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- CAT12.8.1 r2040: 1/1: ./sub-0025887/ses-2/sub-0025887_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 36s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 82s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 45s
- Update probability maps 9s
- 93s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 115s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0802 0.0010 0.0813 | 29.4886
- 3 | 2.50 | 0.0796 0.0016 0.0812 | 26.9772
- 4 | 2.50 | 0.0792 0.0018 0.0810 | 24.6107
- 5 | 2.50 | 0.0789 0.0020 0.0809 | 22.6548
- 6 | 2.50 | 0.0787 0.0021 0.0807 | 20.6989
- 7 | 2.50 | 0.0784 0.0022 0.0806 | 18.9688
- 8 | 2.50 | 0.0782 0.0023 0.0804 | 17.4455
- 9 | 2.50 | 0.0779 0.0023 0.0802 | 15.9223
- 10 | 2.50 | 0.0776 0.0024 0.0800 | 14.6627
- 11 | 2.50 | 0.0773 0.0025 0.0798 | 13.4764
- 12 | 2.50 | 0.0770 0.0026 0.0796 | 12.3015
- 13 | 2.50 | 0.0767 0.0027 0.0794 | 11.3776
- 14 | 2.50 | 0.0764 0.0027 0.0792 | 10.4537
- 15 | 2.25 | 0.0750 0.0028 0.0778 | 9.5920
- 16 | 2.25 | 0.0724 0.0041 0.0766 | 8.8725
- 29 | 2.00 | 0.0737 0.0019 0.0756 | 3.3283
- 30 | 2.00 | 0.0677 0.0043 0.0719 | 3.1221
- 31 | 2.00 | 0.0657 0.0053 0.0709 | 2.9160
- 43 | 1.75 | 0.0645 0.0030 0.0675 | 1.5785
- 44 | 1.75 | 0.0603 0.0052 0.0655 | 1.5194
- 45 | 1.75 | 0.0590 0.0060 0.0650 | 1.4626
- 57 | 1.50 | 0.0574 0.0043 0.0618 | 1.0900
- 58 | 1.50 | 0.0544 0.0063 0.0607 | 1.0730
- 59 | 1.50 | 0.0534 0.0070 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 178s
- Prepare output 11s
- 190s
- Jacobian determinant (RMS): 0.011 0.039 0.058 0.083 0.106 | 0.112855
- Template Matching: 0.082 0.217 0.197 0.177 0.160 | 0.160172
- Write result maps: 67s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 66s
- CSF distance: 16s
- PBT2x thickness: 46s
- 135s
- Create initial surface 90s
- Topology correction: 99s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 79s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 15s
- PBT2x thickness: 46s
- 107s
- Create initial surface 87s
- Topology correction: 103s
- Surface refinement: 99s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 97s
- Spherical registration 318s
- Final surface processing results:
- Average thickness (FS): 2.4506 0.6386 mm
- Surface intensity / position RMSE: 0.0678 / 0.0760
- Euler number / defect number / defect size: 42.0 / 19.0 / 1.71%
- Display thickness: /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/surf/lh.thickness.sub-0025887_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/surf/rh.thickness.sub-0025887_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/sub-0025887_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1858s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- 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 18s
- ROI estimation of 'mori' atlas 28s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 68s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 86s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 118s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 560s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/report/catreport_sub-0025887_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 4 second(s).
- Image Quality Rating (IQR): 82.17% (B-)
- GM volume (GMV): 46.23% (718.88 / 1554.94 ml)
- GM thickness (GMT): 2.45 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_479549/ds/BNU_1/sub-0025887/ses-2/label
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