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- CAT12.8.1 r2040: 1/1: ./sub-0027304/ses-1/sub-0027304_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 26s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 29s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 66s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 75s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 55s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0832 0.0000 0.0832 | 32.0000
- 2 | 2.50 | 0.0808 0.0012 0.0820 | 29.4886
- 3 | 2.50 | 0.0801 0.0017 0.0818 | 26.9772
- 4 | 2.50 | 0.0798 0.0019 0.0817 | 24.6107
- 5 | 2.50 | 0.0795 0.0020 0.0816 | 22.6548
- 6 | 2.50 | 0.0793 0.0021 0.0814 | 20.6989
- 7 | 2.50 | 0.0790 0.0022 0.0812 | 18.9688
- 8 | 2.50 | 0.0788 0.0023 0.0810 | 17.4455
- 9 | 2.50 | 0.0785 0.0023 0.0808 | 15.9223
- 10 | 2.50 | 0.0782 0.0024 0.0806 | 14.6627
- 11 | 2.50 | 0.0779 0.0025 0.0804 | 13.4764
- 12 | 2.50 | 0.0776 0.0025 0.0802 | 12.3015
- 13 | 2.50 | 0.0773 0.0026 0.0800 | 11.3776
- 14 | 2.50 | 0.0770 0.0027 0.0797 | 10.4537
- 15 | 2.25 | 0.0759 0.0028 0.0786 | 9.5920
- 16 | 2.25 | 0.0731 0.0041 0.0772 | 8.8725
- 29 | 2.00 | 0.0746 0.0018 0.0764 | 3.3283
- 30 | 2.00 | 0.0686 0.0043 0.0728 | 3.1221
- 31 | 2.00 | 0.0666 0.0052 0.0718 | 2.9160
- 43 | 1.75 | 0.0658 0.0030 0.0688 | 1.5785
- 44 | 1.75 | 0.0615 0.0053 0.0668 | 1.5194
- 45 | 1.75 | 0.0600 0.0061 0.0662 | 1.4626
- 57 | 1.50 | 0.0587 0.0044 0.0631 | 1.0900
- 58 | 1.50 | 0.0554 0.0065 0.0620 | 1.0730
- 59 | 1.50 | 0.0543 0.0072 0.0616 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 8s
- 161s
- Jacobian determinant (RMS): 0.011 0.037 0.055 0.077 0.099 | 0.105717
- Template Matching: 0.083 0.219 0.200 0.180 0.163 | 0.163011
- Write result maps: 74s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 13s
- PBT2x thickness: 37s
- 80s
- Create initial surface 70s
- Topology correction: 87s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 71s
- Spherical registration 216s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 13s
- PBT2x thickness: 38s
- 78s
- Create initial surface 70s
- Topology correction: 86s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 72s
- Spherical registration 226s
- Final surface processing results:
- Average thickness (FS): 2.5588 0.6764 mm
- Surface intensity / position RMSE: 0.0718 / 0.0889
- Euler number / defect number / defect size: 20.0 / 13.5 / 1.37%
- Display thickness: /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/surf/lh.thickness.sub-0027304_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/surf/rh.thickness.sub-0027304_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/sub-0027304_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1434s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 20s
- ROI estimation of 'neuromorphometrics' atlas 80s
- ROI estimation of 'lpba40' atlas 27s
- ROI estimation of 'hammers' atlas 65s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 23s
- ROI estimation of 'aal3' atlas 39s
- ROI estimation of 'mori' atlas 58s
- ROI estimation of 'anatomy3' atlas 83s
- ROI estimation of 'julichbrain' atlas 109s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 84s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 158s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 159s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 960s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/report/catreport_sub-0027304_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 36 second(s).
- Image Quality Rating (IQR): 80.30% (B-)
- GM volume (GMV): 49.25% (810.05 / 1644.81 ml)
- GM thickness (GMT): 2.56 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2873766/ds/IPCAS_5/sub-0027304/ses-1/label
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