------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_21479/ds/sub-35/sub-35_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 261s APP: Rough bias correction: Initialize 12s Estimate background 10s Initial correction 34s Refine background 5s Final correction 29s Final scaling 61s 191s Correct center-of-mass 8s Affine registration 38s =============================================================================== ALERT 01: cat_run_job1639:StrokeLesionButNoCorrection There are 39.78 cm of zeros within the brain but Stroke Lesion Correction (SLC) inactive (available in the expert mode). =============================================================================== SPM preprocessing 1 (estimate 1 - TPM registration): 28s Use previous fine affine registration. 66s SPM preprocessing 1 (estimate 2): 68s ---------------------------------------------------------------------------- WARNING 01: 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 113s Update segmentation 318s Update skull-stripping 131s Update probability maps 10s Update registration 97s 668s Global intensity correction: SANLM denoising after intensity normalization (medium): 68s ------------------------------------------------------------------------ NOTE 01: cat_main:skipLAS Skip LAS due to image contrast. Use global normalization. ------------------------------------------------------------------------ 634s SANLM denoising after LAS (medium) 144s 212s --- Update Ym and Ymi --- ROI segmentation (partitioning): Atlas -> subject space 25s Major structures 1s Ventricle detection 8s Blood vessel detection 1s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 28s 66s Amap using initial SPM12 segmentations (MRF filter strength 0.07): 538s AMAP peaks: [0.390.15,0.980.04,0.580.05] --- 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 | 0.2362 0.0000 0.2362 | 32.0000 2 | 2.50 | 0.2214 0.0046 0.2259 | 29.4886 3 | 2.50 | 0.2156 0.0078 0.2235 | 26.9772 4 | 2.50 | 0.2123 0.0096 0.2219 | 24.6107 5 | 2.50 | 0.2096 0.0110 0.2205 | 22.6548 6 | 2.50 | 0.2072 0.0119 0.2192 | 20.6989 7 | 2.50 | 0.2047 0.0129 0.2176 | 18.9688 8 | 2.50 | 0.2024 0.0138 0.2162 | 17.4455 9 | 2.50 | 0.2001 0.0146 0.2147 | 15.9223 10 | 2.50 | 0.1976 0.0157 0.2132 | 14.6627 11 | 2.50 | 0.1951 0.0166 0.2117 | 13.4764 12 | 2.50 | 0.1925 0.0174 0.2099 | 12.3015 13 | 2.50 | 0.1897 0.0185 0.2083 | 11.3776 14 | 2.50 | 0.1871 0.0194 0.2065 | 10.4537 15 | 2.25 | 0.2315 0.0208 0.2523 | 9.5920 16 | 2.25 | 0.2165 0.0295 0.2460 | 8.8725 17 | 2.25 | 0.2092 0.0331 0.2423 | 8.1530 18 | 2.25 | 0.2034 0.0355 0.2388 | 7.5234 19 | 2.25 | 0.1982 0.0373 0.2355 | 6.9630 20 | 2.25 | 0.1933 0.0386 0.2318 | 6.4027 21 | 2.25 | 0.1883 0.0402 0.2285 | 5.9447 22 | 2.25 | 0.1835 0.0415 0.2250 | 5.5083 23 | 2.25 | 0.1788 0.0425 0.2213 | 5.0803 24 | 2.25 | 0.1731 0.0441 0.2172 | 4.7404 25 | 2.25 | 0.1687 0.0449 0.2135 | 4.4005 26 | 2.25 | 0.1641 0.0458 0.2099 | 4.0868 27 | 2.25 | 0.1595 0.0470 0.2065 | 3.8221 28 | 2.25 | 0.1551 0.0477 0.2028 | 3.5574 29 | 2.00 | 0.1548 0.0484 0.2032 | 3.3283 30 | 2.00 | 0.1483 0.0501 0.1984 | 3.1221 31 | 2.00 | 0.1442 0.0504 0.1945 | 2.9160 32 | 2.00 | 0.1393 0.0512 0.1905 | 2.7495 33 | 2.00 | 0.1355 0.0516 0.1872 | 2.5890 34 | 2.00 | 0.1318 0.0519 0.1837 | 2.4330 35 | 2.00 | 0.1281 0.0527 0.1808 | 2.3080 36 | 2.00 | 0.1247 0.0530 0.1777 | 2.1830 37 | 2.00 | 0.1213 0.0534 0.1747 | 2.0688 38 | 2.00 | 0.1181 0.0539 0.1720 | 1.9714 39 | 2.00 | 0.1150 0.0542 0.1691 | 1.8740 40 | 2.00 | 0.1112 0.0546 0.1658 | 1.7907 41 | 2.00 | 