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- CAT12.8.1 r2040: 1/1: ./sub-0027248/ses-2/sub-0027248_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 49s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 42s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 61s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 53s
- Update probability maps 12s
- 107s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 53s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 78s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.05]
- 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
- 14s
- 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 | 0.0877 0.0000 0.0877 | 32.0000
- 2 | 2.50 | 0.0845 0.0013 0.0858 | 29.4886
- 3 | 2.50 | 0.0836 0.0020 0.0856 | 26.9772
- 4 | 2.50 | 0.0832 0.0023 0.0854 | 24.6107
- 5 | 2.50 | 0.0828 0.0024 0.0852 | 22.6548
- 6 | 2.50 | 0.0825 0.0025 0.0850 | 20.6989
- 7 | 2.50 | 0.0821 0.0026 0.0848 | 18.9688
- 8 | 2.50 | 0.0818 0.0028 0.0846 | 17.4455
- 9 | 2.50 | 0.0815 0.0029 0.0843 | 15.9223
- 10 | 2.50 | 0.0811 0.0030 0.0841 | 14.6627
- 11 | 2.50 | 0.0807 0.0031 0.0838 | 13.4764
- 12 | 2.50 | 0.0804 0.0031 0.0835 | 12.3015
- 13 | 2.50 | 0.0800 0.0033 0.0832 | 11.3776
- 14 | 2.50 | 0.0796 0.0033 0.0829 | 10.4537
- 15 | 2.25 | 0.0796 0.0034 0.0830 | 9.5920
- 16 | 2.25 | 0.0764 0.0050 0.0814 | 8.8725
- 17 | 2.25 | 0.0751 0.0056 0.0807 | 8.1530
- 18 | 2.25 | 0.0742 0.0059 0.0801 | 7.5234
- 29 | 2.00 | 0.0762 0.0028 0.0790 | 3.3283
- 30 | 2.00 | 0.0707 0.0052 0.0759 | 3.1221
- 31 | 2.00 | 0.0687 0.0061 0.0748 | 2.9160
- 43 | 1.75 | 0.0676 0.0035 0.0711 | 1.5785
- 44 | 1.75 | 0.0632 0.0058 0.0690 | 1.5194
- 45 | 1.75 | 0.0616 0.0067 0.0683 | 1.4626
- 57 | 1.50 | 0.0601 0.0049 0.0650 | 1.0900
- 58 | 1.50 | 0.0568 0.0070 0.0638 | 1.0730
- 59 | 1.50 | 0.0558 0.0076 0.0634 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 213s
- Prepare output 14s
- 227s
- Jacobian determinant (RMS): 0.013 0.047 0.072 0.099 0.125 | 0.131460
- Template Matching: 0.088 0.223 0.206 0.185 0.167 | 0.167368
- Write result maps: 59s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 19s
- PBT2x thickness: 56s
- 117s
- Create initial surface 96s
- Topology correction: 86s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 91s
- Spherical registration 330s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 17s
- PBT2x thickness: 53s
- 108s
- Create initial surface 94s
- Topology correction: 85s
- Surface refinement: 78s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 90s
- Spherical registration 350s
- Final surface processing results:
- Average thickness (FS): 2.5157 0.6770 mm
- Surface intensity / position RMSE: 0.0637 / 0.0649
- Euler number / defect number / defect size: 16.0 / 9.5 / 0.33%
- Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/surf/lh.thickness.sub-0027248_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/surf/rh.thickness.sub-0027248_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/sub-0027248_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1842s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 55s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 93s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 147s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s
- Write results 16s
- 576s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/report/catreport_sub-0027248_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 59 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 84.54% (B)
- GM volume (GMV): 48.90% (654.01 / 1337.53 ml)
- GM thickness (GMT): 2.52 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/label
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