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- CAT12.8.1 r1980: 1/1: ./ds/sub-AL027/sub-AL027_ses-4_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 3s
- 23s
- Correct center-of-mass 12s
- Affine registration 60s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 36s
- SPM preprocessing 1 (estimate 2): 27s
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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 6s
- Update probability maps 1s
- Update registration 29s
- 53s
- 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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- 15s
- SANLM denoising after LAS (medium) 15s
- 16s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 3s
- Major structures 1s
- Ventricle detection 4s
- Blood vessel detection 0s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 2s
- 10s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 18s
- AMAP peaks: [1.100.04,0.400.05,0.610.07]
- --- 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 | 0.2734 0.0000 0.2734 | 32.0000
- 2 | 2.50 | 0.2570 0.0054 0.2624 | 29.4886
- 3 | 2.50 | 0.2514 0.0090 0.2604 | 26.9772
- 4 | 2.50 | 0.2483 0.0108 0.2591 | 24.6107
- 5 | 2.50 | 0.2459 0.0121 0.2580 | 22.6548
- 6 | 2.50 | 0.2436 0.0131 0.2567 | 20.6989
- 7 | 2.50 | 0.2408 0.0141 0.2550 | 18.9688
- 8 | 2.50 | 0.2384 0.0152 0.2536 | 17.4455
- 9 | 2.50 | 0.2358 0.0162 0.2520 | 15.9223
- 10 | 2.50 | 0.2330 0.0175 0.2504 | 14.6627
- 11 | 2.50 | 0.2301 0.0186 0.2487 | 13.4764
- 12 | 2.50 | 0.2271 0.0197 0.2468 | 12.3015
- 13 | 2.50 | 0.2238 0.0212 0.2450 | 11.3776
- 14 | 2.50 | 0.2205 0.0224 0.2430 | 10.4537
- 15 | 2.25 | 0.2783 0.0239 0.3022 | 9.5920
- 16 | 2.25 | 0.2601 0.0351 0.2952 | 8.8725
- 17 | 2.25 | 0.2508 0.0400 0.2908 | 8.1530
- 18 | 2.25 | 0.2434 0.0432 0.2867 | 7.5234
- 19 | 2.25 | 0.2368 0.0459 0.2826 | 6.9630
- 20 | 2.25 | 0.2304 0.0478 0.2782 | 6.4027
- 21 | 2.25 | 0.2239 0.0502 0.2741 | 5.9447
- 22 | 2.25 | 0.2176 0.0521 0.2697 | 5.5083
- 23 | 2.25 | 0.2114 0.0537 0.2650 | 5.0803
- 24 | 2.25 | 0.2035 0.0560 0.2595 | 4.7404
- 25 | 2.25 | 0.1975 0.0573 0.2548 | 4.4005
- 26 | 2.25 | 0.1913 0.0587 0.2500 | 4.0868
- 27 | 2.25 | 0.1850 0.0605 0.2456 | 3.8221
- 28 | 2.25 | 0.1790 0.0617 0.2407 | 3.5574
- 29 | 2.00 | 0.1773 0.0631 0.2403 | 3.3283
- 30 | 2.00 | 0.1699 0.0643 0.2342 | 3.1221
- 31 | 2.00 | 0.1645 0.0647 0.2292 | 2.9160
- 32 | 2.00 | 0.1576 0.0660 0.2237 | 2.7495
- 33 | 2.00 | 0.1524 0.0668 0.2192 | 2.5890
- 34 | 2.00 | 0.1471 0.0675 0.2145 | 2.4330
- 35 | 2.00 | 0.1417 0.0688 0.2105 | 2.3080
- 36 | 2.00 | 0.1367 0.0696 0.2063 | 2.1830
- 37 | 2.00 | 0.1317 0.0704 0.2021 | 2.0688
- 38 | 2.00 | 0.1269 0.0715 0.1984 | 1.9714
- 39 | 2.00 | 0.1223 0.0721 0.1944 | 1.8740
- 40 | 2.00 | 0.1165 0.0730 0.1895 | 1.7907
- 41 | 2.00 | 0.1124 0.0735 0.1859 | 1.7148
- 42 | 2.00 | 0.1085 0.0738 0.1822 | 1.6390
- 43 | 1.75 | 0.1046 0.0747 0.1793 | 1.5785
- 44 | 1.75 | 0.1002 0.0760 0.1762 | 1.5194
- 45 | 1.75 | 0.0968 0.0764 0.1732 | 1.4626
- 46 | 1.75 | 0.0937 0.0769 0.1706 | 1.4166
- 47 | 1.75 | 0.0909 0.0770 0.1679 | 1.3706
- 48 | 1.75 | 0.0882 0.0772 0.1654 | 1.3290
