------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season104_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 37s APP: Rough bias correction: Initialize 11s Estimate background 12s Initial correction 11s Refine background 6s Final correction 10s Final scaling 12s 73s Correct center-of-mass 5s Affine registration 17s SPM preprocessing 1 (estimate 1 - TPM registration): 8s Use initial fine affine registration. 141s SPM preprocessing 1 (estimate 2): 129s SPM preprocessing 2 (write): Write Segmentation 30s Update Segmentation 35s Update Skull-Stripping 75s Update probability maps 15s 155s Global intensity correction: 29s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 53s Local adaptive segmentation (LASstr=0.50): Prepare maps 9s Prepare partitions 4s Prepare segments (LASmod = 1.03) 30s Estimate local tissue thresholds (WM) 31s Estimate local tissue thresholds (GM) 42s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 157s ROI segmentation (partitioning): Atlas -> subject space 16s Major structures 8s Ventricle detection 29s Blood vessel detection 18s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 50s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 7s Final corrections 8s 137s Blood vessel correction (BVCstr=0.50): 3s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 69s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 9s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 5s 21s 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 | 0.0800 0.0000 0.0800 | 32.0000 2 | 2.50 | 0.0778 0.0011 0.0789 | 29.4886 3 | 2.50 | 0.0771 0.0016 0.0787 | 26.9772 4 | 2.50 | 0.0768 0.0018 0.0786 | 24.6107 5 | 2.50 | 0.0765 0.0019 0.0785 | 22.6548 6 | 2.50 | 0.0763 0.0020 0.0783 | 20.6989 7 | 2.50 | 0.0760 0.0021 0.0782 | 18.9688 8 | 2.50 | 0.0758 0.0022 0.0780 | 17.4455 9 | 2.50 | 0.0755 0.0023 0.0778 | 15.9223 10 | 2.50 | 0.0752 0.0024 0.0776 | 14.6627 11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764 12 | 2.50 | 0.0747 0.0025 0.0772 | 12.3015 13 | 2.50 | 0.0744 0.0026 0.0770 | 11.3776 14 | 2.50 | 0.0741 0.0026 0.0768 | 10.4537 15 | 2.25 | 0.0731 0.0027 0.0758 | 9.5920 16 | 2.25 | 0.0703 0.0041 0.0744 | 8.8725 29 | 2.00 | 0.0718 0.0019 0.0736 | 3.3283 30 | 2.00 | 0.0659 0.0042 0.0702 | 3.1221 31 | 2.00 | 0.0639 0.0052 0.0691 | 2.9160 43 | 1.75 | 0.0630 0.0030 0.0660 | 1.5785 44 | 1.75 | 0.0588 0.0052 0.0640 | 1.5194 45 | 1.75 | 0.0574 0.0060 0.0633 | 1.4626 57 | 1.50 | 0.0559 0.0043 0.0603 | 1.0900 58 | 1.50 | 0.0528 0.0063 0.0592 | 1.0730 59 | 1.50 | 0.0518 0.0070 0.0588 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 247s Prepare output 15s 262s Jacobian determinant (RMS): 0.010 0.038 0.056 0.078 0.100 | 0.107037 Template Matching: 0.080 0.211 0.192 0.172 0.155 | 0.155427 Write result maps: 42s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 65s CSF distance: 20s PBT2x thickness: 62s 157s Create initial surface 111s Topology correction: 130s Surface refinement: 147s Reduction of surface collisions with optimization: 98s Spherical mapping with areal smoothing 109s Spherical registration 281s rh: Thickness estimation (0.50 mm): WM distance: 47s CSF distance: 18s PBT2x thickness: 57s 132s Create initial surface 102s Topology correction: 111s Surface refinement: 100s Reduction of surface collisions with optimization: 94s Spherical mapping with areal smoothing 97s Spherical registration 256s Final surface processing results: Average thickness (FS): 2.5893  0.6774 mm Surface intensity / position RMSE: 0.0763 / 0.0875 Euler number / defect number / defect size: 46.0 / 20.0 / 1.16% Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/lh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/rh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 2046s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s ROI estimation of 'neuromorphometrics' atlas 66s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 47s ROI estimation of 'thalamus' atlas 4s ROI estimation of 'ibsr' atlas 17s ROI estimation of 'aal3' atlas 27s ROI estimation of 'mori' atlas 40s ROI estimation of 'anatomy3' atlas 59s ROI estimation of 'julichbrain' atlas 77s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 186s Write results 187s 751s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_32760/ds/sub-season104/report/catreport_sub-season104_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 71 minute(s) and 47 second(s). Image Quality Rating (IQR): 87.04% (B+) GM volume (GMV): 49.79% (715.80 / 1437.54 ml) GM thickness (GMT): 2.59  0.68 mm Segmentations are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/mri Reports are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/report Labels are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/label ------------------------------------------------------------------------