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- CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027438_ses-1_acq-inv1_run-1_T1w.n
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- SANLM denoising (medium): 351s
- APP: Rough bias correction:
- Initialize 12s
- Estimate background 15s
- Initial correction 14s
- Refine background 7s
- Final correction 10s
- Final scaling 16s
- 86s
- Correct center-of-mass 3s
- Affine registration 47s
- SPM preprocessing 1 (estimate 1 - TPM registration): 44s
- SPM preprocessing 1 (estimate 2): 49s
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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 37s
- Update segmentation 61s
- Update skull-stripping 31s
- Update probability maps 3s
- Update registration 49s
- 180s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 94s
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- NOTE 01: cat_main:skipLAS
- Skip LAS due to image contrast. Use global normalization.
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- 212s
- SANLM denoising after LAS (medium) 160s
- 254s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 1s
- Ventricle detection 3s
- Blood vessel detection 1s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 9s
- 26s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 103s
- AMAP peaks: [0.950.06,0.340.08,0.580.06]
- --- 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 | 0.0890 0.0000 0.0890 | 32.0000
- 2 | 2.50 | 0.0846 0.0017 0.0863 | 29.4886
- 3 | 2.50 | 0.0832 0.0027 0.0859 | 26.9772
- 4 | 2.50 | 0.0825 0.0031 0.0856 | 24.6107
- 5 | 2.50 | 0.0820 0.0033 0.0853 | 22.6548
- 6 | 2.50 | 0.0815 0.0035 0.0850 | 20.6989
- 7 | 2.50 | 0.0809 0.0037 0.0846 | 18.9688
- 8 | 2.50 | 0.0804 0.0039 0.0843 | 17.4455
- 9 | 2.50 | 0.0799 0.0040 0.0839 | 15.9223
- 10 | 2.50 | 0.0793 0.0043 0.0835 | 14.6627
- 11 | 2.50 | 0.0787 0.0044 0.0831 | 13.4764
- 12 | 2.50 | 0.0781 0.0046 0.0827 | 12.3015
- 13 | 2.50 | 0.0774 0.0048 0.0822 | 11.3776
- 14 | 2.50 | 0.0768 0.0050 0.0818 | 10.4537
- 15 | 2.25 | 0.0771 0.0052 0.0822 | 9.5920
- 16 | 2.25 | 0.0733 0.0071 0.0805 | 8.8725
- 29 | 2.00 | 0.0738 0.0032 0.0770 | 3.3283
- 30 | 2.00 | 0.0655 0.0068 0.0722 | 3.1221
- 31 | 2.00 | 0.0627 0.0080 0.0707 | 2.9160
- 43 | 1.75 | 0.0613 0.0048 0.0661 | 1.5785
- 44 | 1.75 | 0.0568 0.0073 0.0641 | 1.5194
- 45 | 1.75 | 0.0554 0.0081 0.0635 | 1.4626
- 57 | 1.50 | 0.0546 0.0062 0.0607 | 1.0900
- 58 | 1.50 | 0.0513 0.0084 0.0597 | 1.0730
- 59 | 1.50 | 0.0503 0.0091 0.0594 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 159s
- Prepare output 22s
- 181s
- Jacobian determinant (RMS): 0.016 0.062 0.100 0.148 0.193 | 0.205384
- Template Matching: 0.089 0.220 0.188 0.166 0.151 | 0.150820
- Write result maps: 68s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 16s
- PBT2x thickness: 46s
- 92s
- Create initial surface 72s
- Topology correction: 58s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 60s
- Spherical registration 295s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 19s
- PBT2x thickness: 54s
- 109s
- Create initial surface 86s
- Topology correction: 69s
- Surface refinement: 87s
- Reduction of surface collisions with optimization: 97s
- Spherical mapping with areal smoothing 78s
- Spherical registration 286s
- Final surface processing results:
- Average thickness (FS): 3.0572 1.0302 mm
- Surface intensity / position RMSE: 0.1285 / 0.1357
- Euler number / defect number / defect size: 44.0 / 45.5 / 1.77%
- Display thickness: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/surf/lh.thickness.sub-0027438_ses-1_acq-inv1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/surf/rh.thickness.sub-0027438_ses-1_acq-inv1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/sub-0027438_ses-1_acq-inv1_run-1_T1w.nii
- Surface ROI estimation: 2524s
- Surface and thickness estimation takes: 2130s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 61s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 43s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 15s
- ROI estimation of 'aal3' atlas 26s
- ROI estimation of 'mori' atlas 38s
- ROI estimation of 'anatomy3' atlas 55s
- ROI estimation of 'julichbrain' atlas 72s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 178s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s
- Write results 16s
- 739s
- Quality check: 26s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/report/catreport_sub-0027438_ses-1_acq-inv1_run-1_T1w.pdf
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- CAT preprocessing takes 70 minute(s) and 19 second(s).
- Image Quality Rating (IQR): 21.76% (F)
- GM volume (GMV): 57.37% (790.13 / 1377.15 ml)
- GM thickness (GMT): 3.06 1.03 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/label
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