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Subject:

Re: Error during CAT12 surface thickness estimation & surface data visualization

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Mon, 7 Jan 2019 12:12:20 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (185 lines)

Dear Matthieu,

is this error only occurring for this data set? The error message points do an issue with writing the surface gifti data...

Best,

Christian

On Sun, 6 Jan 2019 20:20:11 +0100, Matthieu Vanhoutte <[log in to unmask]> wrote:

>Dear Christian,
>
>Could you help me about the previous warning below ?
>
>Best,
>Matthieu
>
>> Le 23 déc. 2018 à 21:37, Matthieu Vanhoutte <[log in to unmask]> a écrit :
>> 
>> Dear CAT’s experts,
>> 
>> I got a CAT12 warning during the segmentation and it seems that it causes error when trying to visualize surface data:
>> 
>>  
>>                             < M A T L A B (R) >
>>                   Copyright 1984-2017 The MathWorks, Inc.
>>                    R2017a (9.2.0.538062) 64-bit (maci64)
>>                              February 23, 2017
>>  
>>  
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com <http://www.mathworks.com/>.
>>  
>> CAT parallel processing with MATLAB PID: 56009
>>  
>> ------------------------------------------------------------------------
>> CAT12.5 r1364: 1/1:   CAT12/sub-002S5018_T1w.nii
>> ------------------------------------------------------------------------
>> SANLM denoising (medium):                                            29s
>> Internal resampling (1.20x1.00x1.00mm > 1.00x1.00x1.00mm):            2s
>> APP: Rough bias correction:                                       
>>   Initialize                                                          9s
>>   Estimate background                                                30s
>>   Initial correction                                                 19s
>>   Refine background                                                  11s
>>   Final correction                                                    7s
>>   Background correction                                               1s
>>   Final scaling                                                       3s
>>                                                                      81s
>> Coarse affine registration                                            9s
>> Affine registration                                                   7s
>> SPM preprocessing 1 (estimate 1):                                    13s
>> SPM preprocessing 1 (estimate 2):                                    98s
>> SPM preprocessing 1 (estimate skull-stripped):                       97s
>> SPM preprocessing 1 (estimate skull-stripped):                       75s
>> SPM preprocessing 2 (write):                                      
>>   Write Segmentation                                                 18s
>>   Update Segmentation                                                45s
>>   Update Skull-Stripping                                              7s
>>   Update probability maps                                             8s
>>                                                                      78s
>> Global intensity correction:                                         24s
>> SANLM denoising after intensity normalization (medium):              16s
>> Fast Shooting registration                                           49s
>> Local adaptive segmentation (LASstr=0.50):                        
>>   Prepare maps                                                        4s
>>   Prepare partitions                                                  2s
>>   Prepare segments (LASmod = 1.00)                                   16s
>>   Estimate local tissue thresholds (WM)                              17s
>>   Estimate local tissue thresholds (GM)                              20s
>>   Estimate local tissue thresholds (CSF/BG)                           5s
>>   Intensity transformation                                           69s
>>   SANLM denoising after LAS (medium)                                 18s
>>                                                                      18s
>> ROI segmentation (partitioning):                                  
>>   Atlas -> subject space                                             10s
>>   Major structures                                                    5s
>>   Ventricle detection                                                10s
>>   Blood vessel detection                                             11s
>>   WMH detection (WMHCstr=0.50 > WMHCstr'=0.50)                       29s
>>   Manual stroke lesion detection                                      0s
>>   Closing of deep structures                                          2s
>>   Side alignment                                                      4s
>>   Final corrections                                                   5s
>>                                                                      75s
>> Blood vessel correction (BVCstr=0.50):                                2s
