------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_3568911/ds/sub-049/sub-049_ses-t1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 13s APP: Rough bias correction: Initialize 7s Estimate background 6s Initial correction 8s Refine background 4s Final correction 7s Final scaling 7s 46s Correct center-of-mass 10s Affine registration 11s SPM preprocessing 1 (estimate 1 - TPM registration): 84s SPM preprocessing 1 (estimate 2): 90s SPM preprocessing 2 (write): Write Segmentation 19s Update Segmentation 21s Update Skull-Stripping 49s Update probability maps 10s 99s Global intensity correction: 17s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.10) 15s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 17s 86s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 4s Ventricle detection 15s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 76s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] 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 12s 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 | 0.0901 0.0000 0.0901 | 32.0000 2 | 2.50 | 0.0862 0.0016 0.0877 | 29.4886 3 | 2.50 | 0.0850 0.0024 0.0874 | 26.9772 4 | 2.50 | 0.0844 0.0028 0.0871 | 24.6107 5 | 2.50 | 0.0839 0.0030 0.0869 | 22.6548 6 | 2.50 | 0.0835 0.0031 0.0866 | 20.6989 7 | 2.50 | 0.0831 0.0032 0.0864 | 18.9688 8 | 2.50 | 0.0827 0.0034 0.0861 | 17.4455 9 | 2.50 | 0.0823 0.0035 0.0857 | 15.9223 10 | 2.50 | 0.0818 0.0036 0.0854 | 14.6627 11 | 2.50 | 0.0813 0.0037 0.0851 | 13.4764 12 | 2.50 | 0.0809 0.0038 0.0847 | 12.3015 13 | 2.50 | 0.0804 0.0040 0.0844 | 11.3776 14 | 2.50 | 0.0799 0.0041 0.0840 | 10.4537 15 | 2.25 | 0.0802 0.0042 0.0844 | 9.5920 16 | 2.25 | 0.0763 0.0061 0.0824 | 8.8725 17 | 2.25 | 0.0747 0.0068 0.0815 | 8.1530 29 | 2.00 | 0.0759 0.0031 0.0790 | 3.3283 30 | 2.00 | 0.0694 0.0059 0.0753 | 3.1221 31 | 2.00 | 0.0672 0.0069 0.0741 | 2.9160 43 | 1.75 | 0.0660 0.0040 0.0700 | 1.5785 44 | 1.75 | 0.0617 0.0062 0.0679 | 1.5194 45 | 1.75 | 0.0603 0.0070 0.0673 | 1.4626 57 | 1.50 | 0.0588 0.0052 0.0639 | 1.0900 58 | 1.50 | 0.0557 0.0071 0.0628 | 1.0730 59 | 1.50 | 0.0547 0.0078 0.0624 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 213s Prepare output 11s 224s Jacobian determinant (RMS): 0.012 0.049 0.076 0.103 0.126 | 0.133633 Template Matching: 0.090 0.224 0.202 0.181 0.164 | 0.164048 Write result maps: 30s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 50s CSF distance: 18s PBT2x thickness: 51s 125s Create initial surface 81s Topology correction: 103s Surface refinement: 81s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 132s Spherical registration 277s rh: Thickness estimation (0.50 mm): WM distance: 43s CSF distance: 17s PBT2x thickness: 51s 118s Create initial surface 83s Topology correction: 96s Surface refinement: 80s Reduction of surface collisions with optimization: 60s Spherical mapping with areal smoothing 88s Spherical registration 286s Final surface processing results: Average thickness (FS): 2.5045  0.6198 mm Surface intensity / position RMSE: 0.0655 / 0.0689 Euler number / defect number / defect size: 28.0 / 14.5 / 1.27% Display thickness: /var/lib/condor/execute/dir_3568911/ds/sub-049/surf/lh.thickness.sub-049_ses-t1_T1w Display thickness: /var/lib/condor/execute/dir_3568911/ds/sub-049/surf/rh.thickness.sub-049_ses-t1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3568911/ds/sub-049/sub-049_ses-t1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1769s ROI estimation in native space: ROI estimation of 'cobra' atlas 15s ROI estimation of 'neuromorphometrics' atlas 54s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 38s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 21s ROI estimation of 'mori' atlas 31s ROI estimation of 'anatomy3' atlas 45s ROI estimation of 'julichbrain' atlas 60s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 142s Write results 142s 581s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3568911/ds/sub-049/report/catreport_sub-049_ses-t1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 55 minute(s) and 33 second(s). Image Quality Rating (IQR): 83.71% (B) GM volume (GMV): 46.80% (657.89 / 1405.86 ml) GM thickness (GMT): 2.50  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/mri Reports are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/report Labels are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/label ------------------------------------------------------------------------