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- CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027441_ses-1_acq-inv1_run-1_T1w.n
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- SANLM denoising (medium): 377s
- APP: Rough bias correction:
- Initialize 14s
- Estimate background 16s
- Initial correction 14s
- Refine background 7s
- Final correction 10s
- Final scaling 17s
- 93s
- Correct center-of-mass 3s
- Affine registration 18s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 94s
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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 40s
- Update segmentation 65s
- Update skull-stripping 33s
- Update probability maps 3s
- Update registration 53s
- 194s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 101s
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- NOTE 01: cat_main:skipLAS
- Skip LAS due to image contrast. Use global normalization.
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- 224s
- SANLM denoising after LAS (medium) 169s
- 270s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 1s
- Ventricle detection 4s
- Blood vessel detection 1s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 10s
- 28s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 94s
- AMAP peaks: [0.980.05,0.370.08,0.620.05]
- --- 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 | 0.0984 0.0000 0.0984 | 32.0000
- 2 | 2.50 | 0.0889 0.0026 0.0915 | 29.4886
- 3 | 2.50 | 0.0855 0.0044 0.0899 | 26.9772
- 4 | 2.50 | 0.0840 0.0052 0.0891 | 24.6107
- 5 | 2.50 | 0.0829 0.0056 0.0885 | 22.6548
- 6 | 2.50 | 0.0821 0.0058 0.0879 | 20.6989
- 7 | 2.50 | 0.0813 0.0060 0.0873 | 18.9688
- 8 | 2.50 | 0.0806 0.0062 0.0868 | 17.4455
- 9 | 2.50 | 0.0798 0.0063 0.0861 | 15.9223
- 10 | 2.50 | 0.0790 0.0065 0.0855 | 14.6627
- 11 | 2.50 | 0.0783 0.0066 0.0849 | 13.4764
- 12 | 2.50 | 0.0775 0.0067 0.0842 | 12.3015
- 13 | 2.50 | 0.0767 0.0069 0.0836 | 11.3776
- 14 | 2.50 | 0.0760 0.0069 0.0829 | 10.4537
- 15 | 2.25 | 0.0770 0.0074 0.0844 | 9.5920
- 16 | 2.25 | 0.0728 0.0095 0.0823 | 8.8725
- 17 | 2.25 | 0.0708 0.0102 0.0811 | 8.1530
- 29 | 2.00 | 0.0717 0.0048 0.0766 | 3.3283
- 30 | 2.00 | 0.0642 0.0081 0.0723 | 3.1221
- 31 | 2.00 | 0.0616 0.0092 0.0708 | 2.9160
- 43 | 1.75 | 0.0605 0.0055 0.0660 | 1.5785
- 44 | 1.75 | 0.0561 0.0080 0.0641 | 1.5194
- 45 | 1.75 | 0.0546 0.0087 0.0633 | 1.4626
- 57 | 1.50 | 0.0539 0.0067 0.0606 | 1.0900
- 58 | 1.50 | 0.0507 0.0089 0.0596 | 1.0730
- 59 | 1.50 | 0.0496 0.0096 0.0592 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 21s
- 202s
- Jacobian determinant (RMS): 0.014 0.058 0.096 0.140 0.184 | 0.197642
- Template Matching: 0.098 0.212 0.185 0.164 0.149 | 0.148929
- Write result maps: 74s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 17s
- PBT2x thickness: 49s
- 97s
- Create initial surface 76s
- Topology correction: 63s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 68s
- Spherical registration 297s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 17s
- PBT2x thickness: 49s
- 100s
- Create initial surface 75s
- Topology correction: 70s
- Surface refinement: 64s
- Reduction of surface collisions with optimization: 101s
- Spherical mapping with areal smoothing 68s
- Spherical registration 295s
- Final surface processing results:
- Average thickness (FS): 3.0636 0.9654 mm
- Surface intensity / position RMSE: 0.1284 / 0.1286
- Euler number / defect number / defect size: 60.0 / 37.0 / 2.12%
- Display thickness: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/surf/lh.thickness.sub-0027441_ses-1_acq-inv1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/surf/rh.thickness.sub-0027441_ses-1_acq-inv1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/sub-0027441_ses-1_acq-inv1_run-1_T1w.nii
- Surface ROI estimation: 2569s
- Surface and thickness estimation takes: 2120s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 65s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 46s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 27s
- ROI estimation of 'mori' atlas 39s
- ROI estimation of 'anatomy3' atlas 56s
- ROI estimation of 'julichbrain' atlas 75s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 52s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 119s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 179s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s
- Write results 16s
- 762s
- Quality check: 26s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/report/catreport_sub-0027441_ses-1_acq-inv1_run-1_T1w.pdf
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- CAT preprocessing takes 72 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 30.98% (F)
- GM volume (GMV): 60.03% (811.06 / 1351.08 ml)
- GM thickness (GMT): 3.06 0.97 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/label
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