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- CAT12.8.1 r2040: 1/1: ./sub-0027430/ses-1/sub-0027430_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 238s
- Skip initial affine registration due to high-intensity background 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 36s
- SPM preprocessing 1 (estimate 2): 87s
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- WARNING 01: cat_run_job1639:nonT1contrast
- A non-T1 contrast was detected and the NEW EXPERIMENTAL
- PIPELINE is used! If it is was a high-resolution T1 image,
- the initial segmentation might have failed, probably due
- to alignment problems (please check the image orientation).
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- SPM preprocessing 2 (write):
- Write Segmentation 25s
- Update segmentation 44s
- Update skull-stripping 20s
- Update probability maps 2s
- Update registration 30s
- 121s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 82s
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- NOTE 01: cat_main:skipLAS
- Skip LAS due to image contrast. Use global normalization.
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- 161s
- SANLM denoising after LAS (medium) 83s
- 165s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 1s
- Ventricle detection 2s
- Blood vessel detection 1s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 7s
- 18s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 53s
- AMAP peaks: [0.910.05,0.640.08,0.360.04]
- --- Update Ym and Ymi ---
- 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 | 0.0867 0.0000 0.0867 | 32.0000
- 2 | 2.50 | 0.0824 0.0017 0.0841 | 29.4886
- 3 | 2.50 | 0.0811 0.0026 0.0837 | 26.9772
- 4 | 2.50 | 0.0804 0.0030 0.0834 | 24.6107
- 5 | 2.50 | 0.0799 0.0032 0.0831 | 22.6548
- 6 | 2.50 | 0.0795 0.0033 0.0828 | 20.6989
- 7 | 2.50 | 0.0790 0.0035 0.0825 | 18.9688
- 8 | 2.50 | 0.0785 0.0037 0.0822 | 17.4455
- 9 | 2.50 | 0.0780 0.0038 0.0818 | 15.9223
- 10 | 2.50 | 0.0775 0.0040 0.0814 | 14.6627
- 11 | 2.50 | 0.0769 0.0041 0.0810 | 13.4764
- 12 | 2.50 | 0.0764 0.0042 0.0806 | 12.3015
- 13 | 2.50 | 0.0758 0.0044 0.0802 | 11.3776
- 14 | 2.50 | 0.0753 0.0045 0.0798 | 10.4537
- 15 | 2.25 | 0.0740 0.0047 0.0787 | 9.5920
- 16 | 2.25 | 0.0705 0.0065 0.0770 | 8.8725
- 29 | 2.00 | 0.0700 0.0029 0.0729 | 3.3283
- 30 | 2.00 | 0.0632 0.0058 0.0690 | 3.1221
- 31 | 2.00 | 0.0610 0.0068 0.0678 | 2.9160
- 43 | 1.75 | 0.0594 0.0040 0.0634 | 1.5785
- 44 | 1.75 | 0.0557 0.0060 0.0617 | 1.5194
- 45 | 1.75 | 0.0545 0.0067 0.0612 | 1.4626
- 57 | 1.50 | 0.0531 0.0050 0.0581 | 1.0900
- 58 | 1.50 | 0.0503 0.0068 0.0572 | 1.0730
- 59 | 1.50 | 0.0495 0.0074 0.0569 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 104s
- Prepare output 12s
- 116s
- Jacobian determinant (RMS): 0.015 0.057 0.088 0.122 0.151 | 0.159718
- Template Matching: 0.087 0.211 0.183 0.163 0.148 | 0.148405
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 11s
- PBT2x thickness: 26s
- 58s
- Create initial surface 47s
- Topology correction: 50s
- Surface refinement: 39s
- Reduction of surface collisions with optimization: 36s
- Spherical mapping with areal smoothing 47s
- Spherical registration 185s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 9s
- PBT2x thickness: 27s
- 56s
- Create initial surface 47s
- Topology correction: 53s
- Surface refinement: 41s
- Reduction of surface collisions with optimization: 38s
- Spherical mapping with areal smoothing 48s
- Spherical registration 185s
- Final surface processing results:
- Average thickness (FS): 2.6171 0.8203 mm
- Surface intensity / position RMSE: 0.0928 / 0.1028
- Euler number / defect number / defect size: 18.0 / 13.5 / 1.65%
- Display thickness: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/surf/lh.thickness.sub-0027430_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/surf/rh.thickness.sub-0027430_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/sub-0027430_ses-1_run-1_T1w.nii
- Surface ROI estimation: 1559s
- Surface and thickness estimation takes: 1298s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 33s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 38s
- ROI estimation of 'julichbrain' atlas 51s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 122s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 527s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/report/catreport_sub-0027430_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 44 minute(s) and 31 second(s).
- Image Quality Rating (IQR): 83.45% (B)
- GM volume (GMV): 49.24% (696.23 / 1413.85 ml)
- GM thickness (GMT): 2.62 0.82 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/label
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