CAT12 - expert mode -modulated normalization error

Bugs
1

19-Dec-2020 17:40:31 - Failed 'CAT12: Segmentation (current release)'
Reference to non-existent field 'vol_rel_WMH'.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_main_reportstr.m" (v1730), function "cat_main_reportstr" at line 320.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_io_report.m" (???), function "cat_io_report" at line 208.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 204.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "run_job" at line 866.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "cat_run" at line 455.

The following modules did not run:
Failed: CAT12: Segmentation (current release)

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command
window, starting with the lines (look for the line showing the exact #job as
displayed in this error message)

Running job #1

I am getting this error and don't know what is causing it or how to solve it.
Can you please help me?
Thanks

2

@emdim Please copy-paste the entire CAT log you get in the Matlab command window (from the CAT startup message).

@CGaser Any suggestion?

3

@emdim
Have you changed any WMH setttings?

4

Here is my Matlab code. I didn't change any setting (at least intentionally):

addpath /home/emdim/scratch/spm12    
[~, files] = system('dir /home/emdim/scratch/workspace/done/*.nii')
files = split(files)

for i=20:120
    s = cell2mat(files(i))
    g = with_affine_segm(s)
end

function x = with_affine_segm(s)
    %in_put = '/home/emdim/scratch/workspace/done/'
    x=1
    %filename =x;
    %s = strcat(in_put, filename)
    %s = strcat(s, ',1')
    matlabbatch{1}.spm.tools.cat.estwrite.data = {s};
    matlabbatch{1}.spm.tools.cat.estwrite.data_wmh = {''};
    matlabbatch{1}.spm.tools.cat.estwrite.nproc = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.useprior = '';
    matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {'/home/emdim/scratch/spm12/tpm/TPM.nii'};
    matlabbatch{1}.spm.tools.cat.estwrite.opts.affreg = 'mni';
    matlabbatch{1}.spm.tools.cat.estwrite.opts.biasacc = 0.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.APP = 1070;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.spm_kamap = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.LASstr = 0.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.gcutstr = 2;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.WMHC = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.shooting.shootingtpm = {'/home/emdim/scratch/spm12/toolbox/cat12/templates_volumes/Template_0_IXI555_MNI152_GS.nii'};
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.shooting.regstr = 0.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.vox = 1.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.restypes.optimal = [1 0.1];
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.ignoreErrors = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.ownatlas = {''};
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ct.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ct.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ct.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.pp.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.pp.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.pp.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.SL.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.SL.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.SL.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.SL.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.labelnative = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.las.native = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.las.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.las.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.jacobianwarped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [0 0];
    matlabbatch{1}.spm.tools.cat.estwrite.output.rmat = 0;
    spm_jobman('initcfg');
    spm_jobman('run',matlabbatch);
end

Thank you @CGaser

5

@Francois @CGaser
As requested here is the log file output:

------------------------------------------------------------------------
21-Dec-2020 12:31:04 - Running job #1
------------------------------------------------------------------------


------------------------------------------------------------------------
21-Dec-2020 12:31:04 - Running job #1
------------------------------------------------------------------------
21-Dec-2020 12:31:04 - Running 'CAT12: Segmentation (current release)'
21-Dec-2020 12:31:04 - Running 'CAT12: Segmentation (current release)'
Warning: File not found or permission denied
> In cat_run_job1639 (line 68)
  In cat_run_newcatch (line 34)
  In cat_run>run_job (line 866)
  In cat_run (line 455)
  In cfg_run_cm (line 29)
  In cfg_util>local_runcj (line 1717)
  In cfg_util (line 972)
  In spm_jobman>fill_run_job (line 469)
  In spm_jobman (line 247)
  In matlab_seq>with_affine_segm (line 102)
  In matlab_seq (line 25)

------------------------------------------------------------------------
CAT12.7 r1739: 1/1:   /home/emdim/scratch/workspace/done/1063167_MNI.nii
------------------------------------------------------------------------

