------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0026031/ses-2/sub-0026031_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 357s Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 3s APP: Rough bias correction: Initialize 16s Estimate background 12s Initial correction 16s Refine background 7s Final correction 14s Final scaling 12s 93s Correct center-of-mass 5s Affine registration 20s SPM preprocessing 1 (estimate 1 - TPM registration): 170s SPM preprocessing 1 (estimate 2): 90s SPM preprocessing 2 (write): Write Segmentation 42s Update Segmentation 49s Update Skull-Stripping 119s Update probability maps 25s 235s Global intensity correction: 44s SANLM denoising after intensity normalization (medium): 75s Fast Optimized Shooting registration 66s Local adaptive segmentation (LASstr=0.50): Prepare maps 10s Prepare partitions 8s Prepare segments (LASmod = 1.00) 40s Estimate local tissue thresholds (WM) 54s Estimate local tissue thresholds (GM) 87s Intensity transformation 0s SANLM denoising after LAS (medium) 110s 319s ROI segmentation (partitioning): Atlas -> subject space 21s Major structures 10s Ventricle detection 50s Blood vessel detection 32s WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 70s Manual stroke lesion detection 0s Closing of deep structures 5s Side alignment 10s Final corrections 10s 208s Blood vessel correction (BVCstr=0.50): 4s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 75s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 12s Level 1 cleanup (brain masking) 6s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 7s 29s 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 | 0.0846 0.0011 0.0857 | 29.4886 3 | 2.50 | 0.0840 0.0016 0.0856 | 26.9772 4 | 2.50 | 0.0837 0.0018 0.0854 | 24.6107 5 | 2.50 | 0.0834 0.0019 0.0853 | 22.6548 6 | 2.50 | 0.0832 0.0020 0.0851 | 20.6989 7 | 2.50 | 0.0830 0.0020 0.0850 | 18.9688 8 | 2.50 | 0.0827 0.0021 0.0848 | 17.4455 9 | 2.50 | 0.0825 0.0022 0.0846 | 15.9223 10 | 2.50 | 0.0822 0.0023 0.0845 | 14.6627 11 | 2.50 | 0.0819 0.0023 0.0843 | 13.4764 12 | 2.50 | 0.0817 0.0024 0.0840 | 12.3015 13 | 2.50 | 0.0814 0.0025 0.0838 | 11.3776 14 | 2.50 | 0.0811 0.0025 0.0836 | 10.4537 15 | 2.25 | 0.0823 0.0025 0.0848 | 9.5920 16 | 2.25 | 0.0790 0.0041 0.0831 | 8.8725 17 | 2.25 | 0.0777 0.0047 0.0824 | 8.1530 18 | 2.25 | 0.0770 0.0049 0.0819 | 7.5234 19 | 2.25 | 0.0764 0.0050 0.0814 | 6.9630 20 | 2.25 | 0.0759 0.0051 0.0810 | 6.4027 21 | 2.25 | 0.0754 0.0051 0.0805 | 5.9447 22 | 2.25 | 0.0749 0.0052 0.0801 | 5.5083 29 | 2.00 | 0.0780 0.0032 0.0812 | 3.3283 30 | 2.00 | 0.0736 0.0054 0.0789 | 3.1221 31 | 2.00 | 0.0721 0.0061 0.0781 | 2.9160 43 | 1.75 | 0.0720 0.0034 0.0754 | 1.5785 44 | 1.75 | 0.0668 0.0062 0.0731 | 1.5194 45 | 1.75 | 0.0652 0.0071 0.0723 | 1.4626 57 | 1.50 | 0.0643 0.0051 0.0694 | 1.0900 58 | 1.50 | 0.0603 0.0078 0.0681 | 1.0730 59 | 1.50 | 0.0591 0.0085 0.0676 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 224s Prepare output 22s 247s Jacobian determinant (RMS): 0.009 0.034 0.062 0.097 0.138 | 0.142405 Template Matching: 0.087 0.225 0.216 0.196 0.177 | 0.177396 Write result maps: 260s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 49s CSF distance: 24s PBT2x thickness: 68s 148s Create initial surface 112s Topology correction: 123s Surface refinement: 147s Reduction of surface collisions with optimization: 100s Spherical mapping with areal smoothing 121s Spherical registration 335s rh: Thickness estimation (0.50 mm): WM distance: 52s CSF distance: 23s PBT2x thickness: 71s 154s Create initial surface 117s Topology correction: 127s Surface refinement: 121s Reduction of surface collisions with optimization: 106s Spherical mapping with areal smoothing 119s Spherical registration 337s Final surface processing results: Average thickness (FS): 2.6553  0.6258 mm Surface intensity / position RMSE: 0.0814 / 0.0773 Euler number / defect number / defect size: 44.0 / 30.5 / 0.82% Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/surf/lh.thickness.sub-0026031_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/surf/rh.thickness.sub-0026031_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/sub-0026031_ses-2_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2367s ROI estimation in native space: ROI estimation of 'cobra' atlas 20s ROI estimation of 'neuromorphometrics' atlas 72s ROI estimation of 'lpba40' atlas 21s ROI estimation of 'hammers' atlas 51s ROI estimation of 'thalamus' atlas 4s ROI estimation of 'ibsr' atlas 18s ROI estimation of 'aal3' atlas 28s ROI estimation of 'mori' atlas 41s ROI estimation of 'anatomy3' atlas 59s ROI estimation of 'julichbrain' atlas 79s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 54s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 128s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 192s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s Write results 18s 817s Quality check: 67s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/report/catreport_sub-0026031_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 94 minute(s) and 30 second(s). Image Quality Rating (IQR): 70.52% (C-) GM volume (GMV): 52.88% (886.70 / 1676.80 ml) GM thickness (GMT): 2.66  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/report Labels are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/label ------------------------------------------------------------------------