50 | 0.0799 0.0018 0.0817 | 26.9772 4 | 2.50 | 0.0795 0.0020 0.0816 | 24.6107 5 | 2.50 | 0.0792 0.0022 0.0814 | 22.6548 6 | 2.50 | 0.0789 0.0023 0.0812 | 20.6989 7 | 2.50 | 0.0786 0.0024 0.0810 | 18.9688 8 | 2.50 | 0.0783 0.0025 0.0808 | 17.4455 9 | 2.50 | 0.0780 0.0026 0.0806 | 15.9223 10 | 2.50 | 0.0777 0.0027 0.0804 | 14.6627 11 | 2.50 | 0.0773 0.0028 0.0802 | 13.4764 12 | 2.50 | 0.0770 0.0029 0.0799 | 12.3015 13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776 14 | 2.50 | 0.0763 0.0031 0.0794 | 10.4537 15 | 2.25 | 0.0751 0.0032 0.0783 | 9.5920 16 | 2.25 | 0.0719 0.0047 0.0766 | 8.8725 29 | 2.00 | 0.0723 0.0021 0.0745 | 3.3283 30 | 2.00 | 0.0657 0.0048 0.0705 | 3.1221 31 | 2.00 | 0.0635 0.0059 0.0693 | 2.9160 43 | 1.75 | 0.0619 0.0034 0.0653 | 1.5785 44 | 1.75 | 0.0577 0.0056 0.0633 | 1.5194 45 | 1.75 | 0.0563 0.0064 0.0627 | 1.4626 57 | 1.50 | 0.0543 0.0047 0.0590 | 1.0900 58 | 1.50 | 0.0515 0.0065 0.0580 | 1.0730 59 | 1.50 | 0.0506 0.0071 0.0577 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 171s Prepare output 12s 183s Jacobian determinant (RMS): 0.012 0.044 0.067 0.094 0.119 | 0.127053 Template Matching: 0.083 0.216 0.190 0.169 0.152 | 0.151657 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 31s CSF distance: 14s PBT2x thickness: 39s 90s Create initial surface 74s Topology correction: 70s Surface refinement: 67s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 74s Spherical registration 293s rh: Thickness estimation (0.50 mm): WM distance: 37s CSF distance: 13s PBT2x thickness: 39s 95s Create initial surface 74s Topology correction: 68s Surface refinement: 69s Reduction of surface collisions with optimization: 54s Spherical mapping with areal smoothing 68s Spherical registration 265s Final surface processing results: Average thickness (FS): 2.6493  0.6298 mm Surface intensity / position RMSE: 0.0599 / 0.0597 Euler number / defect number / defect size: 6.0 / 7.0 / 0.04% Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/lh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/rh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_9449/ds/sub-season216/sub-season216_ses-2_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1510s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 35s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 25s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 21s ROI estimation of 'anatomy3' atlas 29s ROI estimation of 'julichbrain' atlas 39s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 93s Write results 93s 393s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_9449/ds/sub-season216/report/catreport_sub-season216_ses-2_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 51 minute(s) and 22 second(s). Image Quality Rating (IQR): 87.33% (B+) GM volume (GMV): 45.55% (649.12 / 1424.94 ml) GM thickness (GMT): 2.65  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/mri Reports are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/report Labels are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/label ------------------------------------------------------------------------