------------------------------------------------------------------------
CAT12.7 r1739: 1/1:   /home/emdim/scratch/workspace/done/1063167_MNI.nii
------------------------------------------------------------------------
SANLM denoising (medium):                                         SANLM denoising (medium):                                            28s
   28s
    -----------------------------------------------------------------------------
     WARNING 01:  cat_run_job1639cat_run_job:skullStrippedInputWithSkullStripping
                  Detected skull-stripped or strongly masked image. Skip APP.
                  Use skull-stripped initial affine registration template and
                  TPM without head tissues (class 4 and 5)!
    -----------------------------------------------------------------------------    -----------------------------------------------------------------------------
     WARNING 01:  cat_run_job1639cat_run_job:skullStrippedInputWithSkullStripping
                  Detected skull-stripped or strongly masked image. Skip APP.
                  Use skull-stripped initial affine registration template and
                  TPM without head tissues (class 4 and 5)!
    -----------------------------------------------------------------------------

APP: Rough bias correction:                                       APP: Rough bias correction:

  Initialize                                                        Initialize                                                          7s
  Estimate background                                                 7s
  Estimate background                                                 7s
  Initial correction                                                  7s
  Initial correction                                                  6s
  Refine background                                                   6s
  Refine background                                                   3s
  Final correction                                                    3s
  Final correction                                                    6s
  Final scaling                                                       6s
  Final scaling                                                       7s
                                                                      7s
                                                                     42s
Affine registration                                                  42s
Affine registration                                                   3s
Affine registration                                                   3s
Affine registration                                                   6s
SPM preprocessing 1 (estimate 1):                                     6s
SPM preprocessing 1 (estimate 1):
Final fine affine registration failed.
Use fine affine registration from previous step.

