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- CAT12.8.1 r1980: 1/1: ./ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.n
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- SANLM denoising (medium): 1s
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- WARNING 01: cat_run_job:failedBGD
- cat_run_job1639: Detection of background failed.
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- Internal resampling (1.50x4.50x1.50mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 2s
- Estimate background 3s
- Initial correction 3s
- Refine background 1s
- Final correction 2s
- Final scaling 3s
- 17s
- Correct center-of-mass 10s
- Affine registration 45s
- SPM preprocessing 1 (estimate 1 - TPM registration): 11s
- Use initial fine affine registration. 28s
- SPM preprocessing 1 (estimate 2): 29s
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- WARNING 02: 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 6s
- Update segmentation 7s
- Update skull-stripping 5s
- Update probability maps 1s
- Update registration 23s
- 41s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 1s
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- NOTE 01: cat_main:skipLAS
- Skip LAS due to image contrast. Use global normalization.
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- 13s
- SANLM denoising after LAS (medium) 12s
- 14s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 2s
- 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 1s
- 10s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 9s
- AMAP peaks: [1.090.12,0.360.10,0.660.05]
- --- 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 | 0.2658 0.0000 0.2658 | 32.0000
- 2 | 2.50 | 0.2487 0.0056 0.2543 | 29.4886
- 3 | 2.50 | 0.2428 0.0093 0.2521 | 26.9772
- 4 | 2.50 | 0.2395 0.0112 0.2507 | 24.6107
- 5 | 2.50 | 0.2368 0.0126 0.2495 | 22.6548
- 6 | 2.50 | 0.2345 0.0136 0.2481 | 20.6989
- 7 | 2.50 | 0.2316 0.0147 0.2463 | 18.9688
- 8 | 2.50 | 0.2291 0.0158 0.2449 | 17.4455
- 9 | 2.50 | 0.2265 0.0167 0.2432 | 15.9223
- 10 | 2.50 | 0.2236 0.0180 0.2416 | 14.6627
- 11 | 2.50 | 0.2207 0.0191 0.2398 | 13.4764
- 12 | 2.50 | 0.2177 0.0202 0.2378 | 12.3015
- 13 | 2.50 | 0.2143 0.0217 0.2360 | 11.3776
- 14 | 2.50 | 0.2111 0.0228 0.2339 | 10.4537
- 15 | 2.25 | 0.2646 0.0244 0.2890 | 9.5920
- 16 | 2.25 | 0.2469 0.0351 0.2820 | 8.8725
- 17 | 2.25 | 0.2380 0.0396 0.2776 | 8.1530
- 18 | 2.25 | 0.2309 0.0426 0.2736 | 7.5234
- 19 | 2.25 | 0.2245 0.0450 0.2696 | 6.9630
- 20 | 2.25 | 0.2185 0.0467 0.2652 | 6.4027
- 21 | 2.25 | 0.2123 0.0489 0.2612 | 5.9447
- 22 | 2.25 | 0.2064 0.0506 0.2570 | 5.5083
- 23 | 2.25 | 0.2005 0.0519 0.2525 | 5.0803
- 24 | 2.25 | 0.1932 0.0540 0.2472 | 4.7404
- 25 | 2.25 | 0.1875 0.0551 0.2427 | 4.4005
- 26 | 2.25 | 0.1817 0.0564 0.2381 | 4.0868
- 27 | 2.25 | 0.1758 0.0580 0.2338 | 3.8221
- 28 | 2.25 | 0.1702 0.0590 0.2292 | 3.5574
- 29 | 2.00 | 0.1694 0.0603 0.2297 | 3.3283
- 30 | 2.00 | 0.1621 0.0618 0.2239 | 3.1221
- 31 | 2.00 | 0.1567 0.0623 0.2191 | 2.9160
- 32 | 2.00 | 0.1502 0.0636 0.2138 | 2.7495
- 33 | 2.00 | 0.1452 0.0643 0.2095 | 2.5890
- 34 | 2.00 | 0.1401 0.0649 0.2050 | 2.4330
- 35 | 2.00 | 0.1351 0.0660 0.2012 | 2.3080
- 36 | 2.00 | 0.1304 0.0667 0.1971 | 2.1830
- 37 | 2.00 | 0.1257 0.0674 0.1931 | 2.0688
- 38 | 2.00 | 0.1212 0.0683 0.1895 | 1.9714
- 39 | 2.00 | 0.1169 0.0688 0.1857 | 1.8740
