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- ------------------------------------------------------------------------
- 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
- ------------------------------------------------------------------------
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