Print

Print
Hi Vladimir,

Thanks, I managed to re-install SPM12b and the updates properly and the batch function is working now. However, when I specify the forward model as BEM the job still crashes. I tried to run it using the experimental 3-shell sphere and this seems to work. But I'd like to know why I can't use BEM, have you any idea what could be causing this?

I've copied below the output in the command window:
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Head model specification'

SPM12b: spm_eeg_inv_mesh_ui (v4027)                13:34:44 - 30/08/2013
========================================================================
       template: 1
         Affine: [4x4 double]
           sMRI: 'C:\Users\G\Desktop\spm12b\canonical\single_subj_T1.nii'
          Msize: 2
       tess_mni: [1x1 struct]
       tess_ctx: 'C:\Users\G\Desktop\spm12b\canonical\cortex_8196.surf.gii'
     tess_scalp: 'C:\Users\G\Desktop\spm12b\canonical\scalp_2562.surf.gii'
    tess_oskull: 'C:\Users\G\Desktop\spm12b\canonical\oskull_2562.surf.gii'
    tess_iskull: 'C:\Users\G\Desktop\spm12b\canonical\iskull_2562.surf.gii'
            fid: [1x1 struct]

creating layout from cfg.elec
creating layout for ext1020 system
reordering the boundaries to: 1 2 3
Failed  'Head model specification'
Error using horzcat
Dimensions of matrices being concatenated are not consistent.
In file "C:\Users\G\Desktop\spm12b\external\fieldtrip\forward\private\triangle4pt.m" (v7123), function "triangle4pt" at line 58.
In file "C:\Users\G\Desktop\spm12b\external\fieldtrip\forward\ft_headmodel_bemcp.m" (v7310), function "ft_headmodel_bemcp" at line 102.
In file "C:\Users\G\Desktop\spm12b\external\fieldtrip\ft_prepare_headmodel.m" (v8304), function "ft_prepare_headmodel" at line 222.
In file "C:\Users\G\Desktop\spm12b\spm_eeg_inv_forward.m" (v5139), function "spm_eeg_inv_forward" at line 81.
In file "C:\Users\G\Desktop\spm12b\config\spm_cfg_eeg_inv_headmodel.m" (v5377), function "specify_headmodel" at line 314.

No executable modules, but still unresolved dependencies or incomplete module inputs.
The following modules did not run:
Failed: Head model specification
Skipped: Source inversion
Skipped: Inversion results

Please let me know if you have any ideas why I can't seem to use the BEM. If you require any of my files please also let me know.

Best Wishes,
Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: Vladimir Litvak [[log in to unmask]]
Sent: 29 August 2013 16:04
To: Gemma Barnacle
Cc: [log in to unmask]
Subject: Re: [SPM] source localisation error

Dear Gemma,

It looks like you didn't install the full SPM version but just the updates. Try running spm_update in the SPM version that worked before or just download a full version of SPM via registration form.

Best,

Vladimir


On Thu, Aug 29, 2013 at 2:34 PM, Gemma Barnacle <[log in to unmask]> wrote:
Hi Vladimir,

I have done what you suggested, but this has not helped. When I tried to used the Batch function there was no 'SPM' menu to select a module to run. I tried instead using the GUI and '3D Source Reconstr.' but when I tried to load a file (from before the averaging step for one subject) I got this error:

Inputs to cfg_getfile('CPath',...) must be cellstr.
Error using char
Cell elements must be character arrays.

Error in spm_file (line 162)
    str = char(str);

Error in spm_eeg_load (line 32)
P = spm_file(spm_file(P, 'ext', '.mat'), 'cpath');

Error in spm_eeg_inv_imag_api>Load_Callback (line 124)
D = spm_eeg_load(S);


Error in spm_eeg_inv_imag_api (line 53)
        feval(varargin{:}); % FEVAL switchyard
 
Error while evaluating uicontrol Callback

I'm also copying below the text I got when I started SPM12b because there seemed to be a lot going on, and this was not the case with the previous version I was using.

