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- CAT12.8.1 r1980: 1/1: ./ds/sub-AL035/sub-AL035_ses-2_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 11s
- Affine registration 30s
- SPM preprocessing 1 (estimate 1 - TPM registration): 9s
- Use initial fine affine registration. 43s
- SPM preprocessing 1 (estimate 2): 55s
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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 7s
- Update segmentation 8s
- Update skull-stripping 7s
- Update probability maps 1s
- Update registration 27s
- 50s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 2s
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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 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 2s
- 10s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 13s
- AMAP peaks: [1.040.05,0.370.07,0.640.05]
- --- 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 | 0.2957 0.0000 0.2957 | 32.0000
- 2 | 2.50 | 0.2788 0.0056 0.2844 | 29.4886
- 3 | 2.50 | 0.2730 0.0094 0.2824 | 26.9772
- 4 | 2.50 | 0.2698 0.0113 0.2811 | 24.6107
- 5 | 2.50 | 0.2672 0.0127 0.2799 | 22.6548
- 6 | 2.50 | 0.2649 0.0137 0.2786 | 20.6989
- 7 | 2.50 | 0.2618 0.0149 0.2767 | 18.9688
- 8 | 2.50 | 0.2592 0.0161 0.2753 | 17.4455
- 9 | 2.50 | 0.2565 0.0171 0.2736 | 15.9223
- 10 | 2.50 | 0.2534 0.0185 0.2719 | 14.6627
- 11 | 2.50 | 0.2503 0.0198 0.2702 | 13.4764
- 12 | 2.50 | 0.2471 0.0210 0.2681 | 12.3015
- 13 | 2.50 | 0.2435 0.0227 0.2662 | 11.3776
- 14 | 2.50 | 0.2400 0.0241 0.2641 | 10.4537
- 15 | 2.25 | 0.3080 0.0257 0.3337 | 9.5920
- 16 | 2.25 | 0.2874 0.0385 0.3259 | 8.8725
- 17 | 2.25 | 0.2768 0.0442 0.3210 | 8.1530
- 18 | 2.25 | 0.2685 0.0479 0.3164 | 7.5234
- 19 | 2.25 | 0.2610 0.0510 0.3119 | 6.9630
- 20 | 2.25 | 0.2539 0.0531 0.3070 | 6.4027
- 21 | 2.25 | 0.2466 0.0559 0.3025 | 5.9447
- 22 | 2.25 | 0.2396 0.0581 0.2977 | 5.5083
- 23 | 2.25 | 0.2327 0.0598 0.2925 | 5.0803
- 24 | 2.25 | 0.2239 0.0624 0.2862 | 4.7404
- 25 | 2.25 | 0.2172 0.0638 0.2810 | 4.4005
- 26 | 2.25 | 0.2104 0.0654 0.2758 | 4.0868
- 27 | 2.25 | 0.2034 0.0674 0.2709 | 3.8221
- 28 | 2.25 | 0.1968 0.0688 0.2655 | 3.5574
- 29 | 2.00 | 0.1923 0.0704 0.2627 | 3.3283
- 30 | 2.00 | 0.1851 0.0705 0.2556 | 3.1221
- 31 | 2.00 | 0.1797 0.0705 0.2502 | 2.9160
- 32 | 2.00 | 0.1724 0.0716 0.2441 | 2.7495
- 33 | 2.00 | 0.1670 0.0723 0.2393 | 2.5890
- 34 | 2.00 | 0.1614 0.0730 0.2344 | 2.4330
- 35 | 2.00 | 0.1557 0.0744 0.2301 | 2.3080
- 36 | 2.00 | 0.1503 0.0753 0.2256 | 2.1830
- 37 | 2.00 | 0.1450 0.0762 0.2211 | 2.0688
- 38 | 2.00 | 0.1398 0.0774 0.2171 | 1.9714
- 39 | 2.00 | 0.1348 0.0780 0.2129 | 1.8740
- 40 | 2.00 | 0.1284 0.0790 0.2075 | 1.7907
- 41 | 2.00 | 0.1240 0.0796 0.2037 | 1.7148
- 42 | 2.00 | 0.1198 0.0799 0.1997 | 1.6390
- 43 | 1.75 | 0.1154 0.0812 0.1967 | 1.5785
- 44 | 1.75 | 0.1109 0.0824 0.1933 | 1.5194
- 45 | 1.75 | 0.1073 0.0827 0.1900 | 1.4626
- 46 | 1.75 | 0.1039 0.0833 0.1873 | 1.4166
- 47 | 1.75 | 0.1009 0.0835 0.1844 | 1.3706
- 48 | 1.75 | 0.0979 0.0838 0.1817 | 1.3290
- 49 | 1.75 | 0.0937 0.0842 0.1779 | 1.2932
