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- CAT12.8.1 r2040: 1/1: ./sub-0025935/ses-1/sub-0025935_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 51s
- 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 4s
- Final correction 6s
- Final scaling 6s
- 47s
- Correct center-of-mass 5s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 84s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 24s
- Update Skull-Stripping 51s
- Update probability maps 10s
- 107s
- 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 = 1.00) 18s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 52s
- 143s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 85s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- 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 | 0.0804 0.0000 0.0804 | 32.0000
- 2 | 2.50 | 0.0778 0.0011 0.0789 | 29.4886
- 3 | 2.50 | 0.0770 0.0017 0.0787 | 26.9772
- 4 | 2.50 | 0.0766 0.0020 0.0786 | 24.6107
- 5 | 2.50 | 0.0763 0.0021 0.0784 | 22.6548
- 6 | 2.50 | 0.0760 0.0022 0.0782 | 20.6989
- 7 | 2.50 | 0.0758 0.0023 0.0781 | 18.9688
- 8 | 2.50 | 0.0755 0.0024 0.0779 | 17.4455
- 9 | 2.50 | 0.0752 0.0025 0.0777 | 15.9223
- 10 | 2.50 | 0.0749 0.0026 0.0775 | 14.6627
- 11 | 2.50 | 0.0746 0.0027 0.0772 | 13.4764
- 12 | 2.50 | 0.0743 0.0027 0.0770 | 12.3015
- 13 | 2.50 | 0.0739 0.0028 0.0768 | 11.3776
- 14 | 2.50 | 0.0736 0.0029 0.0765 | 10.4537
- 15 | 2.25 | 0.0723 0.0030 0.0753 | 9.5920
- 16 | 2.25 | 0.0696 0.0043 0.0739 | 8.8725
- 29 | 2.00 | 0.0706 0.0019 0.0725 | 3.3283
- 30 | 2.00 | 0.0648 0.0042 0.0691 | 3.1221
- 31 | 2.00 | 0.0628 0.0052 0.0680 | 2.9160
- 43 | 1.75 | 0.0617 0.0030 0.0647 | 1.5785
- 44 | 1.75 | 0.0577 0.0051 0.0628 | 1.5194
- 45 | 1.75 | 0.0564 0.0058 0.0622 | 1.4626
- 57 | 1.50 | 0.0550 0.0042 0.0592 | 1.0900
- 58 | 1.50 | 0.0521 0.0061 0.0582 | 1.0730
- 59 | 1.50 | 0.0511 0.0067 0.0579 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 210s
- Prepare output 15s
- 225s
- Jacobian determinant (RMS): 0.012 0.043 0.063 0.087 0.109 | 0.116339
- Template Matching: 0.080 0.209 0.188 0.169 0.153 | 0.153335
- Write result maps: 75s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 21s
- PBT2x thickness: 63s
- 135s
- Create initial surface 110s
- Topology correction: 129s
- Surface refinement: 140s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 120s
- Spherical registration 332s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 21s
- PBT2x thickness: 63s
- 131s
- Create initial surface 109s
- Topology correction: 128s
- Surface refinement: 143s
- Reduction of surface collisions with optimization: 93s
- Spherical mapping with areal smoothing 115s
- Spherical registration 351s
- Final surface processing results:
- Average thickness (FS): 2.5145 0.6085 mm
- Surface intensity / position RMSE: 0.0714 / 0.0858
- Euler number / defect number / defect size: 40.0 / 20.5 / 1.44%
- Display thickness: /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/surf/lh.thickness.sub-0025935_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/surf/rh.thickness.sub-0025935_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/sub-0025935_ses-1_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 2264s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 38s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 54s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 104s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 12s
- 562s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/report/catreport_sub-0025935_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 67 minute(s) and 16 second(s).
- Image Quality Rating (IQR): 81.66% (B-)
- GM volume (GMV): 49.75% (781.73 / 1571.30 ml)
- GM thickness (GMT): 2.51 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3318795/ds/BNU_2/sub-0025935/ses-1/label
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