- 49 | 1.75 | 0.0845 0.0775 0.1620 | 1.2932
- 50 | 1.75 | 0.0823 0.0774 0.1597 | 1.2574
- 51 | 1.75 | 0.0802 0.0776 0.1577 | 1.2271
- 52 | 1.75 | 0.0781 0.0777 0.1558 | 1.1992
- 53 | 1.75 | 0.0762 0.0777 0.1539 | 1.1713
- 54 | 1.75 | 0.0744 0.0779 0.1524 | 1.1493
- 57 | 1.50 | 0.0759 0.0772 0.1531 | 1.0900
- Problem with Shooting (dets: 0.00380401 .. 3.17158)
- 58 | 1.50 | 0.0701 0.0809 0.1510 | 1.0730
- 59 | 1.50 | 0.0675 0.0819 0.1494 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 370s
- Prepare output 7s
- 377s
- Jacobian determinant (RMS): 0.032 0.180 0.556 1.309 2.640 | 2.500340
- Template Matching: 0.273 0.278 0.177 0.223 0.203 | 0.202579
- Write result maps: 18s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 4s
- CSF distance: 2s
- PBT2x thickness: 5s
- 13s
- Create initial surface 20s
- Topology correction: 20s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 21s
- Spherical mapping with areal smoothing 36s
- Spherical registration 336s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 4s
- CSF distance: 2s
- PBT2x thickness: 6s
- 13s
- Create initial surface 17s
- Topology correction: 93s
- Surface refinement: 117s
- Reduction of surface collisions with optimization: 47s
- Spherical mapping with areal smoothing 36s
- Spherical registration 370s
- Final surface processing results:
- Average thickness (FS): 0.7937 0.2502 mm
- Surface intensity / position RMSE: 0.1478 / 0.4435
- Euler number / defect number / defect size: 30.0 / 10.0 / 8.35%
- Display thickness: /var/lib/condor/execute/dir_27215/ds/sub-AL027/surf/lh.thickness.sub-AL027_ses-4_acq-RARE_T1w
- Display thickness: /var/lib/condor/execute/dir_27215/ds/sub-AL027/surf/rh.thickness.sub-AL027_ses-4_acq-RARE_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_27215/ds/sub-AL027/sub-AL027_ses-4_acq-RARE_T1w.nii
- Surface ROI estimation: 1686s
- Surface and thickness estimation takes: 1655s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 4s
- ROI estimation of 'neuromorphometrics' atlas 15s
- ROI estimation of 'lpba40' atlas 5s
- ROI estimation of 'hammers' atlas 11s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 4s
- ROI estimation of 'aal3' atlas 6s
- ROI estimation of 'mori' atlas 9s
- ROI estimation of 'anatomy3' atlas 13s
- ROI estimation of 'julichbrain' atlas 17s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 7s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 42s
- Write results 43s
- 174s
- Quality check: 1s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_27215/ds/sub-AL027/report/catreport_sub-AL027_ses-4_acq-RARE_T1w.pdf
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- CAT preprocessing takes 35 minute(s) and 28 second(s).
- Image Quality Rating (IQR): 52.32% (E-)
- GM volume (GMV): 1.04% ( 2.26 / 216.98 ml)
- GM thickness (GMT): 0.79 0.26 mm
- Segmentations are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/mri
- Reports are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/report
- Labels are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/label
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