0.1085 0.0548 0.1633 | 1.7148 42 | 2.00 | 0.1059 0.0548 0.1607 | 1.6390 43 | 1.75 | 0.1038 0.0548 0.1586 | 1.5785 44 | 1.75 | 0.1001 0.0561 0.1562 | 1.5194 45 | 1.75 | 0.0976 0.0564 0.1540 | 1.4626 46 | 1.75 | 0.0954 0.0568 0.1522 | 1.4166 47 | 1.75 | 0.0934 0.0569 0.1503 | 1.3706 48 | 1.75 | 0.0916 0.0570 0.1486 | 1.3290 49 | 1.75 | 0.0891 0.0572 0.1463 | 1.2932 50 | 1.75 | 0.0875 0.0571 0.1446 | 1.2574 51 | 1.75 | 0.0860 0.0571 0.1432 | 1.2271 52 | 1.75 | 0.0846 0.0572 0.1419 | 1.1992 53 | 1.75 | 0.0833 0.0572 0.1405 | 1.1713 54 | 1.75 | 0.0820 0.0574 0.1394 | 1.1493 55 | 1.75 | 0.0809 0.0574 0.1383 | 1.1276 56 | 1.75 | 0.0798 0.0574 0.1372 | 1.1069 57 | 1.50 | 0.0811 0.0580 0.1391 | 1.0900 Problem with Shooting (dets: 0.00385781 .. 6.30551) 58 | 1.50 | 0.0772 0.0611 0.1383 | 1.0730 59 | 1.50 | 0.0752 0.0618 0.1370 | 1.0579 60 | 1.50 | 0.0740 0.0622 0.1362 | 1.0447 Shooting registration with 2.50:-0.25:1.50 mm takes: 387s Prepare output 50s 437s Jacobian determinant (RMS): 0.028 0.147 0.421 0.865 1.965 | 1.612386 Template Matching: 0.236 0.231 0.155 0.104 0.222 | 0.222035 Write result maps: 146s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 14s CSF distance: 6s PBT2x thickness: 18s 44s Create initial surface 62s Topology correction: 46s Surface refinement: 50s Reduction of surface collisions with optimization: 28s Spherical mapping with areal smoothing 39s Spherical registration 292s rh: Thickness estimation (0.50 mm): WM distance: 10s CSF distance: 6s PBT2x thickness: 17s 39s Create initial surface 57s Topology correction: 52s Surface refinement: 68s Reduction of surface collisions with optimization: 33s Spherical mapping with areal smoothing 45s Spherical registration 306s Final surface processing results: Average thickness (FS): 0.5007  0.2558 mm Surface intensity / position RMSE: 0.1152 / 0.2587 Euler number / defect number / defect size: 116.0 / 61.0 / 7.40% Display thickness: /var/lib/condor/execute/dir_21479/ds/sub-35/surf/lh.thickness.sub-35_T1w Display thickness: /var/lib/condor/execute/dir_21479/ds/sub-35/surf/rh.thickness.sub-35_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_21479/ds/sub-35/sub-35_T1w.nii Surface ROI estimation: 3715s Surface and thickness estimation takes: 2880s ROI estimation in native space: ROI estimation of 'cobra' atlas 56s ROI estimation of 'neuromorphometrics' atlas 205s ROI estimation of 'lpba40' atlas 59s ROI estimation of 'hammers' atlas 137s ROI estimation of 'thalamus' atlas 10s ROI estimation of 'ibsr' atlas 46s ROI estimation of 'aal3' atlas 77s ROI estimation of 'mori' atlas 117s ROI estimation of 'anatomy3' atlas 172s ROI estimation of 'julichbrain' atlas 235s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 97s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 173s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 357s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 531s Write results 532s 2275s Quality check: 30s Print 'Graphics' figure to: /var/lib/condor/execute/dir_21479/ds/sub-35/report/catreport_sub-35_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 128 minute(s) and 47 second(s). Image Quality Rating (IQR): 8.71% (F) GM volume (GMV): 6.68% (54.17 / 811.07 ml) GM thickness (GMT): 0.50  0.26 mm Segmentations are saved in /var/lib/condor/execute/dir_21479/ds/sub-35/mri Reports are saved in /var/lib/condor/execute/dir_21479/ds/sub-35/report Labels are saved in /var/lib/condor/execute/dir_21479/ds/sub-35/label ------------------------------------------------------------------------