Final fine affine registration failed.
Use fine affine registration from previous step.
   17s
SPM preprocessing 1 (estimate 2):                                    17s
SPM preprocessing 1 (estimate 2):                                    33s
   33s
SPM preprocessing 2 (write):
Warning: File not found or permission denied
> In cat_main1639>cat_main_updatepara (line 1031)
  In cat_main1639 (line 25)
  In cat_run_job1639 (line 912)
  Write Segmentation                                                In cat_run_newcatch (line 34)
  In cat_run>run_job (line 866)
  In cat_run (line 455)
  In cfg_run_cm (line 29)
  In cfg_util>local_runcj (line 1717)
  In cfg_util (line 972)
  In spm_jobman>fill_run_job (line 469)
  In spm_jobman (line 247)
  In matlab_seq>with_affine_segm (line 102)
  In matlab_seq (line 25)
SPM preprocessing 2 (write):
  Write Segmentation                                                 14s
   14s
  Update Segmentation                                               Update Segmentation                                                36s
  Update Skull-Stripping                                             36s
  Update Skull-Stripping                                             10s
  Update probability maps                                            10s
  Update probability maps                                            18s
                                                                     77s
Global intensity correction:                                         18s
                                                                     78s
Global intensity correction:                                         19s
SANLM denoising after intensity normalization (medium):              19s
SANLM denoising after intensity normalization (medium):              18s
Fast registration                                                    19s
Fast registration                                                    65s
Local adaptive segmentation (LASstr=0.50):
  Prepare maps                                                       66s
Local adaptive segmentation (LASstr=0.50):
  Prepare maps                                                        8s
  Prepare partitions                                                  8s
  Prepare partitions                                                  2s
    2s
  Prepare segments (LASmod = 1.00)                                  Prepare segments (LASmod = 1.00)                                   23s
  Estimate local tissue thresholds (WM)                              23s
  Estimate local tissue thresholds (WM)                              17s
  Estimate local tissue thresholds (GM)                              17s
  Estimate local tissue thresholds (GM)                              20s
  Estimate local tissue thresholds (CSF/BG)                          20s
  Estimate local tissue thresholds (CSF/BG)                           4s
  Intensity transformation                                            4s
  Intensity transformation                                           76s
  SANLM denoising after LAS (medium)                                 76s
  SANLM denoising after LAS (medium)                                 31s
                                                                     31s
ROI segmentation (partitioning):
  Atlas -> subject space                                             32s
                                                                     32s
ROI segmentation (partitioning):
  Atlas -> subject space                                             12s
  Major structures                                                   11s
  Major structures                                                    7s
  Ventricle detection                                                 7s
  Ventricle detection                                                16s
  Blood vessel detection                                             16s
  Blood vessel detection                                             18s
  WMH detection (WMHCstr=0.50 > WMHCstr'=0.50)                       18s
  WMH detection (WMHCstr=0.50 > WMHCstr'=0.50)                       28s
  Manual stroke lesion detection                                      0s
  Closing of deep structures                                         29s
  Manual stroke lesion detection                                      0s
  Closing of deep structures                                          3s
  Side alignment                                                      3s
  Side alignment                                                      6s
  Final corrections                                                   6s
  Final corrections                                                   5s
                                                                     94s
Blood vessel correction (BVCstr=0.50):                                5s
                                                                     94s
Blood vessel correction (BVCstr=0.50):                                1s
    1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06):Amap using initial SPM12 segmentations (MRF filter strength 0.06):   33s
    AMAP peaks: [CSF,GM,WM] = [0.52±0.12,0.79±0.04,0.96±0.04]
   33s
    AMAP peaks: [CSF,GM,WM] = [0.52±0.12,0.79±0.04,0.96±0.04]
Final cleanup (gcutstr=0.25):
  Level 1 cleanup (ROI estimation)                                Final cleanup (gcutstr=0.25):