- 50 | 1.75 | 0.0912 0.0842 0.1754 | 1.2574
- 51 | 1.75 | 0.0888 0.0844 0.1732 | 1.2271
- 52 | 1.75 | 0.0865 0.0846 0.1712 | 1.1992
- 53 | 1.75 | 0.0844 0.0847 0.1691 | 1.1713
- 54 | 1.75 | 0.0824 0.0851 0.1674 | 1.1493
- 55 | 1.75 | 0.0805 0.0853 0.1657 | 1.1276
- 56 | 1.75 | 0.0787 0.0854 0.1641 | 1.1069
- 57 | 1.50 | 0.0792 0.0880 0.1673 | 1.0900
- Problem with Shooting (dets: 0.00437255 .. 2.8682)
- 58 | 1.50 | 0.0753 0.0906 0.1659 | 1.0730
- 59 | 1.50 | 0.0731 0.0913 0.1644 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 331s
- Prepare output 6s
- 337s
- Jacobian determinant (RMS): 0.033 0.195 0.611 1.462 2.987 | 2.918903
- Template Matching: 0.296 0.308 0.192 0.115 0.219 | 0.219373
- Write result maps: 14s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 3s
- CSF distance: 1s
- PBT2x thickness: 5s
- 10s
- Create initial surface 17s
- Topology correction: 16s
- Surface refinement: 40s
- Reduction of surface collisions with optimization: 20s
- Spherical mapping with areal smoothing 32s
- Spherical registration 327s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 3s
- CSF distance: 1s
- PBT2x thickness: 5s
- 11s
- Create initial surface 18s
- Topology correction: 21s
- Surface refinement: 47s
- Reduction of surface collisions with optimization: 21s
- Spherical mapping with areal smoothing 35s
- Spherical registration 340s
- Final surface processing results:
- Average thickness (FS): 0.5887 0.1179 mm
- Surface intensity / position RMSE: 0.0755 / 0.1613
- Euler number / defect number / defect size: 10.0 / 7.5 / 1.70%
- Display thickness: /var/lib/condor/execute/dir_29850/ds/sub-AL035/surf/lh.thickness.sub-AL035_ses-2_acq-RARE_T1w
- Display thickness: /var/lib/condor/execute/dir_29850/ds/sub-AL035/surf/rh.thickness.sub-AL035_ses-2_acq-RARE_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29850/ds/sub-AL035/sub-AL035_ses-2_acq-RARE_T1w.nii
- Surface ROI estimation: 1406s
- Surface and thickness estimation takes: 1375s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 4s
- ROI estimation of 'neuromorphometrics' atlas 13s
- ROI estimation of 'lpba40' atlas 4s
- ROI estimation of 'hammers' atlas 9s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 3s
- ROI estimation of 'aal3' atlas 5s
- ROI estimation of 'mori' atlas 8s
- ROI estimation of 'anatomy3' atlas 11s
- ROI estimation of 'julichbrain' atlas 15s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 36s
- Write results 37s
- 150s
- Quality check: 1s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29850/ds/sub-AL035/report/catreport_sub-AL035_ses-2_acq-RARE_T1w.pdf
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- CAT preprocessing takes 30 minute(s) and 31 second(s).
- Image Quality Rating (IQR): 52.32% (E-)
- GM volume (GMV): 0.33% ( 0.66 / 201.92 ml)
- GM thickness (GMT): 0.59 0.12 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29850/ds/sub-AL035/mri
- Reports are saved in /var/lib/condor/execute/dir_29850/ds/sub-AL035/report
- Labels are saved in /var/lib/condor/execute/dir_29850/ds/sub-AL035/label
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