>> Amap using initial SPM12 segmentations (MRF filter strength 0.06):   17s
>>     AMAP peaks: [CSF,GM,WM] = [0.45±0.08,0.71±0.07,0.96±0.05]
>> Final cleanup (gcutstr=0.23):                                     
>>   Level 1 cleanup (ROI estimation)                                    4s
>>   Level 1 cleanup (brain masking)                                     2s
>>   Level 2 cleanup (CSF correction)                                    1s
>>   Level 3 cleanup (CSF/WM PVE)                                        2s
>>                                                                       9s
>>  
>>  
>> Dartel registration with 1.50 mm on a 1.50 mm Template:           
>>   Template: "/matlab/spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii"
>>     1 | 0.1436 |   457208        0   457208    0.000 
>>     2 | 0.1187 |   377833    19830   397663    0.000 
>>     3 | 0.1134 |   361070    27562   388631    0.000 
>>     4 | 0.1121 |   357001    15403   372404    0.000 
>>     5 | 0.1026 |   326658    33935   360593    0.000 
>>     6 | 0.1011 |   321857    36864   358721    0.000 
>>     7 | 0.1011 |   322094    19295   341389    0.000 
>>     8 | 0.0921 |   293440    37119   330559    0.000 
>>     9 | 0.0912 |   290482    38694   329176    0.000 
>>    10 | 0.0913 |   290628    20193   310821    0.000 
>>    11 | 0.0823 |   262013    37932   299944    0.000 
>>    12 | 0.0815 |   259445    39005   298450    0.000 
>>    13 | 0.0819 |   260909    20499   281408    0.000 
>>    14 | 0.0741 |   235957    35520   271477    0.000 
>>    15 | 0.0731 |   232846    37035   269881    0.000 
>>    16 | 0.0728 |   231930    38939   270869    0.000 
>>    17 | 0.0724 |   230649    39399   270048    0.000 
>>    18 | 0.0721 |   229712    40143   269854    0.000 
>>                                                                     193s
>>   Jacobian determinant (RMS):  0.119812 
>>            Template Matching:  0.072136 
>> Write result maps:                                                   19s
>> Surface and thickness estimation:                                 
>> lh:
>>   Thickness estimation (0.50 mm³):                                
>>     WM distance:                                                     36s
>>     CSF distance:                                                    31s
>>     PBT2x thickness:                                                 19s
>>                                                                      95s
>>                                                                      98s
>>   Create initial surface                                             37s
>>   Topology correction and surface refinement:                        59s
>>   Refine central surface                                             63s
>>   Correction of central surface in highly folded areas 2              3s
>>   Spherical mapping with areal smoothing                            140s
>>   Spherical registration                                            272s
>>  Surface Euler number: -10
>>  Overall size of topology defects: 831
>> [Warning: A value of class "int32" was indexed with no subscripts specified.
>> Currently the result of this operation is the indexed value itself, but in a
>> future release, it will be an error.] 
>> [> In gifti/subsref (line 45)
>>   In cat_surf_createCS (line 861)
>>   In cat_main (line 1822)
>>   In cat_run_job1070 (line 721)
>>   In cat_run_newcatch (line 16)
>>   In cat_run>run_job (line 398)
>>   In cat_run (line 161)] 
>> 
>> Then when trying to visualize central surface with the « Display Surface Results » I got this error:
>> 
>> Warning: A value of class "int32" was indexed with no subscripts specified. Currently the result of this operation is the
>> indexed value itself, but in a future release, it will be an error. 
>> > In gifti/subsref (line 45)
>>   In cat_surf_info (line 438)
>>   In cat_surf_results (line 357)
>>   In cat_surf_results>select_data (line 1648) 
>> Warning: A value of class "int32" was indexed with no subscripts specified. Currently the result of this operation is the
>> indexed value itself, but in a future release, it will be an error. 
>> > In gifti/subsref (line 45)
>>   In spm_mesh_adjacency (line 15)
>>   In cat_surf_results (line 382)
>>   In cat_surf_results>select_data (line 1648) 
>> Error using cat_surf_results (line 415)
>> No data in surfaces found.
>> 
>> Error in cat_surf_results>select_data (line 1648)
>> cat_surf_results('disp', H.S{1}.name, H.S{2}.name);
>>  
>> Error while evaluating DestroyedObject Callback.
>> 
>> Index exceeds matrix dimensions.
>> 
>> Error in cat_surf_results (line 317)
>>             [pth{1}, nm1, ext1] = spm_fileparts(H.S{1}.name(1, :));
>> 
>> Error in cat_surf_results>select_data (line 1648)
>> cat_surf_results('disp', H.S{1}.name, H.S{2}.name);
>>  
>> Error while evaluating DestroyedObject Callback.
>> 
>> Many thanks in advance for your feedback.
>> 
>> Best,
>> Matt
>
>

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