------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./ds/sub-AL020/sub-AL020_ses-3_acq-RARE_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 2s ------------------------------------------------------------------------ WARNING 01: cat_run_job:failedBGD cat_run_job1639: Detection of background failed. ------------------------------------------------------------------------ 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 22s Correct center-of-mass 10s Affine registration 57s SPM preprocessing 1 (estimate 1 - TPM registration): 14s Use initial fine affine registration. 37s SPM preprocessing 1 (estimate 2): 42s ---------------------------------------------------------------------------- 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). ---------------------------------------------------------------------------- SPM preprocessing 2 (write): Write Segmentation 7s Update segmentation 8s Update skull-stripping 6s Update probability maps 1s Update registration 29s 51s Global intensity correction: SANLM denoising after intensity normalization (medium): 1s ------------------------------------------------------------------------ NOTE 01: cat_main:skipLAS Skip LAS due to image contrast. Use global normalization. ------------------------------------------------------------------------ 16s SANLM denoising after LAS (medium) 15s 17s --- Update Ym and Ymi --- Update of intensities failed! 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 11s Amap using initial SPM12 segmentations (MRF filter strength 0.07): 11s AMAP peaks: [1.020.08,0.380.09,0.650.04] --- 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 | 0.2623 0.0000 0.2623 | 32.0000 2 | 2.50 | 0.2457 0.0054 0.2512 | 29.4886 3 | 2.50 | 0.2400 0.0091 0.2491 | 26.9772 4 | 2.50 | 0.2368 0.0109 0.2477 | 24.6107 5 | 2.50 | 0.2342 0.0123 0.2465 | 22.6548 6 | 2.50 | 0.2319 0.0133 0.2452 | 20.6989 7 | 2.50 | 0.2291 0.0144 0.2434 | 18.9688 8 | 2.50 | 0.2265 0.0155 0.2420 | 17.4455 9 | 2.50 | 0.2238 0.0164 0.2403 | 15.9223 10 | 2.50 | 0.2209 0.0177 0.2387 | 14.6627 11 | 2.50 | 0.2180 0.0189 0.2369 | 13.4764 12 | 2.50 | 0.2150 0.0199 0.2350 | 12.3015 13 | 2.50 | 0.2117 0.0215 0.2331 | 11.3776 14 | 2.50 | 0.2085 0.0226 0.2311 | 10.4537 15 | 2.25 | 0.2614 0.0242 0.2856 | 9.5920 16 | 2.25 | 0.2435 0.0351 0.2786 | 8.8725 17 | 2.25 | 0.2345 0.0396 0.2741 | 8.1530 18 | 2.25 | 0.2273 0.0426 0.2700 | 7.5234 19 | 2.25 | 0.2209 0.0450 0.2659 | 6.9630 20 | 2.25 | 0.2148 0.0467 0.2615 | 6.4027 21 | 2.25 | 0.2086 0.0489 0.2575 | 5.9447 22 | 2.25 | 0.2027 0.0505 0.2533 | 5.5083 23 | 2.25 | 0.1969 0.0518 0.2487 | 5.0803 24 | 2.25 | 0.1896 0.0539 0.2435 | 4.7404 25 | 2.25 | 0.1840 0.0549 0.2389 | 4.4005 26 | 2.25 | 0.1782 0.0562 0.2344 | 4.0868 27 | 2.25 | 0.1724 0.0577 0.2301 | 3.8221 28 | 2.25 | 0.1668 0.0587 0.2255 | 3.5574 29 | 2.00 | 0.1664 0.0599 0.2263 | 3.3283 30 | 2.00 | 0.1590 0.0615 0.2205 | 3.1221 31 | 2.00 | 0.1537 0.0620 0.2157 | 2.9160 32 | 2.00 | 0.1472 0.0632 0.2105 | 2.7495 33 | 2.00 | 0.1422 0.0639 0.2062 | 2.5890 34 | 2.00 | 0.1372 0.0645 0.2017 | 2.4330 35 | 2.00 | 0.1322 0.0657 0.1979 | 2.3080 36 | 2.00 | 0.1275 0.0663 0.1938 | 2.1830 37 | 2.00 | 0.1228 0.0670 0.1898 | 2.0688 38 | 2.00 | 0.1183 0.0679 0.1863 | 1.9714 39 | 2.00 | 0.1141 0.0684 0.1825 | 1.8740 40 | 2.00 | 0.1089 0.0691 0.1780 | 1.7907 41 | 2.00 | 0.1051 0.0695 0.1746 | 1.7148 42 | 2.00 | 0.1015 0.0697 0.1712 | 1.6390 43 | 1.75 | 0.0982 0.0704 0.1686 | 1.5785 44 | 1.75 | 0.0939 0.0717 0.1656 | 1.5194 45 | 1.75 | 0.0908 0.0720 0.1627 | 1.4626 46 | 1.75 | 0.0879 0.0724 0.1603 | 1.4166 47 | 1.75 | 0.0854 0.0725 0.1578 | 1.3706 48 | 1.75 | 0.0829 0.0726 0.1555 | 1.3290 49 | 1.75 | 0.0796 0.0728 0.1524 | 1.2932 50 | 1.75 | 0.0776 0.0727 0.1503 | 1.2574 51 | 1.75 | 0.0757 0.0727 0.1484 | 1.2271 52 | 1.75 | 0.0739 0.0728 0.1467 | 1.1992 57 | 1.50 | 0.0753 0.0691 0.1445 | 1.0900 Problem with Shooting (dets: 0.00344788 .. 3.36079) 58 | 1.50 | 0.0687 0.0737 0.1425 | 1.0730 59 | 1.50 | 0.0657 0.0751 0.1409 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 305s Prepare output 7s 312s Jacobian determinant (RMS): 0.032 0.176 0.528 1.202 2.446 | 2.208779 Template Matching: 0.262 0.261 0.166 0.222 0.197 | 0.197181 Write result maps: 15s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 3s CSF distance: 2s PBT2x thickness: 6s 12s Create initial surface 19s Topology correction: 18s Surface refinement: 39s Reduction of surface collisions with optimization: 18s Spherical mapping with areal smoothing 32s Spherical registration 301s rh: Thickness estimation (0.50 mm): WM distance: 3s CSF distance: 2s PBT2x thickness: 6s 13s Create initial surface 19s Topology correction: 20s Surface refinement: 50s Reduction of surface collisions with optimization: 20s Spherical mapping with areal smoothing 33s Spherical registration 308s Final surface processing results: Average thickness (FS): 0.8546  0.1474 mm Surface intensity / position RMSE: 0.1237 / 0.3657 Euler number / defect number / defect size: 8.0 / 5.0 / 1.65% Display thickness: /var/lib/condor/execute/dir_28436/ds/sub-AL020/surf/lh.thickness.sub-AL020_ses-3_acq-RARE_T1w Display thickness: /var/lib/condor/execute/dir_28436/ds/sub-AL020/surf/rh.thickness.sub-AL020_ses-3_acq-RARE_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_28436/ds/sub-AL020/sub-AL020_ses-3_acq-RARE_T1w.nii Surface ROI estimation: 1327s Surface and thickness estimation takes: 1295s 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 11s 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 140s Quality check: 2s Print 'Graphics' figure to: /var/lib/condor/execute/dir_28436/ds/sub-AL020/report/catreport_sub-AL020_ses-3_acq-RARE_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 29 minute(s) and 11 second(s). Image Quality Rating (IQR): 52.32% (E-) GM volume (GMV): 0.23% ( 0.71 / 313.91 ml) GM thickness (GMT): 0.86  0.17 mm Segmentations are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/mri Reports are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/report Labels are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/label ------------------------------------------------------------------------