 ___  ____  __  __                                           
/ __)(  _ \(  \/  )                                          
\__ \ )___/ )    (   Statistical Parametric Mapping          
(___/(__)  (_/\/\_)  SPM12b - http://www.fil.ion.ucl.ac.uk/spm/


SPM12b: v5616                                      14:28:00 - 29/08/2013
========================================================================
Initialising SPM                        :                   ..Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Serial Longitudinal Registration', field 'prog': Value must be a function or function handle on MATLAB path.
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Failed to load C:\Users\G\Desktop\SPM\spm8\config\cfg_mlbatch_appcfg.m
Error using subsasgn (line 88)
Reference to unknown field 'rewrite_job'.
To assign to a field in the job structure, use a reference like '(x).rewrite_job'.
In file "subsasgn.m" (???), function "subsasgn" at line 88.
In file "spm_cfg.m" (v5545), function "spm_cfg" at line 128.
In file "cfg_mlbatch_appcfg.m" (v2086), function "cfg_mlbatch_appcfg" at line 10.
In file "cfg_util.m" (v4252), function "local_initapps" at line 1297.
In file "cfg_util.m" (v4252), function "cfg_util" at line 619.
In file "spm_jobman.m" (v4242), function "spm_jobman" at line 160.
In file "spm.m" (v5604), function "spm" at line 341.

.....

Is it possible to go back to the old version of SPM that I was using? That version seemed to get me a little further than this.

Please let me know if you require me to send any files etc. to assist with figuring this out.

Best Wishes,

Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: Vladimir Litvak [[log in to unmask]]
Sent: 28 August 2013 13:55
To: Gemma Barnacle
Cc: [log in to unmask]

Subject: Re: [SPM] source localisation error

That's quite strange.I would suggest that you download the latest SPM12b version from the website, reset your Matlab path to default and add just SPM top folder to it, then rerun SPM, delete the previous reconstructions in 3D tool and start from scratch. If you still have the problem then, I'll need to look at a data example.

Vladimir


On Wed, Aug 28, 2013 at 1:39 PM, Gemma Barnacle <[log in to unmask]> wrote:
Thanks Vladimir,

I am actually not getting as far as the invert step, with the error arising at the Forward Model step. I specify BEM but it will not process the request. Here is what appears in the Command Window:


reordering the boundaries to: 1 2 3
Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Error in triangle4pt (line 58)
    sph_pnt = pnt([tri(jj,:) lv],:);

Error in ft_headmodel_bemcp (line 102)
vol = triangle4pt(vol);

Error in ft_prepare_headmodel (line 206)
      vol = ft_headmodel_bemcp(geometry,'conductivity',cfg.conductivity);

Error in spm_eeg_inv_forward (line 83)
                vol = ft_prepare_headmodel(cfg, vol);

Error in spm_eeg_inv_forward_ui (line 42)
D = spm_eeg_inv_forward(D);

Error in spm_eeg_inv_imag_api>Forward_Callback (line 87)
handles.D = spm_eeg_inv_forward_ui(handles.D);

Error in spm_eeg_inv_imag_api (line 53)
        feval(varargin{:}); % FEVAL switchyard
 
Error while evaluating uicontrol Callback

>>

Hopefully this will give you some info as to what I'm doing wrong.
Thanks,


Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Vladimir Litvak [[log in to unmask]]
Sent: 28 August 2013 13:23
To: [log in to unmask]
Subject: Re: [SPM] source localisation error

Dear Gemma,

Could you use the GUI and send everything that is printed in the command window from the point when you pressed the 'invert' button?

Thanks,

Vladimir


On Wed, Aug 28, 2013 at 1:11 PM, Gemma Barnacle <[log in to unmask]> wrote:
Dear Experts,

I have followed the instructions from the SPM training day earlier this year to complete source reconstruction on my EEG data. I have tried using the GUI and the batch function but both are not working for me. The common error I seem to get is:

Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Please could anyone tell me what this refers to? And how to correct this error?

Many thanks in advance,
Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.




Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: Vladimir Litvak [[log in to unmask]]
Sent: 29 August 2013 16:04
To: Gemma Barnacle
Cc: [log in to unmask]
Subject: Re: [SPM] source localisation error

Dear Gemma,

It looks like you didn't install the full SPM version but just the updates. Try running spm_update in the SPM version that worked before or just download a full version of SPM via registration form.

Best,

Vladimir


On Thu, Aug 29, 2013 at 2:34 PM, Gemma Barnacle <[log in to unmask]> wrote:
Hi Vladimir,

I have done what you suggested, but this has not helped. When I tried to used the Batch function there was no 'SPM' menu to select a module to run. I tried instead using the GUI and '3D Source Reconstr.' but when I tried to load a file (from before the averaging step for one subject) I got this error:

Inputs to cfg_getfile('CPath',...) must be cellstr.
Error using char
Cell elements must be character arrays.

