------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 218s Internal resampling (1.20x0.50x0.50mm > 0.80x0.50x0.80mm): 3s APP: Rough bias correction: Initialize 8s Estimate background 6s Initial correction 8s Refine background 3s Final correction 7s Final scaling 11s 57s Correct center-of-mass 4s Affine registration 26s SPM preprocessing 1 (estimate 1 - TPM registration): 63s SPM preprocessing 1 (estimate 2): 35s SPM preprocessing 2 (write): Write Segmentation 37s Update Segmentation 44s Update Skull-Stripping 104s Update probability maps 19s 205s Global intensity correction: 33s SANLM denoising after intensity normalization (medium): 154s Fast Optimized Shooting registration 39s Local adaptive segmentation (LASstr=0.50): Prepare maps 8s Prepare partitions 6s Prepare segments (LASmod = 1.07) 39s Estimate local tissue thresholds (WM) 29s Estimate local tissue thresholds (GM) 39s Intensity transformation 0s SANLM denoising after LAS (medium) 137s 266s ROI segmentation (partitioning): Atlas -> subject space 13s Major structures 4s Ventricle detection 12s Blood vessel detection 12s WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 24s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 10s 82s Blood vessel correction (BVCstr=0.50): 4s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 73s AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 10s Level 1 cleanup (brain masking) 6s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 7s 27s 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 | 0.0903 0.0000 0.0903 | 32.0000 2 | 2.50 | 0.0869 0.0014 0.0883 | 29.4886 3 | 2.50 | 0.0859 0.0022 0.0880 | 26.9772 4 | 2.50 | 0.0853 0.0025 0.0878 | 24.6107 5 | 2.50 | 0.0849 0.0027 0.0876 | 22.6548 6 | 2.50 | 0.0846 0.0028 0.0874 | 20.6989 7 | 2.50 | 0.0842 0.0029 0.0871 | 18.9688 8 | 2.50 | 0.0838 0.0030 0.0869 | 17.4455 9 | 2.50 | 0.0835 0.0031 0.0866 | 15.9223 10 | 2.50 | 0.0830 0.0033 0.0863 | 14.6627 11 | 2.50 | 0.0827 0.0034 0.0860 | 13.4764 12 | 2.50 | 0.0822 0.0034 0.0857 | 12.3015 13 | 2.50 | 0.0818 0.0036 0.0854 | 11.3776 14 | 2.50 | 0.0814 0.0036 0.0850 | 10.4537 15 | 2.25 | 0.0814 0.0037 0.0852 | 9.5920 16 | 2.25 | 0.0780 0.0054 0.0834 | 8.8725 17 | 2.25 | 0.0767 0.0060 0.0826 | 8.1530 18 | 2.25 | 0.0758 0.0062 0.0820 | 7.5234 19 | 2.25 | 0.0752 0.0063 0.0815 | 6.9630 20 | 2.25 | 0.0746 0.0062 0.0809 | 6.4027 29 | 2.00 | 0.0769 0.0035 0.0803 | 3.3283 30 | 2.00 | 0.0720 0.0057 0.0777 | 3.1221 31 | 2.00 | 0.0704 0.0064 0.0768 | 2.9160 43 | 1.75 | 0.0699 0.0036 0.0735 | 1.5785 44 | 1.75 | 0.0652 0.0061 0.0714 | 1.5194 45 | 1.75 | 0.0637 0.0070 0.0707 | 1.4626 57 | 1.50 | 0.0622 0.0050 0.0672 | 1.0900 58 | 1.50 | 0.0586 0.0074 0.0660 | 1.0730 59 | 1.50 | 0.0574 0.0082 0.0656 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 115s Prepare output 16s 131s Jacobian determinant (RMS): 0.013 0.047 0.071 0.092 0.116 | 0.122991 Template Matching: 0.090 0.224 0.211 0.191 0.172 | 0.172219 Write result maps: 143s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 37s CSF distance: 13s PBT2x thickness: 36s 91s Create initial surface 68s Topology correction: 75s Surface refinement: 72s Reduction of surface collisions with optimization: 59s Spherical mapping with areal smoothing 69s Spherical registration 196s rh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 13s PBT2x thickness: 36s 91s Create initial surface 66s Topology correction: 76s Surface refinement: 70s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 81s Spherical registration 196s Final surface processing results: Average thickness (FS): 2.4824  0.5970 mm Surface intensity / position RMSE: 0.0662 / 0.0705 Euler number / defect number / defect size: 14.0 / 9.0 / 0.60% Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/lh.thickness.sub-0026043_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/rh.thickness.sub-0026043_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1395s 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 50s ROI estimation of 'thalamus' atlas 4s ROI estimation of 'ibsr' atlas 17s ROI estimation of 'aal3' atlas 29s ROI estimation of 'mori' atlas 42s ROI estimation of 'anatomy3' atlas 61s ROI estimation of 'julichbrain' atlas 79s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 57s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s Write results 17s 807s Quality check: 31s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report/catreport_sub-0026043_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 64 minute(s) and 57 second(s). Image Quality Rating (IQR): 82.72% (B-) GM volume (GMV): 43.84% (798.12 / 1820.48 ml) GM thickness (GMT): 2.48  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report Labels are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/label ------------------------------------------------------------------------