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- CAT12.8.1 r2040: 1/1: ./sub-0027313/ses-1/sub-0027313_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 35s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 35s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 40s
- Update probability maps 9s
- 83s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 28s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.02) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 100s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 56s
- Blood vessel correction (BVCstr=0.50): 2s
- 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) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 10s
- 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 | 0.0859 0.0000 0.0859 | 32.0000
- 2 | 2.50 | 0.0830 0.0013 0.0842 | 29.4886
- 3 | 2.50 | 0.0821 0.0020 0.0841 | 26.9772
- 4 | 2.50 | 0.0817 0.0022 0.0839 | 24.6107
- 5 | 2.50 | 0.0813 0.0024 0.0837 | 22.6548
- 6 | 2.50 | 0.0810 0.0025 0.0835 | 20.6989
- 7 | 2.50 | 0.0807 0.0026 0.0833 | 18.9688
- 8 | 2.50 | 0.0804 0.0027 0.0831 | 17.4455
- 9 | 2.50 | 0.0801 0.0028 0.0828 | 15.9223
- 10 | 2.50 | 0.0797 0.0029 0.0826 | 14.6627
- 11 | 2.50 | 0.0794 0.0030 0.0824 | 13.4764
- 12 | 2.50 | 0.0790 0.0031 0.0821 | 12.3015
- 13 | 2.50 | 0.0786 0.0032 0.0818 | 11.3776
- 14 | 2.50 | 0.0783 0.0033 0.0815 | 10.4537
- 15 | 2.25 | 0.0783 0.0034 0.0816 | 9.5920
- 16 | 2.25 | 0.0750 0.0050 0.0799 | 8.8725
- 29 | 2.00 | 0.0763 0.0022 0.0785 | 3.3283
- 30 | 2.00 | 0.0695 0.0050 0.0745 | 3.1221
- 31 | 2.00 | 0.0672 0.0061 0.0733 | 2.9160
- 43 | 1.75 | 0.0661 0.0035 0.0696 | 1.5785
- 44 | 1.75 | 0.0615 0.0059 0.0674 | 1.5194
- 45 | 1.75 | 0.0599 0.0068 0.0667 | 1.4626
- 57 | 1.50 | 0.0584 0.0049 0.0633 | 1.0900
- 58 | 1.50 | 0.0551 0.0070 0.0622 | 1.0730
- 59 | 1.50 | 0.0540 0.0077 0.0618 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 165s
- Prepare output 9s
- 174s
- Jacobian determinant (RMS): 0.013 0.046 0.068 0.093 0.116 | 0.122684
- Template Matching: 0.086 0.225 0.202 0.180 0.162 | 0.162126
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 11s
- PBT2x thickness: 33s
- 72s
- Create initial surface 63s
- Topology correction: 79s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 72s
- Spherical registration 226s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 11s
- PBT2x thickness: 32s
- 71s
- Create initial surface 63s
- Topology correction: 78s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 75s
- Spherical registration 238s
- Final surface processing results:
- Average thickness (FS): 2.3907 0.6441 mm
- Surface intensity / position RMSE: 0.0774 / 0.1087
- Euler number / defect number / defect size: 52.0 / 24.0 / 2.35%
- Display thickness: /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/surf/lh.thickness.sub-0027313_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/surf/rh.thickness.sub-0027313_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/sub-0027313_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1395s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 52s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 23s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 44s
- ROI estimation of 'julichbrain' atlas 48s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 96s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 500s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/report/catreport_sub-0027313_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 75.20% (C)
- GM volume (GMV): 48.63% (689.13 / 1417.23 ml)
- GM thickness (GMT): 2.39 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1963981/ds/DC_1/sub-0027313/ses-1/label
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