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- CAT12.8.1 r2040: 1/1: ./sub-0025781/ses-1/sub-0025781_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 28s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 52s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 15s
- Update Skull-Stripping 33s
- Update probability maps 7s
- 68s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.06) 11s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 90s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 47s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0845 0.0012 0.0858 | 29.4886
- 3 | 2.50 | 0.0837 0.0018 0.0856 | 26.9772
- 4 | 2.50 | 0.0833 0.0021 0.0854 | 24.6107
- 5 | 2.50 | 0.0830 0.0022 0.0852 | 22.6548
- 6 | 2.50 | 0.0827 0.0023 0.0850 | 20.6989
- 7 | 2.50 | 0.0824 0.0024 0.0849 | 18.9688
- 8 | 2.50 | 0.0821 0.0025 0.0846 | 17.4455
- 9 | 2.50 | 0.0818 0.0026 0.0844 | 15.9223
- 10 | 2.50 | 0.0815 0.0027 0.0842 | 14.6627
- 11 | 2.50 | 0.0811 0.0028 0.0839 | 13.4764
- 12 | 2.50 | 0.0808 0.0029 0.0837 | 12.3015
- 13 | 2.50 | 0.0804 0.0030 0.0834 | 11.3776
- 14 | 2.50 | 0.0801 0.0031 0.0832 | 10.4537
- 15 | 2.25 | 0.0806 0.0031 0.0838 | 9.5920
- 16 | 2.25 | 0.0774 0.0048 0.0822 | 8.8725
- 17 | 2.25 | 0.0761 0.0053 0.0815 | 8.1530
- 18 | 2.25 | 0.0753 0.0056 0.0809 | 7.5234
- 19 | 2.25 | 0.0747 0.0057 0.0804 | 6.9630
- 29 | 2.00 | 0.0773 0.0029 0.0802 | 3.3283
- 30 | 2.00 | 0.0716 0.0054 0.0771 | 3.1221
- 31 | 2.00 | 0.0697 0.0064 0.0761 | 2.9160
- 43 | 1.75 | 0.0689 0.0036 0.0725 | 1.5785
- 44 | 1.75 | 0.0639 0.0063 0.0702 | 1.5194
- 45 | 1.75 | 0.0623 0.0072 0.0695 | 1.4626
- 57 | 1.50 | 0.0609 0.0053 0.0661 | 1.0900
- 58 | 1.50 | 0.0572 0.0077 0.0649 | 1.0730
- 59 | 1.50 | 0.0560 0.0084 0.0644 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 155s
- Prepare output 8s
- 162s
- Jacobian determinant (RMS): 0.011 0.040 0.065 0.091 0.119 | 0.124709
- Template Matching: 0.087 0.224 0.209 0.187 0.168 | 0.168105
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 12s
- PBT2x thickness: 34s
- 79s
- Create initial surface 63s
- Topology correction: 70s
- Surface refinement: 56s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 62s
- Spherical registration 222s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 12s
- PBT2x thickness: 34s
- 78s
- Create initial surface 62s
- Topology correction: 70s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 62s
- Spherical registration 220s
- Final surface processing results:
- Average thickness (FS): 2.6773 0.6842 mm
- Surface intensity / position RMSE: 0.0661 / 0.0650
- Euler number / defect number / defect size: 22.0 / 12.5 / 0.89%
- Display thickness: /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/surf/lh.thickness.sub-0025781_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/surf/rh.thickness.sub-0025781_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/sub-0025781_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1283s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 33s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 51s
- ROI estimation of 'julichbrain' atlas 66s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 127s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 174s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 12s
- 697s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/report/catreport_sub-0025781_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 82.23% (B-)
- GM volume (GMV): 47.06% (725.41 / 1541.61 ml)
- GM thickness (GMT): 2.68 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_321317/ds/SWU_4/sub-0025781/ses-1/label
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