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- CAT12.8.1 r2040: 1/1: ./sub-0025981/ses-1/sub-0025981_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 42s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 8s
- Refine background 3s
- Final correction 6s
- Final scaling 6s
- 45s
- Correct center-of-mass 5s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 93s
- SPM preprocessing 1 (estimate 2): 94s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 24s
- Update Skull-Stripping 53s
- Update probability maps 11s
- 109s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.09) 18s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 143s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 5s
- Ventricle detection 16s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 84s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0808 0.0011 0.0819 | 29.4886
- 3 | 2.50 | 0.0800 0.0017 0.0817 | 26.9772
- 4 | 2.50 | 0.0796 0.0019 0.0816 | 24.6107
- 5 | 2.50 | 0.0794 0.0021 0.0815 | 22.6548
- 6 | 2.50 | 0.0791 0.0022 0.0813 | 20.6989
- 7 | 2.50 | 0.0789 0.0023 0.0811 | 18.9688
- 8 | 2.50 | 0.0786 0.0024 0.0810 | 17.4455
- 9 | 2.50 | 0.0783 0.0024 0.0808 | 15.9223
- 10 | 2.50 | 0.0781 0.0025 0.0806 | 14.6627
- 11 | 2.50 | 0.0778 0.0026 0.0804 | 13.4764
- 12 | 2.50 | 0.0775 0.0026 0.0801 | 12.3015
- 13 | 2.50 | 0.0772 0.0027 0.0799 | 11.3776
- 14 | 2.50 | 0.0769 0.0028 0.0797 | 10.4537
- 15 | 2.25 | 0.0768 0.0028 0.0796 | 9.5920
- 16 | 2.25 | 0.0740 0.0043 0.0782 | 8.8725
- 29 | 2.00 | 0.0761 0.0019 0.0780 | 3.3283
- 30 | 2.00 | 0.0698 0.0044 0.0742 | 3.1221
- 31 | 2.00 | 0.0677 0.0054 0.0731 | 2.9160
- 43 | 1.75 | 0.0670 0.0031 0.0701 | 1.5785
- 44 | 1.75 | 0.0625 0.0055 0.0680 | 1.5194
- 45 | 1.75 | 0.0610 0.0064 0.0673 | 1.4626
- 57 | 1.50 | 0.0598 0.0046 0.0643 | 1.0900
- 58 | 1.50 | 0.0564 0.0068 0.0632 | 1.0730
- 59 | 1.50 | 0.0553 0.0075 0.0628 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 216s
- Prepare output 14s
- 230s
- Jacobian determinant (RMS): 0.010 0.036 0.055 0.080 0.105 | 0.110966
- Template Matching: 0.083 0.222 0.203 0.183 0.166 | 0.165880
- Write result maps: 77s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 22s
- PBT2x thickness: 67s
- 141s
- Create initial surface 125s
- Topology correction: 134s
- Surface refinement: 151s
- Reduction of surface collisions with optimization: 106s
- Spherical mapping with areal smoothing 125s
- Spherical registration 344s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 21s
- PBT2x thickness: 66s
- 133s
- Create initial surface 120s
- Topology correction: 139s
- Surface refinement: 149s
- Reduction of surface collisions with optimization: 105s
- Spherical mapping with areal smoothing 126s
- Spherical registration 353s
- Final surface processing results:
- Average thickness (FS): 2.4702 0.6099 mm
- Surface intensity / position RMSE: 0.0680 / 0.0693
- Euler number / defect number / defect size: 22.0 / 14.0 / 0.59%
- Display thickness: /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/surf/lh.thickness.sub-0025981_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/surf/rh.thickness.sub-0025981_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/sub-0025981_ses-1_run-1_T1w.nii
- Surface ROI estimation: 15s
- Surface and thickness estimation takes: 2390s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 47s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 49s
- ROI estimation of 'julichbrain' atlas 64s
- 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 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 111s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 556s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/report/catreport_sub-0025981_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 69 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 84.05% (B)
- GM volume (GMV): 48.82% (781.58 / 1600.91 ml)
- GM thickness (GMT): 2.47 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3318420/ds/BNU_2/sub-0025981/ses-1/label
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