------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_19436/ds/sub-009/sub-009_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 18s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 4s Final scaling 5s 35s Correct center-of-mass 4s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 70s SPM preprocessing 1 (estimate 2): 59s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 39s Update probability maps 8s 79s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 17s Fast Optimized Shooting registration 33s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.12) 13s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 19s Intensity transformation 0s SANLM denoising after LAS (medium) 24s 80s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 11s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 24s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 1s 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 | 0.0855 0.0000 0.0855 | 32.0000 2 | 2.50 | 0.0822 0.0014 0.0836 | 29.4886 3 | 2.50 | 0.0812 0.0021 0.0833 | 26.9772 4 | 2.50 | 0.0807 0.0024 0.0831 | 24.6107 5 | 2.50 | 0.0803 0.0026 0.0829 | 22.6548 6 | 2.50 | 0.0799 0.0027 0.0827 | 20.6989 7 | 2.50 | 0.0796 0.0029 0.0824 | 18.9688 8 | 2.50 | 0.0792 0.0030 0.0822 | 17.4455 9 | 2.50 | 0.0788 0.0031 0.0819 | 15.9223 10 | 2.50 | 0.0784 0.0032 0.0816 | 14.6627 11 | 2.50 | 0.0780 0.0034 0.0813 | 13.4764 12 | 2.50 | 0.0775 0.0034 0.0810 | 12.3015 13 | 2.50 | 0.0771 0.0036 0.0807 | 11.3776 14 | 2.50 | 0.0767 0.0037 0.0803 | 10.4537 15 | 2.25 | 0.0761 0.0038 0.0799 | 9.5920 16 | 2.25 | 0.0728 0.0055 0.0783 | 8.8725 29 | 2.00 | 0.0733 0.0025 0.0758 | 3.3283 30 | 2.00 | 0.0664 0.0053 0.0717 | 3.1221 31 | 2.00 | 0.0640 0.0064 0.0704 | 2.9160 43 | 1.75 | 0.0624 0.0037 0.0661 | 1.5785 44 | 1.75 | 0.0581 0.0059 0.0640 | 1.5194 45 | 1.75 | 0.0566 0.0067 0.0633 | 1.4626 57 | 1.50 | 0.0549 0.0050 0.0599 | 1.0900 58 | 1.50 | 0.0520 0.0068 0.0588 | 1.0730 59 | 1.50 | 0.0511 0.0074 0.0585 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 163s Prepare output 10s 173s Jacobian determinant (RMS): 0.013 0.050 0.075 0.103 0.125 | 0.131886 Template Matching: 0.086 0.218 0.192 0.170 0.153 | 0.153215 Write result maps: 22s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 56s CSF distance: 13s PBT2x thickness: 38s 112s Create initial surface 77s Topology correction: 69s Surface refinement: 55s Reduction of surface collisions with optimization: 50s Spherical mapping with areal smoothing 65s Spherical registration 293s rh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 12s PBT2x thickness: 35s 81s Create initial surface 74s Topology correction: 68s Surface refinement: 65s Reduction of surface collisions with optimization: 51s Spherical mapping with areal smoothing 66s Spherical registration 287s Final surface processing results: Average thickness (FS): 2.4845  0.6111 mm Surface intensity / position RMSE: 0.0632 / 0.0630 Euler number / defect number / defect size: 10.0 / 7.0 / 0.48% Display thickness: /var/lib/condor/execute/dir_19436/ds/sub-009/surf/lh.thickness.sub-009_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_19436/ds/sub-009/surf/rh.thickness.sub-009_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_19436/ds/sub-009/sub-009_ses-t0_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1492s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 29s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s Write results 84s 306s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_19436/ds/sub-009/report/catreport_sub-009_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 43 minute(s) and 33 second(s). Image Quality Rating (IQR): 82.80% (B-) GM volume (GMV): 45.25% (574.13 / 1268.90 ml) GM thickness (GMT): 2.48  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/mri Reports are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/report Labels are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/label ------------------------------------------------------------------------