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- CAT12.8.1 r2040: 1/1: ./sub-0026019/ses-2/sub-0026019_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 158s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 6s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 6s
- 44s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 77s
- SPM preprocessing 1 (estimate 2): 28s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 52s
- Update probability maps 12s
- 108s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 35s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 135s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 74s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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
- 13s
- 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 | 0.0839 0.0000 0.0839 | 32.0000
- 2 | 2.50 | 0.0804 0.0014 0.0818 | 29.4886
- 3 | 2.50 | 0.0794 0.0022 0.0816 | 26.9772
- 4 | 2.50 | 0.0789 0.0024 0.0813 | 24.6107
- 5 | 2.50 | 0.0785 0.0026 0.0811 | 22.6548
- 6 | 2.50 | 0.0782 0.0027 0.0809 | 20.6989
- 7 | 2.50 | 0.0778 0.0028 0.0806 | 18.9688
- 8 | 2.50 | 0.0774 0.0030 0.0804 | 17.4455
- 9 | 2.50 | 0.0771 0.0030 0.0801 | 15.9223
- 10 | 2.50 | 0.0767 0.0032 0.0798 | 14.6627
- 11 | 2.50 | 0.0763 0.0033 0.0795 | 13.4764
- 12 | 2.50 | 0.0759 0.0033 0.0792 | 12.3015
- 13 | 2.50 | 0.0755 0.0034 0.0789 | 11.3776
- 14 | 2.50 | 0.0751 0.0035 0.0786 | 10.4537
- 15 | 2.25 | 0.0747 0.0036 0.0783 | 9.5920
- 16 | 2.25 | 0.0712 0.0053 0.0765 | 8.8725
- 29 | 2.00 | 0.0722 0.0024 0.0746 | 3.3283
- 30 | 2.00 | 0.0657 0.0050 0.0706 | 3.1221
- 31 | 2.00 | 0.0635 0.0060 0.0694 | 2.9160
- 43 | 1.75 | 0.0624 0.0035 0.0658 | 1.5785
- 44 | 1.75 | 0.0582 0.0057 0.0638 | 1.5194
- 45 | 1.75 | 0.0567 0.0064 0.0632 | 1.4626
- 57 | 1.50 | 0.0553 0.0047 0.0600 | 1.0900
- 58 | 1.50 | 0.0522 0.0067 0.0589 | 1.0730
- 59 | 1.50 | 0.0512 0.0073 0.0585 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 107s
- Prepare output 10s
- 117s
- Jacobian determinant (RMS): 0.013 0.046 0.067 0.091 0.113 | 0.120371
- Template Matching: 0.084 0.214 0.190 0.170 0.154 | 0.153634
- Write result maps: 164s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 10s
- PBT2x thickness: 29s
- 63s
- Create initial surface 52s
- Topology correction: 61s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 53s
- Spherical registration 190s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 9s
- PBT2x thickness: 28s
- 58s
- Create initial surface 49s
- Topology correction: 60s
- Surface refinement: 48s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 53s
- Spherical registration 197s
- Final surface processing results:
- Average thickness (FS): 2.5829 0.6385 mm
- Surface intensity / position RMSE: 0.0720 / 0.0664
- Euler number / defect number / defect size: 12.0 / 14.0 / 0.30%
- Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/surf/lh.thickness.sub-0026019_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/surf/rh.thickness.sub-0026019_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/sub-0026019_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1121s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 44s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 35s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 74s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 111s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 479s
- Quality check: 36s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/report/catreport_sub-0026019_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 80.79% (B-)
- GM volume (GMV): 50.87% (679.18 / 1335.23 ml)
- GM thickness (GMT): 2.58 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-2/label
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