ds003468_ReproVBM/sub-AL038/report/catlog_sub-AL038_ses-7_acq-RARE_T1w.nii.txt

------------------------------------------------------------------------
CAT12.8.1 r1980: 1/1:      ./ds/sub-AL038/sub-AL038_ses-7_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                                                    2s
  Final scaling                                                       3s
                                                                     20s
Correct center-of-mass                                                9s
Affine registration                                                   5s
SPM preprocessing 1 (estimate 1 - TPM registration):                 13s
  Use initial fine affine registration.                              38s
SPM preprocessing 1 (estimate 2):                                    41s
    ----------------------------------------------------------------------------
     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                                                  8s
  Update segmentation                                                10s
  Update skull-stripping                                              8s
  Update probability maps                                             1s
  Update registration                                                29s
                                                                     55s
Global intensity correction:                                      SANLM denoising after intensity normalization (medium):               4s
    ------------------------------------------------------------------------
     NOTE 01:     cat_main:skipLAS
                  Skip LAS due to image contrast. Use global normalization.
    ------------------------------------------------------------------------
   20s
  SANLM denoising after LAS (medium)                                 17s
                                                                     21s
 --- Update Ym and Ymi --- 
ROI segmentation (partitioning):                                  
  Atlas -> subject space                                              3s
  Major structures                                                    1s
  Ventricle detection                                                 5s
  Blood vessel detection                                              1s
  Manual stroke lesion detection                                      0s
  Closing of deep structures                                          1s
  Side alignment                                                      1s
  Final corrections                                                   2s
                                                                     13s
Amap using initial SPM12 segmentations (MRF filter strength 0.07):   17s
    AMAP peaks: [0.860.13,0.250.09,0.640.09]
 --- 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"
    ------------------------------------------------------------------------------------------------------
     WARNING 03:  cat_main_registration:Hydrocephalus
                  Very large ventricles detected (1.00
    1 | 2.50 | 0.2999  0.0000  0.2999 |  32.0000 
    2 | 2.50 | 0.2692  0.0088  0.2779 |  29.4886 
    3 | 2.50 | 0.2501  0.0189  0.2689 |  26.9772 
    4 | 2.50 | 0.2405  0.0242  0.2647 |  24.6107 
    5 | 2.50 | 0.2373  0.0249  0.2622 |  22.6548 
    6 | 2.50 | 0.2345  0.0253  0.2598 |  20.6989 
    7 | 2.50 | 0.2308  0.0260  0.2568 |  18.9688 
    8 | 2.50 | 0.2271  0.0272  0.2543 |  17.4455 
    9 | 2.50 | 0.2245  0.0271  0.2516 |  15.9223 
   10 | 2.50 | 0.2209  0.0283  0.2491 |  14.6627 
   11 | 2.50 | 0.2182  0.0284  0.2466 |  13.4764 
   12 | 2.50 | 0.2145  0.0293  0.2438 |  12.3015 
   13 | 2.50 | 0.2114  0.0299  0.2413 |  11.3776 
   14 | 2.50 | 0.2078  0.0309  0.2386 |  10.4537 
   15 | 2.25 | 0.2561  0.0326  0.2887 |  10.0000 
   16 | 2.25 | 0.2394  0.0427  0.2821 |   9.2366 
   17 | 2.25 | 0.2324  0.0445  0.2769 |   8.4743 
   18 | 2.25 | 0.2256  0.0469  0.2725 |   7.8084 
   19 | 2.25 | 0.2197  0.0485  0.2682 |   7.2165 
   20 | 2.25 | 0.2140  0.0497  0.2636 |   6.6255 
   21 | 2.25 | 0.2081  0.0514  0.2595 |   6.1431 
   22 | 2.25 | 0.2026  0.0527  0.2553 |   5.6842 
   23 | 2.25 | 0.1971  0.0537  0.2508 |   5.2347 
   24 | 2.25 | 0.1902  0.0557  0.2459 |   4.8782 
   25 | 2.25 | 0.1848  0.0566  0.2413 |   4.5223 
   26 | 2.25 | 0.1790  0.0577  0.2367 |   4.1941 
   27 | 2.25 | 0.1732  0.0589  0.2322 |   3.9176 
   28 | 2.25 | 0.1677  0.0598  0.2275 |   3.6415 
   29 | 2.00 | 0.1830  0.1418  0.3248 |   8.0000 
   30 | 2.00 | 0.1965  0.0943  0.2908 |   7.1626 
   31 | 2.00 | 0.2008  0.0721  0.2730 |   6.3645 
   32 | 2.00 | 0.1990  0.0657  0.2647 |   5.7493 
   33 | 2.00 | 0.1948  0.0626  0.2575 |   5.1811 
   34 | 2.00 | 0.1917  0.0593  0.2510 |   4.6535 
   35 | 2.00 | 0.1831  0.0618  0.2449 |   4.2477 
   36 | 2.00 | 0.1783  0.0603  0.2386 |   3.8576 
   37 | 2.00 | 0.1705  0.0615  0.2320 |   3.5153 
   38 | 2.00 | 0.1634  0.0641  0.2275 |   3.2341 
   39 | 2.00 | 0.1569  0.0627  0.2196 |   2.9628 
   40 | 2.00 | 0.1490  0.0642  0.2132 |   2.7387 
   41 | 2.00 | 0.1428  0.0657  0.2085 |   2.5412 
   42 | 2.00 | 0.1369  0.0652  0.2022 |   2.3500 
   43 | 1.75 | 0.1359  0.1808  0.3166 |   6.0000 
