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- CAT12.8.1 r2040: 1/1: ./sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 40s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 30s
- Correct center-of-mass 4s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 64s
- SPM preprocessing 1 (estimate 2): 58s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 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 = 1.06) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 89s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 58s
- 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) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 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 | 0.0860 0.0000 0.0860 | 32.0000
- 2 | 2.50 | 0.0839 0.0011 0.0850 | 29.4886
- 3 | 2.50 | 0.0833 0.0016 0.0848 | 26.9772
- 4 | 2.50 | 0.0829 0.0018 0.0847 | 24.6107
- 5 | 2.50 | 0.0827 0.0019 0.0846 | 22.6548
- 6 | 2.50 | 0.0824 0.0020 0.0844 | 20.6989
- 7 | 2.50 | 0.0822 0.0021 0.0843 | 18.9688
- 8 | 2.50 | 0.0819 0.0022 0.0841 | 17.4455
- 9 | 2.50 | 0.0817 0.0022 0.0839 | 15.9223
- 10 | 2.50 | 0.0814 0.0023 0.0837 | 14.6627
- 11 | 2.50 | 0.0811 0.0024 0.0835 | 13.4764
- 12 | 2.50 | 0.0809 0.0025 0.0833 | 12.3015
- 13 | 2.50 | 0.0806 0.0026 0.0831 | 11.3776
- 14 | 2.50 | 0.0803 0.0026 0.0829 | 10.4537
- 15 | 2.25 | 0.0798 0.0027 0.0825 | 9.5920
- 16 | 2.25 | 0.0768 0.0041 0.0810 | 8.8725
- 17 | 2.25 | 0.0757 0.0046 0.0803 | 8.1530
- 18 | 2.25 | 0.0749 0.0049 0.0798 | 7.5234
- 29 | 2.00 | 0.0766 0.0023 0.0789 | 3.3283
- 30 | 2.00 | 0.0710 0.0047 0.0757 | 3.1221
- 31 | 2.00 | 0.0691 0.0057 0.0747 | 2.9160
- 43 | 1.75 | 0.0680 0.0032 0.0712 | 1.5785
- 44 | 1.75 | 0.0635 0.0056 0.0691 | 1.5194
- 45 | 1.75 | 0.0621 0.0064 0.0685 | 1.4626
- 57 | 1.50 | 0.0605 0.0046 0.0651 | 1.0900
- 58 | 1.50 | 0.0572 0.0068 0.0640 | 1.0730
- 59 | 1.50 | 0.0562 0.0074 0.0636 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 154s
- Prepare output 8s
- 162s
- Jacobian determinant (RMS): 0.010 0.037 0.058 0.081 0.105 | 0.112444
- Template Matching: 0.086 0.225 0.207 0.186 0.169 | 0.168644
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 13s
- PBT2x thickness: 37s
- 91s
- Create initial surface 67s
- Topology correction: 80s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 75s
- Spherical registration 211s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 14s
- PBT2x thickness: 37s
- 91s
- Create initial surface 66s
- Topology correction: 80s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 109s
- Spherical registration 245s
- Final surface processing results:
- Average thickness (FS): 2.5928 0.6404 mm
- Surface intensity / position RMSE: 0.0608 / 0.0731
- Euler number / defect number / defect size: 22.0 / 9.5 / 1.02%
- Display thickness: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/surf/lh.thickness.sub-0025624_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/surf/rh.thickness.sub-0025624_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1444s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 61s
- ROI estimation of 'lpba40' atlas 18s
- ROI estimation of 'hammers' atlas 48s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 28s
- ROI estimation of 'mori' atlas 40s
- ROI estimation of 'anatomy3' atlas 58s
- ROI estimation of 'julichbrain' atlas 76s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 185s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s
- Write results 16s
- 787s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/report/catreport_sub-0025624_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 83.99% (B)
- GM volume (GMV): 43.73% (764.28 / 1747.61 ml)
- GM thickness (GMT): 2.59 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/label
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