------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_11102/ds/sub-22/sub-22_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 30s APP: Rough bias correction: Initialize 6s Estimate background 10s Initial correction 7s Refine background 4s Final correction 5s Final scaling 7s 44s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 60s SPM preprocessing 1 (estimate 2): 46s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 17s Update Skull-Stripping 36s Update probability maps 8s 75s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 5s Fast Optimized Shooting registration 30s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 11s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 23s 83s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 12s Blood vessel detection 7s WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 20s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 57s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 28s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.05] Final cleanup (gcutstr=0.24): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 9s 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 | 0.0869 0.0000 0.0869 | 32.0000 2 | 2.50 | 0.0839 0.0012 0.0852 | 29.4886 3 | 2.50 | 0.0830 0.0019 0.0850 | 26.9772 4 | 2.50 | 0.0826 0.0022 0.0848 | 24.6107 5 | 2.50 | 0.0822 0.0024 0.0846 | 22.6548 6 | 2.50 | 0.0819 0.0025 0.0844 | 20.6989 7 | 2.50 | 0.0816 0.0026 0.0842 | 18.9688 8 | 2.50 | 0.0812 0.0028 0.0840 | 17.4455 9 | 2.50 | 0.0809 0.0029 0.0837 | 15.9223 10 | 2.50 | 0.0805 0.0030 0.0835 | 14.6627 11 | 2.50 | 0.0801 0.0031 0.0832 | 13.4764 12 | 2.50 | 0.0797 0.0032 0.0829 | 12.3015 13 | 2.50 | 0.0793 0.0033 0.0827 | 11.3776 14 | 2.50 | 0.0789 0.0034 0.0823 | 10.4537 15 | 2.25 | 0.0807 0.0035 0.0842 | 9.5920 16 | 2.25 | 0.0772 0.0053 0.0825 | 8.8725 17 | 2.25 | 0.0756 0.0060 0.0816 | 8.1530 18 | 2.25 | 0.0746 0.0063 0.0809 | 7.5234 29 | 2.00 | 0.0769 0.0030 0.0800 | 3.3283 30 | 2.00 | 0.0710 0.0056 0.0766 | 3.1221 31 | 2.00 | 0.0688 0.0066 0.0754 | 2.9160 43 | 1.75 | 0.0678 0.0038 0.0716 | 1.5785 44 | 1.75 | 0.0632 0.0062 0.0694 | 1.5194 45 | 1.75 | 0.0616 0.0071 0.0686 | 1.4626 57 | 1.50 | 0.0604 0.0052 0.0656 | 1.0900 58 | 1.50 | 0.0570 0.0074 0.0644 | 1.0730 59 | 1.50 | 0.0559 0.0081 0.0640 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 151s Prepare output 9s 160s Jacobian determinant (RMS): 0.012 0.047 0.074 0.102 0.128 | 0.135534 Template Matching: 0.087 0.224 0.207 0.185 0.168 | 0.167649 Write result maps: 21s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 24s CSF distance: 13s PBT2x thickness: 40s 82s Create initial surface 74s Topology correction: 84s Surface refinement: 88s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 70s Spherical registration 263s rh: Thickness estimation (0.50 mm): WM distance: 24s CSF distance: 13s PBT2x thickness: 39s 82s Create initial surface 74s Topology correction: 81s Surface refinement: 67s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 71s Spherical registration 261s Final surface processing results: Average thickness (FS): 2.6192  0.6192 mm Surface intensity / position RMSE: 0.0656 / 0.0660 Euler number / defect number / defect size: 22.0 / 17.0 / 0.59% Display thickness: /var/lib/condor/execute/dir_11102/ds/sub-22/surf/lh.thickness.sub-22_T1w Display thickness: /var/lib/condor/execute/dir_11102/ds/sub-22/surf/rh.thickness.sub-22_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11102/ds/sub-22/sub-22_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1501s 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 21s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s Write results 68s 285s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11102/ds/sub-22/report/catreport_sub-22_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 42 minute(s) and 20 second(s). Image Quality Rating (IQR): 81.75% (B-) GM volume (GMV): 50.63% (713.14 / 1408.42 ml) GM thickness (GMT): 2.62  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_11102/ds/sub-22/mri Reports are saved in /var/lib/condor/execute/dir_11102/ds/sub-22/report Labels are saved in /var/lib/condor/execute/dir_11102/ds/sub-22/label ------------------------------------------------------------------------