  Level 1 cleanup (ROI estimation)                                    6s
  Level 1 cleanup (brain masking)                                     6s
  Level 1 cleanup (brain masking)                                     3s
  Level 2 cleanup (CSF correction)                                    3s
  Level 2 cleanup (CSF correction)                                    2s
  Level 3 cleanup (CSF/WM PVE)                                        2s
  Level 3 cleanup (CSF/WM PVE)                                        4s
                                                                     14s
    4s
                                                                     14s
Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
  Template: "/home/emdim/scratch/spm12/toolbox/cat12/templates_volumes/Template_0_IXI555_MNI152_GS.nii"
Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
  Template: "/home/emdim/scratch/spm12/toolbox/cat12/templates_volumes/Template_0_IXI555_MNI152_GS.nii"
    1 | 2.50 |    1 | 2.50 | 0.1214  0.0000  0.1214
 0.1214  0.0000  0.1214
    2 | 2.50 |    2 | 2.50 | 0.1150  0.0020  0.1170
 0.1150  0.0020  0.1170
    3 | 2.50 |    3 | 2.50 | 0.1122  0.0033  0.1155
 0.1122  0.0033  0.1155
    4 | 2.50 |    4 | 2.50 | 0.1101  0.0041  0.1142
 0.1101  0.0041  0.1142
    5 | 2.50 |    5 | 2.50 | 0.1080  0.0047  0.1127
 0.1080  0.0047  0.1127
    6 | 2.50 |    6 | 2.50 | 0.1058  0.0053  0.1111
 0.1058  0.0053  0.1111
    7 | 2.50 |    7 | 2.50 | 0.1034  0.0059  0.1093
 0.1034  0.0059  0.1093
    8 | 2.50 |    8 | 2.50 | 0.1011  0.0065  0.1075
 0.1011  0.0065  0.1075
    9 | 2.50 |    9 | 2.50 | 0.0988  0.0070  0.1058
 0.0988  0.0070  0.1058
   10 | 2.50 |   10 | 2.50 | 0.0965  0.0075  0.1041
 0.0965  0.0075  0.1041
   11 | 2.50 |   11 | 2.50 | 0.0944  0.0080  0.1024
 0.0944  0.0080  0.1024
   12 | 2.50 |   12 | 2.50 | 0.0923  0.0085  0.1008
 0.0923  0.0085  0.1008
   13 | 2.50 |   13 | 2.50 | 0.0904  0.0090  0.0994
 0.0904  0.0090  0.0994
   14 | 2.50 |   14 | 2.50 | 0.0887  0.0094  0.0981
 0.0887  0.0094  0.0981
   15 | 2.50 |   15 | 2.50 | 0.0867  0.0099  0.0965
 0.0867  0.0099  0.0965
   16 | 2.25 |   16 | 2.25 | 0.0989  0.0290  0.1279
 0.0989  0.0290  0.1279
   17 | 2.25 |   17 | 2.25 | 0.0894  0.0150  0.1044
 0.0894  0.0150  0.1044
   18 | 2.25 |   18 | 2.25 | 0.0865  0.0157  0.1022
 0.0865  0.0157  0.1022
   30 | 2.00 |   30 | 2.00 | 0.0915  0.0256  0.1170
 0.0915  0.0256  0.1170
   31 | 2.00 |   31 | 2.00 | 0.0819  0.0189  0.1008
 0.0819  0.0189  0.1008
   32 | 2.00 |   32 | 2.00 | 0.0787  0.0203  0.0990
 0.0787  0.0203  0.0990
   44 | 1.75 |   44 | 1.75 | 0.0802  0.0309  0.1111
 0.0802  0.0309  0.1111
   45 | 1.75 |   45 | 1.75 | 0.0743  0.0231  0.0973
 0.0743  0.0231  0.0973
   46 | 1.75 |   46 | 1.75 | 0.0729  0.0236  0.0965
 0.0729  0.0236  0.0965
   58 | 1.50 |   58 | 1.50 | 0.0818  0.0351  0.1170
 0.0818  0.0351  0.1170
   59 | 1.50 |   59 | 1.50 | 0.0726  0.0278  0.1004
 0.0726  0.0278  0.1004
   60 | 1.50 |   60 | 1.50 | 0.0704  0.0286  0.0990
 0.0704  0.0286  0.0990
Shooting registration with 2.50:-0.25:1.50 mm takes:                277s
  Prepare output                                                  Shooting registration with 2.50:-0.25:1.50 mm takes:                277s
  Prepare output                                                     14s
                                                                    291s
  Jacobian determinant (RMS):  0.553985
           Template Matching:    15s
                                                                    291s
  Jacobian determinant (RMS):  0.211176
 0.553985
           Template Matching:  0.211176
Write result maps:                                                Write result maps:                                                Warning: File not found or permission denied
> In cat_io_writenii (line 129)
  In cat_main_write (line 61)
  In cat_main1639 (line 630)
  In cat_run_job1639 (line 912)
  In cat_run_newcatch (line 34)
  In cat_run>run_job (line 866)
  In cat_run (line 455)
  In cfg_run_cm (line 29)
  In cfg_util>local_runcj (line 1717)
  In cfg_util (line 972)
  In spm_jobman>fill_run_job (line 469)
  In spm_jobman (line 247)
  In matlab_seq>with_affine_segm (line 102)
  In matlab_seq (line 25)
Warning: File not found or permission denied
> In cat_io_writenii (line 293)
  In cat_main_write (line 74)
  In cat_main1639 (line 630)
  In cat_run_job1639 (line 912)
  In cat_run_newcatch (line 34)
  In cat_run>run_job (line 866)
  In cat_run (line 455)
  In cfg_run_cm (line 29)
  In cfg_util>local_runcj (line 1717)
  In cfg_util (line 972)
  In spm_jobman>fill_run_job (line 469)
  In spm_jobman (line 247)
  In matlab_seq>with_affine_segm (line 102)
  In matlab_seq (line 25)
Warning: File not found or permission denied
> In cat_io_writenii (line 293)
  In cat_main_write (line 74)
  In cat_main1639 (line 630)
  In cat_run_job1639 (line 912)
  In cat_run_newcatch (line 34)
  In cat_run>run_job (line 866)
  In cat_run (line 455)
  In cfg_run_cm (line 29)
  In cfg_util>local_runcj (line 1717)
  In cfg_util (line 972)
  In spm_jobman>fill_run_job (line 469)
  In spm_jobman (line 247)
  In matlab_seq>with_affine_segm (line 102)
  In matlab_seq (line 25)
    2s
    2s
Surface and thickness estimation:                                 Surface and thickness estimation:
lh:
  Thickness estimation (0.50 mm³):
lh:
  Thickness estimation (0.50 mm³):