   44 | 1.75 | 0.1646  0.1021  0.2666 |   5.1658 
   45 | 1.75 | 0.1732  0.0756  0.2488 |   4.4483 
   46 | 1.75 | 0.1712  0.0670  0.2382 |   3.9240 
   47 | 1.75 | 0.1677  0.0617  0.2293 |   3.4471 
   48 | 1.75 | 0.1616  0.0596  0.2212 |   3.0545 
   49 | 1.75 | 0.1537  0.0598  0.2135 |   2.7438 
   50 | 1.75 | 0.1469  0.0591  0.2060 |   2.4574 
   51 | 1.75 | 0.1392  0.0600  0.1992 |   2.2329 
   52 | 1.75 | 0.1323  0.0609  0.1932 |   2.0402 
   53 | 1.75 | 0.1255  0.0608  0.1863 |   1.8601 
   54 | 1.75 | 0.1191  0.0623  0.1814 |   1.7267 
   55 | 1.75 | 0.1131  0.0626  0.1757 |   1.6021 
   56 | 1.75 | 0.1086  0.0621  0.1708 |   1.4898 
   57 | 1.50 | 0.1129  0.1798  0.2927 |   4.0000 
   58 | 1.50 | 0.1337  0.1072  0.2409 |   3.1096 
   59 | 1.50 | 0.1376  0.0806  0.2182 |   2.4742 
   60 | 1.50 | 0.1331  0.0709  0.2041 |   2.0222 
   61 | 1.50 | 0.1243  0.0629  0.1873 |   1.6486 
   62 | 1.50 | 0.1158  0.0601  0.1759 |   1.3868 
   63 | 1.50 | 0.1069  0.0584  0.1652 |   1.1786 
Shooting registration with 2.50:-0.25:1.50 mm takes:                523s
  Prepare output                                                      7s
                                                                    530s
  Jacobian determinant (RMS): 0.031 0.164 0.332 0.454 0.755 |  1.581609 
           Template Matching: 0.300 0.256 0.183 0.136 0.113 |  0.320608 
Write result maps:                                                   15s
Surface and thickness estimation:                                 
lh:
  Thickness estimation (0.50 mm):                                
    WM distance:                                                      7s
    CSF distance:                                                     2s
    PBT2x thickness:                                                  8s
                                                                     20s
  Create initial surface                                             27s
  Topology correction:                                               22s
  Surface refinement:                                                37s
  Reduction of surface collisions with optimization:                 20s
  Spherical mapping with areal smoothing                             31s
  Spherical registration                                            313s
rh:
  Thickness estimation (0.50 mm):                                
    WM distance:                                                      7s
    CSF distance:                                                     3s
    PBT2x thickness:                                                  8s
                                                                     19s
  Create initial surface                                             25s
  Topology correction:                                               23s
  Surface refinement:                                                30s
  Reduction of surface collisions with optimization:                 15s
  Spherical mapping with areal smoothing                             31s
  Spherical registration                                            340s
Final surface processing results: 
  Average thickness (FS):                     0.8272  0.2915 mm
  Surface intensity / position RMSE:          0.1237 / 0.4714
  Euler number / defect number / defect size: 6.0 / 4.0 / 0.51% 
  Display thickness:          /var/lib/condor/execute/dir_30228/ds/sub-AL038/surf/lh.thickness.sub-AL038_ses-7_acq-RARE_T1w
  Display thickness:          /var/lib/condor/execute/dir_30228/ds/sub-AL038/surf/rh.thickness.sub-AL038_ses-7_acq-RARE_T1w
  Show surfaces in orthview:  /var/lib/condor/execute/dir_30228/ds/sub-AL038/sub-AL038_ses-7_acq-RARE_T1w.nii
  Surface ROI estimation:                                          1617s
Surface and thickness estimation takes:                            1578s
ROI estimation in native space:                                   
  ROI estimation of 'cobra' atlas                                     4s
  ROI estimation of 'neuromorphometrics' atlas                       13s
  ROI estimation of 'lpba40' atlas                                    4s
  ROI estimation of 'hammers' atlas                                   9s
  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                              15s
  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   36s
  Write results                                                      36s
                                                                    148s
Quality check:                                                        2s
Print 'Graphics' figure to: 
  /var/lib/condor/execute/dir_30228/ds/sub-AL038/report/catreport_sub-AL038_ses-7_acq-RARE_T1w.pdf

------------------------------------------------------------------------
CAT preprocessing takes 33 minute(s) and 33 second(s).
Image Quality Rating (IQR):   8.62% (F)
GM volume (GMV):              3.69% (15.40 / 417.51 ml)
GM thickness (GMT):           0.83  0.35 mm
Segmentations are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/mri
Reports are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/report
Labels are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/label
------------------------------------------------------------------------