ds003468_ReproVBM/sub-AL020/report/catlog_sub-AL020_ses-3_acq-RARE_T1w.nii.txt

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CAT12.8.1 r1980: 1/1:      ./ds/sub-AL020/sub-AL020_ses-3_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                                                       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
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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                                              6s
  Update probability maps                                             1s
  Update registration                                                29s
                                                                     51s
Global intensity correction:                                      SANLM denoising after intensity normalization (medium):               1s
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     NOTE 01:     cat_main:skipLAS
                  Skip LAS due to image contrast. Use global normalization.
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   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

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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
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