Dear Jeroen,
I suspect your batch is not fully specified. I suggest that you try to
build the batch in the GUI, using dependencies, run it, make sure it
does want you want, then save it as a script, run it again to make
sure it still runs and only then try to modify it.
Best,
Vladimir
On Mon, Nov 7, 2011 at 8:37 AM, Jeroen Van Schependom
<[log in to unmask]> wrote:
> Dear Vladimir,
>
> I somehow missed the point of actually running the batch. Running it,
> results however in a rather large error message :
>
> spm_jobman('initcfg');
> spm_jobman('run',matlabbatch);
>
> "Cell contents reference from a non-cell array object.
>
> Error in cfg_repeat/initialise>initialise_job (line 119)
> citem{l} = initialise(item.values{1}, ...
>
> Error in cfg_repeat/initialise (line 31)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_choice/initialise>initialise_job (line 71)
> item.cfg_item.val{1} = initialise(item.values{k}, ...
>
> Error in cfg_choice/initialise (line 32)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_branch/initialise>initialise_job (line 49)
> item.cfg_item.val{k} = initialise(item.cfg_item.val{k}, ...
>
> Error in cfg_branch/initialise (line 27)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_choice/initialise>initialise_job (line 71)
> item.cfg_item.val{1} = initialise(item.values{k}, ...
>
> Error in cfg_choice/initialise (line 32)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_choice/initialise>initialise_job (line 71)
> item.cfg_item.val{1} = initialise(item.values{k}, ...
>
> Error in cfg_choice/initialise (line 32)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_choice/initialise>initialise_job (line 71)
> item.cfg_item.val{1} = initialise(item.values{k}, ...
>
> Error in cfg_choice/initialise (line 32)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_repeat/initialise>initialise_job (line 111)
> citem{l} = initialise(item.values{k}, ...
>
> Error in cfg_repeat/initialise (line 31)
> item = initialise_job(item, val, dflag);
>
> Error in cfg_util>local_initjob/@(ucjob)initialise(cjd,ucjob,false)
>
>
> Error in cfg_util>local_initjob (line 1364)
> ucj = cellfun(@(ucjob)initialise(cjd,ucjob,false), job(ui), 'UniformOutput',
> false);
>
> Error in cfg_util (line 678)
> [jobs(cjob) mod_job_idlist] = local_initjob(jobs(cjob), job,
> jobdedup);
>
> Error in spm_jobman (line 216)
> cjob = cfg_util('initjob', mljob);
> "
> The information I find on the internet refers to problems with the
> conversion of a spm5 script to a spm8, but I only use spm8. Do you have any
> clue where the error could be located ?
>
> Many thanks,
>
> Jeroen.
>
>
> 2011/11/4 Vladimir Litvak <[log in to unmask]>
>>
>> Dear Jeroen,
>>
>> Did you actually run the batch with:
>>
>> spm_jobman('run', matlabbatch);
>>
>> ?
>>
>> Vladimir
>>
>> On Fri, Nov 4, 2011 at 9:06 AM, Jeroen Van Schependom
>> <[log in to unmask]> wrote:
>> > Dear Vladimir,
>> >
>> > The code I used untill now does not produce the nifti-images. Please
>> > find an
>> > example below.
>> >
>> > matlabbatch{4}.spm.meeg.source.invert.D =
>> > {['C:\Users\k1787\Documents\PhD -
>> > Matlabfiles\espm8_' naam '.mat']};
>> > matlabbatch{4}.spm.meeg.source.invert.val = 1;
>> > matlabbatch{4}.spm.meeg.source.invert.whatconditions.condlabel = '12';
>> > matlabbatch{4}.spm.meeg.source.invert.isstandard.standard = 1;
>> > matlabbatch{4}.spm.meeg.source.invert.modality = {'All'};
>> > %Inversion results
>> > matlabbatch{5}.spm.meeg.source.results.D = ['espm8_' naam '.mat'];
>> > matlabbatch{5}.spm.meeg.source.results.val = 1;
>> > matlabbatch{5}.spm.meeg.source.results.woi = [-100 900];
>> > matlabbatch{5}.spm.meeg.source.results.foi = [0 100];
>> > matlabbatch{5}.spm.meeg.source.results.ctype = 'evoked';
>> > matlabbatch{5}.spm.meeg.source.results.space = 0;
>> > matlabbatch{5}.spm.meeg.source.results.smoothing = 8;
>> >
>> > Should I add a line or is this code supposed to produce nifti-images. I
>> > also
>> > added following lines :
>> >
>> > matlabbatch{6}.spm.meeg.source.extract.D =
>> > {['C:\Users\k1787\Documents\PhD -
>> > Matlabfiles\espm8_' naam '.mat']};
>> > matlabbatch{6}.spm.meeg.source.extract.val = 1;
>> > matlabbatch{6}.spm.meeg.source.extract.source = struct('label', {},
>> > 'xyz',
>> > {});
>> > matlabbatch{6}.spm.meeg.source.extract.rad = 5;
>> > matlabbatch{6}.spm.meeg.source.extract.type = 'evoked';
>> > matlabbatch{6}.spm.meeg.source.extract.fname = ['spm8_final_' naam];
>> >
>> > But no file, starting with 'spm8_final_' is created either.
>> >
>> > Many thanks,
>> >
>> >
>> > Jeroen Van Schependom
>> >
>> >
>> >
>> > 2011/11/3 Vladimir Litvak <[log in to unmask]>
>> >>
>> >> Dear Jeroen,
>> >>
>> >> The nifti images are constructed automatically by the 'M/EEG inversion
>> >> results' batch tool.
>> >>
>> >> Best,
>> >>
>> >> Vladimir
>> >>
>> >> On Thu, Nov 3, 2011 at 2:36 PM, Jeroen Van Schependom
>> >> <[log in to unmask]> wrote:
>> >> > Dear Vladimir,
>> >> >
>> >> > Is it possible to do the source construction of EEG data in a
>> >> > automatically
>> >> > ? I am able to do several steps via the batch interface, but I cannot
>> >> > find
>> >> > how to construct the nifti images automatically. This would greatly
>> >> > help
>> >> > us
>> >> > in the analysis by enabling us to make enough nifti images for
>> >> > statistical
>> >> > comparison.
>> >> >
>> >> > Many thanks,
>> >> >
>> >> > Jeroen Van Schependom.
>> >> >
>> >
>> >
>
>
|