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SPM  July 2017

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Subject:

Re: CAT12 error - Segmentation/Surface and Thickness Estimation

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Sun, 16 Jul 2017 23:22:30 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (173 lines)

Dear Andreia,

for extracting ROI-values for SBM you can use the functions:
CAT12 -> Extract ROI Data -> Extract ROI-based Surface values
and then
CAT12 -> Extract ROI Data -> Estimate Mean values inside ROI for external analysis

Best,

Christian


On Fri, 7 Jul 2017 16:15:26 +0100, Andreia N. Queirós <[log in to unmask]> wrote:

>Dear Doctor Gaser, 
>
>Thank you so much for your help and sorry for the delayed response. 
>
>We tried your latest suggestions but with no success. However, as we mentioned in our previous post, we have since switched to a computer with a greater RAM memory and it solved our issues.
>
>We stumbled upon a new issue and we would be very grateful if you could help us once again:
>
>We are trying to extract VBM and SBM values for regions such as the Insula. we intend to analyze these values with SPSS so that we can test for associations with self-reported measures.  
>
>We were successful with VBM but don't understand the step-by-step procedure to do the same with SBM. Could you be so kind as to guide in this process? 
>
>
>Furthermore, as requested, please find below the full output from the pc that caused the trouble. 
>
>Thank you so much for your time and consideration.
>
>Best regards, 
>Andreia N. Queirós 
>
>=============================================================================================
>
>To get started, type one of these: helpwin, helpdesk, or demo.
>For product information, visit www.mathworks.com.
> 
>CAT parallel processing with MATLAB PID: 7384
>
>------------------------------------------------------------------------
>CAT12 r1152: 1/1:              .\Nifti\sB003036-0016-00001-000176-01.nii
>------------------------------------------------------------------------
>APP: Rough bias correction:                                        
>  Initialize                                                         36s
>  Estimate background                                                 3s
>  Initial correction                                                 37s
>  Refine background                                                   4s
>  Final correction                                                    6s
>  Background correction                                               1s
>  Final scaling                                                       4s
>                                                                     92s
>Coarse affine registration                                            9s
>Affine registration                                                  11s
>SPM preprocessing 1 (estimate):                                     108s
>SPM preprocessing 2 (write):                                        119s
>Global intensity correction:                                         21s
>SANLM noise correction:                                              42s
>Local adaptive segmentation (LASstr=0.50):                         
>  Prepare maps                                                        6s
>  Prepare partitions                                                  3s
>  Prepare segments (LASmod = 1.13)                                   26s
>  Estimate local tissue thresholds                                   71s
>  SANLM noise correction for LAS                                     20s
>                                                                    126s
>ROI segmentation (partitioning):                                   
>  Atlas -> subject space                                             26s
>  Major structures                                                    9s
>  Ventricle detection                                                16s
>  Blood vessel detection                                              6s
>  WMH detection (WMHCstr=0.50)                                       19s
>  Closing of deep structures                                          2s
>  Side alignment                                                      8s
>  Final corrections                                                   3s
>                                                                     89s
>Blood vessel correction (BVCstr=0.50):                                2s
>Skull-stripping using graph-cut (gcutstr=0.50):                    
>  WM initialisation                                                   6s
>  GM region growing                                                   3s
>  GM-CSF region growing                                               7s
>  CSF region growing                                                  7s
>  Ventricle filling                                                   4s
>                                                                     28s
>Amap using initial SPM12 segmentations (MRF filter strength 0.06):   56s
>    AMAP peaks: [CSF,GM,WM] = [0.38±0.08,0.69±0.09,0.98±0.04]
>Final cleanup (gcutstr=0.50):                                      
>  Level 1 cleanup (ROI estimation)                                    6s
>  Level 1 cleanup (brain masking)                                     4s
>  Level 2 cleanup (CSF correction)                                    3s
>  Level 3 cleanup (CSF/WM PVE)                                        3s
>                                                                     16s
>Internal WMH correction for spatial normalization (WMHCstr=0.50):     4s
>Dartel registration with 1.50 mm:                                  
>    1 | 0.2362 |   501522        0   501522  430.118 
>    2 | 0.1826 |   387676    31974   419649  200.953 
>    3 | 0.1812 |   384672    28787   413459   51.053 
>    4 | 0.1815 |   385417    15046   400464  197.762 
>    5 | 0.1665 |   353491    36139   389630   68.090 
>    6 | 0.1669 |   354277    34510   388787   42.982 
>    7 | 0.1685 |   357754    17953   375707  170.195 
>    8 | 0.1529 |   324679    39356   364035   63.612 
>    9 | 0.1530 |   324721    38131   362852   37.846 
>   10 | 0.1538 |   326477    19999   346476  148.656 
>   11 | 0.1380 |   293043    41020   334062   61.293 
>   12 | 0.1373 |   291548    40739   332288   38.299 
>   13 | 0.1376 |   292217    21533   313750  121.292 
>   14 | 0.1243 |   263928    38575   302502   55.106 
>   15 | 0.1229 |   260869    39679   300548   36.356 
>   16 | 0.1221 |   259306    41781   301088   42.305 
>   17 | 0.1216 |   258153    41948   300101   30.597 
>   18 | 0.1211 |   257014    42856   299869   27.945 
>                                                                    256s
>Write result maps:                                                   34s
>Surface and thickness estimation:                                  
>lh:
>  Thickness estimation (0.50 mm³):                                 
>    WM distance:                                                     85s
>    CSF distance:                                                    66s
>    PBT2x thickness:                                                 63s
>    Final Corrections:                                              229s
>  Create initial surface                                           
>Setting up...
>Starting main process...
>Done with 10 percent.
>Done with 20 percent.
>Done with 30 percent.
>Done with 40 percent.
>Done with 50 percent.
>Done with 60 percent.
>Done with 70 percent.
>Done with 80 percent.
>Done with 90 percent.
>Done with 100 percent.
>Made 54 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 705238  Triangles: 1410492
>Setting up...
>Starting main process...
>Done with 10 percent.
>Done with 20 percent.
>Done with 30 percent.
>Done with 40 percent.
>Done with 50 percent.
>Done with 60 percent.
>Done with 70 percent.
>Done with 80 percent.
>Done with 90 percent.
>Done with 100 percent.
>Made 1 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 705170  Triangles: 1410360
>                                                                     26s
>  Reduce surface to 100000 faces:                                  Resampled into 286268 polygons.
>Extract largest of 129 components.
>  70s
>  Topology correction and surface refinement                       [Warning: Control Character '\P' is not valid. See 'doc sprintf' for control characters valid in the format string.] 
>[> In cat_io_cprintf (line 156)
>  In cat_run_newcatch (line 36)
>  In cat_run>run_job (line 276)
>  In cat_run (line 155)] 
>
>------------------------------------------------------------------------
>CAT Preprocessing error: CAT:system_error: .   27 - cat_check_system_output
>  422 - cat_surf_createCS
> 1644 - cat_main
>  633 - cat_run_job1070
>   14 - cat_run_newcatch
>  276 - run_job
>  155 - cat_run
>------------------------------------------------------------------------
>    Error:cat_io_report:CATgui: Error in cat_io_report GUI parameter report creation > incomple CAT parameters.

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