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- CAT12.8.1 r1980: 1/1: ./ds/sub-AL030/sub-AL030_ses-2_acq-RARE_T1w.n
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- SANLM denoising (medium): 3s
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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
- 21s
- Correct center-of-mass 6s
- Affine registration 58s
- SPM preprocessing 1 (estimate 1 - TPM registration): 11s
- Use initial fine affine registration. 35s
- SPM preprocessing 1 (estimate 2): 48s
- ----------------------------------------------------------------------------
- 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 6s
- Update probability maps 1s
- Update registration 29s
- 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
- 17s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 2s
- Major structures 0s
- Ventricle detection 4s
- Blood vessel detection 0s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 2s
- 9s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 12s
- AMAP peaks: [1.150.05,0.360.06,0.680.07]
- --- 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 | 0.2828 0.0000 0.2828 | 32.0000
- 2 | 2.50 | 0.2663 0.0055 0.2718 | 29.4886
- 3 | 2.50 | 0.2606 0.0092 0.2698 | 26.9772
- 4 | 2.50 | 0.2575 0.0110 0.2685 | 24.6107
- 5 | 2.50 | 0.2549 0.0124 0.2673 | 22.6548
- 6 | 2.50 | 0.2527 0.0134 0.2660 | 20.6989
- 7 | 2.50 | 0.2497 0.0145 0.2642 | 18.9688
- 8 | 2.50 | 0.2472 0.0156 0.2628 | 17.4455
- 9 | 2.50 | 0.2445 0.0166 0.2611 | 15.9223
- 10 | 2.50 | 0.2416 0.0180 0.2595 | 14.6627
- 11 | 2.50 | 0.2386 0.0192 0.2578 | 13.4764
- 12 | 2.50 | 0.2355 0.0203 0.2558 | 12.3015
- 13 | 2.50 | 0.2320 0.0219 0.2540 | 11.3776
- 14 | 2.50 | 0.2287 0.0232 0.2519 | 10.4537
- 15 | 2.25 | 0.2908 0.0248 0.3156 | 9.5920
- 16 | 2.25 | 0.2717 0.0366 0.3083 | 8.8725
- 17 | 2.25 | 0.2620 0.0417 0.3037 | 8.1530
- 18 | 2.25 | 0.2542 0.0452 0.2994 | 7.5234
- 19 | 2.25 | 0.2472 0.0480 0.2951 | 6.9630
- 20 | 2.25 | 0.2405 0.0500 0.2904 | 6.4027
- 21 | 2.25 | 0.2336 0.0525 0.2861 | 5.9447
- 22 | 2.25 | 0.2271 0.0546 0.2816 | 5.5083
- 23 | 2.25 | 0.2205 0.0562 0.2767 | 5.0803
- 24 | 2.25 | 0.2123 0.0586 0.2709 | 4.7404
- 25 | 2.25 | 0.2060 0.0600 0.2660 | 4.4005
- 26 | 2.25 | 0.1994 0.0616 0.2610 | 4.0868
- 27 | 2.25 | 0.1929 0.0635 0.2563 | 3.8221
- 28 | 2.25 | 0.1866 0.0647 0.2513 | 3.5574
- 29 | 2.00 | 0.1837 0.0662 0.2498 | 3.3283
- 30 | 2.00 | 0.1764 0.0671 0.2434 | 3.1221
- 31 | 2.00 | 0.1709 0.0673 0.2382 | 2.9160
- 32 | 2.00 | 0.1638 0.0686 0.2324 | 2.7495
- 33 | 2.00 | 0.1584 0.0693 0.2278 | 2.5890
- 34 | 2.00 | 0.1530 0.0700 0.2230 | 2.4330
- 35 | 2.00 | 0.1475 0.0714 0.2189 | 2.3080
- 36 | 2.00 | 0.1422 0.0722 0.2145 | 2.1830
- 37 | 2.00 | 0.1371 0.0731 0.2102 | 2.0688
- 38 | 2.00 | 0.1321 0.0742 0.2063 | 1.9714
- 39 | 2.00 | 0.1273 0.0748 0.2021 | 1.8740
- 40 | 2.00 | 0.1213 0.0757 0.1970 | 1.7907
- 41 | 2.00 | 0.1171 0.0763 0.1933 | 1.7148
- 42 | 2.00 | 0.1130 0.0766 0.1895 | 1.6390
- 43 | 1.75 | 0.1088 0.0777 0.1865 | 1.5785
- 44 | 1.75 | 0.1043 0.0789 0.1832 | 1.5194
- 45 | 1.75 | 0.1008 0.0792 0.1801 | 1.4626
- 46 | 1.75 | 0.0977 0.0798 0.1774 | 1.4166
- 47 | 1.75 | 0.0947 0.0799 0.1747 | 1.3706