    WM distance:                                                      WM distance:                                                     57s
    CSF distance:                                                    57s
    CSF distance:                                                    30s
    PBT2x thickness:                                                 30s
    PBT2x thickness:                                                 22s
                                                                     22s
                                                                    124s
  124s
  Create initial surface                                            Create initial surface
------------------------------------------------------------------------
CAT Preprocessing error for 1063167_MNI:
------------------------------------------------------------------------
/bin/bash: /lustre04/scratch/emdim/spm12/toolbox/cat12/CAT.glnx86/CAT_Surf2Sphere: Permission denied

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

------------------------------------------------------------------------
CAT Preprocessing error for 1063167_MNI:
------------------------------------------------------------------------
/bin/bash: /lustre04/scratch/emdim/spm12/toolbox/cat12/CAT.glnx86/CAT_Surf2Sphere: Permission denied

------------------------------------------------------------------------
   27 - cat_check_system_output
  747 - cat_surf_createCS
  698 - cat_main1639
  912 - cat_run_job1639
   34 - cat_run_newcatch
  866 - run_job
  455 - cat_run
   29 - cfg_run_cm
 1717 - local_runcj
  972 - cfg_util
  469 - fill_run_job
  247 - spm_jobman
  102 - with_affine_segm
   25 - matlab_seq
------------------------------------------------------------------------
   27 - cat_check_system_output
  747 - cat_surf_createCS
  698 - cat_main1639
  912 - cat_run_job1639
   34 - cat_run_newcatch
  866 - run_job
  455 - cat_run
   29 - cfg_run_cm
 1717 - local_runcj
  972 - cfg_util
  469 - fill_run_job
  247 - spm_jobman
  102 - with_affine_segm
   25 - matlab_seq
------------------------------------------------------------------------
21-Dec-2020 12:49:51 - Failed  'CAT12: Segmentation (current release)'
21-Dec-2020 12:49:51 - Failed  'CAT12: Segmentation (current release)'
Reference to non-existent field 'vol_rel_WMH'.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_main_reportstr.m" (v1730), function "cat_main_reportstr" at line 320.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_io_report.m" (???), function "cat_io_report" at line 208.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 204.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "run_job" at line 866.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "cat_run" at line 455.

Reference to non-existent field 'vol_rel_WMH'.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_main_reportstr.m" (v1730), function "cat_main_reportstr" at line 320.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_io_report.m" (???), function "cat_io_report" at line 208.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 204.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "run_job" at line 866.
In file "/lustre04/scratch/emdim/spm12/toolbox/cat12/cat_run.m" (v1736), function "cat_run" at line 455.

The following modules did not run:
Failed: CAT12: Segmentation (current release)

The following modules did not run:
Failed: CAT12: Segmentation (current release)

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command
window, starting with the lines (look for the line showing the exact #job as
displayed in this error message)
------------------
Running job #1
------------------

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command
window, starting with the lines (look for the line showing the exact #job as
displayed in this error message)
------------------
Running job #1

I think the error may be a permission error as I am running the script on a cluster. However, I am not sure. If that is the case, is there a way to determine what output directory I want using matlabbatch?

Thanks a lot

6

Hello,
I also get this error and I did't change the WMH setting(default "set WMH temporary as WM").The error in command window is:
Reference to non-existent field 'vol_rel_WMH'.

Error in cat_main_reportstr (line 320)
if job.extopts.WMHC<=2 && (qa.subjectmeasures.vol_rel_WMH>0.01 || ...

Error in cat_io_report (line 208)
str = cat_main_reportstr(job,cat_err_res.res,qa);

Error in cat_run_newcatch (line 204)
cat_io_report(job,qa,subj)

Error in cat_run>run_job (line 866)
cat_run_newcatch(job,tpm,subj);

Error in cat_run (line 455)
varargout{1} = run_job(job);'
How can I solve this error?

7

@Mozhdeh123 @emdim
I can't replicate this error and assume that you are using an older version. Please update to r1741 to solve that issue.

8

Thanks for responding. I downloaded latest version of cat means(r1739) and couldn't find r.1741!! Can you give me a website for downloading latest version that you mean?(CAT12.r1741)

9

@Mozhdeh123 @emdim
Ups, my fault. The new release should be now available.

10

I found the error on my side. There was one file used by CAT: CAT_Surf2Sphere in spm12/toolbox/cat12/CAT.glnx86 that didn't have execution permission.

Thanks