- 40 | 2.00 | 0.1117 0.0695 0.1811 | 1.7907
- 41 | 2.00 | 0.1079 0.0699 0.1778 | 1.7148
- 42 | 2.00 | 0.1043 0.0700 0.1743 | 1.6390
- 43 | 1.75 | 0.1009 0.0708 0.1716 | 1.5785
- 44 | 1.75 | 0.0967 0.0720 0.1686 | 1.5194
- 45 | 1.75 | 0.0935 0.0723 0.1658 | 1.4626
- 46 | 1.75 | 0.0907 0.0727 0.1634 | 1.4166
- 47 | 1.75 | 0.0881 0.0727 0.1609 | 1.3706
- 48 | 1.75 | 0.0856 0.0729 0.1585 | 1.3290
- 49 | 1.75 | 0.0823 0.0731 0.1554 | 1.2932
- 50 | 1.75 | 0.0803 0.0730 0.1533 | 1.2574
- 51 | 1.75 | 0.0784 0.0730 0.1514 | 1.2271
- 52 | 1.75 | 0.0765 0.0731 0.1496 | 1.1992
- 53 | 1.75 | 0.0748 0.0730 0.1478 | 1.1713
- 57 | 1.50 | 0.0762 0.0711 0.1473 | 1.0900
- Problem with Shooting (dets: 0.00294326 .. 3.19305)
- 58 | 1.50 | 0.0701 0.0751 0.1452 | 1.0730
- 59 | 1.50 | 0.0673 0.0764 0.1438 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 259s
- Prepare output 5s
- 264s
- Jacobian determinant (RMS): 0.032 0.177 0.530 1.205 2.480 | 2.232162
- Template Matching: 0.266 0.265 0.169 0.224 0.202 | 0.202024
- Write result maps: 12s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 4s
- CSF distance: 1s
- PBT2x thickness: 5s
- 12s
- Create initial surface 18s
- Topology correction: 503s
- Surface refinement: 123s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 58s
- Spherical registration 269s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 4s
- CSF distance: 2s
- PBT2x thickness: 5s
- 12s
- Create initial surface 18s
- Topology correction: 888s
- Surface refinement: 188s
- Reduction of surface collisions with optimization: 192s
- Spherical mapping with areal smoothing 153s
- Spherical registration 265s
- Final surface processing results:
- Average thickness (FS): 0.4933 0.4310 mm
- Surface intensity / position RMSE: 0.2478 / 0.9852
- Euler number / defect number / defect size: 10.0 / 2.5 / 78.25%
- Display thickness: /var/lib/condor/execute/dir_12393/ds/sub-AL011/surf/lh.thickness.sub-AL011_ses-7_acq-RARE_T1w
- Display thickness: /var/lib/condor/execute/dir_12393/ds/sub-AL011/surf/rh.thickness.sub-AL011_ses-7_acq-RARE_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12393/ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.nii
- Surface ROI estimation: 3179s
- Surface and thickness estimation takes: 3153s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 3s
- ROI estimation of 'neuromorphometrics' atlas 11s
- ROI estimation of 'lpba40' atlas 3s
- ROI estimation of 'hammers' atlas 8s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 3s
- ROI estimation of 'aal3' atlas 4s
- ROI estimation of 'mori' atlas 7s
- ROI estimation of 'anatomy3' atlas 9s
- ROI estimation of 'julichbrain' atlas 12s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 5s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 30s
- Write results 31s
- 125s
- Quality check: 1s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12393/ds/sub-AL011/report/catreport_sub-AL011_ses-7_acq-RARE_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 52.32% (E-)
- GM volume (GMV): 1.13% ( 3.77 / 335.08 ml)
- GM thickness (GMT): 0.51 0.48 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/mri
- Reports are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/report
- Labels are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/label
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