- 48 | 1.75 | 0.0919 0.0802 0.1721 | 1.3290
- 49 | 1.75 | 0.0880 0.0805 0.1685 | 1.2932
- 50 | 1.75 | 0.0857 0.0804 0.1661 | 1.2574
- 51 | 1.75 | 0.0835 0.0806 0.1641 | 1.2271
- 52 | 1.75 | 0.0813 0.0808 0.1621 | 1.1992
- 53 | 1.75 | 0.0793 0.0808 0.1601 | 1.1713
- 54 | 1.75 | 0.0774 0.0811 0.1585 | 1.1493
- 55 | 1.75 | 0.0757 0.0812 0.1569 | 1.1276
- 56 | 1.75 | 0.0741 0.0812 0.1553 | 1.1069
- 57 | 1.50 | 0.0745 0.0836 0.1581 | 1.0900
- Problem with Shooting (dets: 0.00463895 .. 3.1338)
- 58 | 1.50 | 0.0707 0.0861 0.1568 | 1.0730
- 59 | 1.50 | 0.0686 0.0868 0.1554 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 334s
- Prepare output 6s
- 339s
- Jacobian determinant (RMS): 0.032 0.185 0.575 1.359 2.735 | 2.652058
- Template Matching: 0.283 0.291 0.184 0.222 0.206 | 0.205910
- Write result maps: 15s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 2s
- CSF distance: 1s
- PBT2x thickness: 4s
- 8s
- Create initial surface 15s
- Topology correction: 16s
- Surface refinement: 60s
- Reduction of surface collisions with optimization: 21s
- Spherical mapping with areal smoothing 32s
- Spherical registration 356s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 2s
- CSF distance: 1s
- PBT2x thickness: 4s
- 9s
- Create initial surface 15s
- Topology correction: 559s
- Surface refinement: 179s
- Reduction of surface collisions with optimization: 127s
- Spherical mapping with areal smoothing 82s
- Spherical registration 357s
- Final surface processing results:
- Average thickness (FS): 0.7513 0.3370 mm
- Surface intensity / position RMSE: 0.1933 / 0.6733
- Euler number / defect number / defect size: 10.0 / 4.5 / 46.23%
- Display thickness: /var/lib/condor/execute/dir_12428/ds/sub-AL030/surf/lh.thickness.sub-AL030_ses-2_acq-RARE_T1w
- Display thickness: /var/lib/condor/execute/dir_12428/ds/sub-AL030/surf/rh.thickness.sub-AL030_ses-2_acq-RARE_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12428/ds/sub-AL030/sub-AL030_ses-2_acq-RARE_T1w.nii
- Surface ROI estimation: 2301s
- Surface and thickness estimation takes: 2270s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 4s
- ROI estimation of 'neuromorphometrics' atlas 14s
- ROI estimation of 'lpba40' atlas 4s
- ROI estimation of 'hammers' atlas 10s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 3s
- ROI estimation of 'aal3' atlas 6s
- ROI estimation of 'mori' atlas 8s
- ROI estimation of 'anatomy3' atlas 12s
- ROI estimation of 'julichbrain' atlas 16s
- 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 35s
- Write results 36s
- 157s
- Quality check: 1s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12428/ds/sub-AL030/report/catreport_sub-AL030_ses-2_acq-RARE_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 39 second(s).
- Image Quality Rating (IQR): 52.32% (E-)
- GM volume (GMV): 0.08% ( 0.12 / 153.73 ml)
- GM thickness (GMT): 0.71 0.48 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12428/ds/sub-AL030/mri
- Reports are saved in /var/lib/condor/execute/dir_12428/ds/sub-AL030/report
- Labels are saved in /var/lib/condor/execute/dir_12428/ds/sub-AL030/label
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