Error in spm_file (line 162)
    str = char(str);

Error in spm_eeg_load (line 32)
P = spm_file(spm_file(P, 'ext', '.mat'), 'cpath');

Error in spm_eeg_inv_imag_api>Load_Callback (line 124)
D = spm_eeg_load(S);


Error in spm_eeg_inv_imag_api (line 53)
        feval(varargin{:}); % FEVAL switchyard
 
Error while evaluating uicontrol Callback

I'm also copying below the text I got when I started SPM12b because there seemed to be a lot going on, and this was not the case with the previous version I was using.

 ___  ____  __  __                                           
/ __)(  _ \(  \/  )                                          
\__ \ )___/ )    (   Statistical Parametric Mapping          
(___/(__)  (_/\/\_)  SPM12b - http://www.fil.ion.ucl.ac.uk/spm/


SPM12b: v5616                                      14:28:00 - 29/08/2013
========================================================================
Initialising SPM                        :                   ..Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Serial Longitudinal Registration', field 'prog': Value must be a function or function handle on MATLAB path.
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Can not initialise generic: job is not a struct.
Failed to load C:\Users\G\Desktop\SPM\spm8\config\cfg_mlbatch_appcfg.m
Error using subsasgn (line 88)
Reference to unknown field 'rewrite_job'.
To assign to a field in the job structure, use a reference like '(x).rewrite_job'.
In file "subsasgn.m" (???), function "subsasgn" at line 88.
In file "spm_cfg.m" (v5545), function "spm_cfg" at line 128.
In file "cfg_mlbatch_appcfg.m" (v2086), function "cfg_mlbatch_appcfg" at line 10.
In file "cfg_util.m" (v4252), function "local_initapps" at line 1297.
In file "cfg_util.m" (v4252), function "cfg_util" at line 619.
In file "spm_jobman.m" (v4242), function "spm_jobman" at line 160.
In file "spm.m" (v5604), function "spm" at line 341.

.....

Is it possible to go back to the old version of SPM that I was using? That version seemed to get me a little further than this.

Please let me know if you require me to send any files etc. to assist with figuring this out.

Best Wishes,

Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: Vladimir Litvak [[log in to unmask]]
Sent: 28 August 2013 13:55
To: Gemma Barnacle
Cc: [log in to unmask]

Subject: Re: [SPM] source localisation error

That's quite strange.I would suggest that you download the latest SPM12b version from the website, reset your Matlab path to default and add just SPM top folder to it, then rerun SPM, delete the previous reconstructions in 3D tool and start from scratch. If you still have the problem then, I'll need to look at a data example.

Vladimir


On Wed, Aug 28, 2013 at 1:39 PM, Gemma Barnacle <[log in to unmask]> wrote:
Thanks Vladimir,

I am actually not getting as far as the invert step, with the error arising at the Forward Model step. I specify BEM but it will not process the request. Here is what appears in the Command Window:


reordering the boundaries to: 1 2 3
Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Error in triangle4pt (line 58)
    sph_pnt = pnt([tri(jj,:) lv],:);

Error in ft_headmodel_bemcp (line 102)
vol = triangle4pt(vol);

Error in ft_prepare_headmodel (line 206)
      vol = ft_headmodel_bemcp(geometry,'conductivity',cfg.conductivity);

Error in spm_eeg_inv_forward (line 83)
                vol = ft_prepare_headmodel(cfg, vol);

Error in spm_eeg_inv_forward_ui (line 42)
D = spm_eeg_inv_forward(D);

Error in spm_eeg_inv_imag_api>Forward_Callback (line 87)
handles.D = spm_eeg_inv_forward_ui(handles.D);

Error in spm_eeg_inv_imag_api (line 53)
        feval(varargin{:}); % FEVAL switchyard
 
Error while evaluating uicontrol Callback

>>

Hopefully this will give you some info as to what I'm doing wrong.
Thanks,


Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Vladimir Litvak [[log in to unmask]]
Sent: 28 August 2013 13:23
To: [log in to unmask]
Subject: Re: [SPM] source localisation error

Dear Gemma,

Could you use the GUI and send everything that is printed in the command window from the point when you pressed the 'invert' button?

Thanks,

Vladimir


On Wed, Aug 28, 2013 at 1:11 PM, Gemma Barnacle <[log in to unmask]> wrote:
Dear Experts,

I have followed the instructions from the SPM training day earlier this year to complete source reconstruction on my EEG data. I have tried using the GUI and the batch function but both are not working for me. The common error I seem to get is:

Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Please could anyone tell me what this refers to? And how to correct this error?

Many thanks in advance,
Gemma.

Miss Gemma E. Barnacle
PhD Student
School of Psychology
Room 119, Zochonis Building
University of Manchester
M13 9PL.