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- CAT12.8.1 r1980: 1/1: ./ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.n
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- SANLM denoising (medium): 2s
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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 3s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 4s
- 23s
- Correct center-of-mass 17s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 20s
- Use initial fine affine registration. 44s
- SPM preprocessing 1 (estimate 2): 48s
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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 8s
- Update segmentation 9s
- Update skull-stripping 7s
- Update probability maps 5s
- Update registration 31s
- 60s
- 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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- 14s
- SANLM denoising after LAS (medium) 16s
- 18s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 2s
- Major structures 0s
- Ventricle detection 2s
- Blood vessel detection 0s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 2s
- 8s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 36s
- AMAP peaks: [0.990.08,0.310.06,0.720.09]
- --- 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 | 0.2594 0.0000 0.2594 | 32.0000
- 2 | 2.50 | 0.2438 0.0051 0.2489 | 29.4886
- 3 | 2.50 | 0.2384 0.0086 0.2470 | 26.9772
- 4 | 2.50 | 0.2354 0.0104 0.2458 | 24.6107
- 5 | 2.50 | 0.2330 0.0117 0.2447 | 22.6548
- 6 | 2.50 | 0.2308 0.0127 0.2435 | 20.6989
- 7 | 2.50 | 0.2281 0.0137 0.2418 | 18.9688
- 8 | 2.50 | 0.2257 0.0148 0.2405 | 17.4455
- 9 | 2.50 | 0.2232 0.0157 0.2389 | 15.9223
- 10 | 2.50 | 0.2204 0.0170 0.2374 | 14.6627
- 11 | 2.50 | 0.2175 0.0182 0.2357 | 13.4764
- 12 | 2.50 | 0.2146 0.0192 0.2338 | 12.3015
- 13 | 2.50 | 0.2113 0.0208 0.2320 | 11.3776
- 14 | 2.50 | 0.2081 0.0220 0.2300 | 10.4537
- 15 | 2.25 | 0.2617 0.0234 0.2851 | 9.5920
- 16 | 2.25 | 0.2445 0.0339 0.2785 | 8.8725
- 17 | 2.25 | 0.2355 0.0387 0.2742 | 8.1530
- 18 | 2.25 | 0.2282 0.0419 0.2701 | 7.5234
- 19 | 2.25 | 0.2216 0.0444 0.2660 | 6.9630
- 20 | 2.25 | 0.2153 0.0463 0.2616 | 6.4027
- 21 | 2.25 | 0.2089 0.0486 0.2576 | 5.9447
- 22 | 2.25 | 0.2028 0.0505 0.2533 | 5.5083
- 23 | 2.25 | 0.1966 0.0520 0.2486 | 5.0803
- 24 | 2.25 | 0.1891 0.0542 0.2433 | 4.7404
- 25 | 2.25 | 0.1832 0.0554 0.2386 | 4.4005
- 26 | 2.25 | 0.1772 0.0568 0.2339 | 4.0868
- 27 | 2.25 | 0.1711 0.0585 0.2295 | 3.8221
- 28 | 2.25 | 0.1652 0.0595 0.2247 | 3.5574
- 29 | 2.00 | 0.1635 0.0608 0.2242 | 3.3283
- 30 | 2.00 | 0.1561 0.0621 0.2181 | 3.1221
- 31 | 2.00 | 0.1507 0.0625 0.2132 | 2.9160
- 32 | 2.00 | 0.1441 0.0637 0.2078 | 2.7495
- 33 | 2.00 | 0.1390 0.0643 0.2034 | 2.5890
- 34 | 2.00 | 0.1339 0.0649 0.1988 | 2.4330
- 35 | 2.00 | 0.1289 0.0660 0.1949 | 2.3080
- 36 | 2.00 | 0.1241 0.0667 0.1907 | 2.1830
- 37 | 2.00 | 0.1193 0.0673 0.1867 | 2.0688
- 38 | 2.00 | 0.1148 0.0682 0.1830 | 1.9714
- 39 | 2.00 | 0.1104 0.0686 0.1791 | 1.8740
- 40 | 2.00 | 0.1051 0.0693 0.1744 | 1.7907
- 41 | 2.00 | 0.1013 0.0697 0.1710 | 1.7148
- 42 | 2.00 | 0.0976 0.0698 0.1675 | 1.6390
- 43 | 1.75 | 0.0939 0.0707 0.1646 | 1.5785
- 44 | 1.75 | 0.0896 0.0718 0.1614 | 1.5194
- 45 | 1.75 | 0.0864 0.0721 0.1585 | 1.4626
- 46 | 1.75 | 0.0835 0.0724 0.1560 | 1.4166
- 47 | 1.75 | 0.0809 0.0725 0.1534 | 1.3706
- 48 | 1.75 | 0.0784 0.0726 0.1509 | 1.3290
- 49 | 1.75 | 0.0751 0.0728 0.1478 | 1.2932
- 50 | 1.75 | 0.0730 0.0725 0.1456 | 1.2574
- 57 | 1.50 | 0.0742 0.0661 0.1403 | 1.0900
- Problem with Shooting (dets: 0.00337295 .. 2.14688)
- 58 | 1.50 | 0.0667 0.0713 0.1380 | 1.0730
- 59 | 1.50 | 0.0631 0.0733 0.1363 | 1.0579
- 60 | 1.50 | 0.0607 0.0745 0.1352 | 1.0447
- Shooting registration with 2.50:-0.25:1.50 mm takes: 320s
- Prepare output 7s
- 327s
- Jacobian determinant (RMS): 0.031 0.173 0.528 1.211 2.388 | 2.273741
- Template Matching: 0.259 0.262 0.163 0.219 0.182 | 0.181965
- Write result maps: 16s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 3s
- CSF distance: 2s
- PBT2x thickness: 4s
- 10s
- Create initial surface 14s
- Topology correction: 17s
- Surface refinement: 37s
- Reduction of surface collisions with optimization: 17s
- Spherical mapping with areal smoothing 31s
- Spherical registration 335s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 3s
- CSF distance: 2s
- PBT2x thickness: 4s
- 10s
- Create initial surface 12s
- Topology correction: 16s
- Surface refinement: 37s
- Reduction of surface collisions with optimization: 18s
- Spherical mapping with areal smoothing 31s
- Spherical registration 326s
- Final surface processing results:
- Average thickness (FS): 0.7421 0.4194 mm
- Surface intensity / position RMSE: 0.0630 / 0.1094
- Euler number / defect number / defect size: 22.0 / 7.0 / 1.97%
- Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/lh.thickness.sub-AL034_ses-1_acq-RARE_T1w
- Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/rh.thickness.sub-AL034_ses-1_acq-RARE_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii
- Surface ROI estimation: 1368s
- Surface and thickness estimation takes: 1336s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 3s
- ROI estimation of 'neuromorphometrics' atlas 12s
- 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 5s
- ROI estimation of 'mori' atlas 7s
- ROI estimation of 'anatomy3' atlas 10s
- ROI estimation of 'julichbrain' atlas 14s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 33s
- Write results 34s
- 138s
- Quality check: 1s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_27041/ds/sub-AL034/report/catreport_sub-AL034_ses-1_acq-RARE_T1w.pdf
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- CAT preprocessing takes 29 minute(s) and 36 second(s).
- Image Quality Rating (IQR): 52.32% (E-)
- GM volume (GMV): 8.92% (12.93 / 144.98 ml)
- GM thickness (GMT): 0.74 0.42 mm
- Segmentations are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/mri
- Reports are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/report
- Labels are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/label
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