Maybe it is possible to create a shell script that first opens all the
figures (main, graphics, interactive?) and then runs your job. Your
problem seems to be caused by some step assuming that there is a window
while actually there isn't.
Maybe that works?
best
Alle Meije
Volkmar Glauche wrote:
> Hi Jon,
>
> I am afraid this would need hacking SPM code :-( There is no adaptation to
> run in text mode.
> And after all, you will definitely want to check each spatial and
> statistical processing step for each of your subjects! There are always
> cases where something goes wrong - if you don't monitor each processing
> step then you end up interpreting some data where you can't trust
> realignment, normalisation, coregistration ...
>
> Volkmar
>
> On Wed, 20 Sep 2006, jon freedlander wrote:
>
>> Hello all,
>>
>> We are running fMRI analyses using SPM5 on Matlab R2006a. The analyses run
>> fine when we are running in graphical mode, however we would like to be able
>> to have a shell script run them from the command line, i.e., without the GUI.
>> However, when we run the same analyses that work within the GUI from the
>> command line, we get the following errors:
>>
>> Running "Slice Timing"
>> ??? Error using ==> figure
>> Width and height must be > 0.
>>
>> Error in ==> spm at 1142
>> Finter = figure('IntegerHandle','off',...
>>
>> Error in ==> spm_figure at 257
>> F = spm('CreateIntWin');
>>
>> Error in ==> spm at 1753
>> Finter = spm_figure('GetWin','Interactive');
>>
>> Error in ==> spm_jobman>run_struct1 at 1454
>> [Finter,unused,CmdLine] = spm('FnUIsetup',c.name);
>>
>> Error in ==> spm_jobman>run_struct1 at 1480
>> run_struct1(c.val{i});
>>
>> Error in ==> spm_jobman>run_struct1 at 1480
>> run_struct1(c.val{i});
>>
>> Error in ==> spm_jobman>run_job at 417
>> run_struct1(c);
>>
>> Error in ==> spm_jobman at 79
>> run_job(varargin{2});
>>
>>>> --------------------------
>> Running "Realign: Estimate & Reslice"
>> ??? Error using ==> figure
>> Width and height must be > 0.
>>
>> Error in ==> spm at 1142
>> Finter = figure('IntegerHandle','off',...
>>
>> Error in ==> spm_figure at 257
>> F = spm('CreateIntWin');
>>
>> Error in ==> spm at 1753
>> Finter = spm_figure('GetWin','Interactive');
>>
>> Error in ==> spm_jobman>run_struct1 at 1454
>> [Finter,unused,CmdLine] = spm('FnUIsetup',c.name);
>>
>> Error in ==> spm_jobman>run_struct1 at 1480
>> run_struct1(c.val{i});
>>
>> Error in ==> spm_jobman>run_struct1 at 1480
>> run_struct1(c.val{i});
>>
>> Error in ==> spm_jobman>run_struct1 at 1480 run_struct1(c.val{i});
>>
>> Error in ==> spm_jobman>run_job at 417
>> run_struct1(c);
>>
>> Error in ==> spm_jobman at 79
>> run_job(varargin{2});
>>
>> Does anyone know if there is anything we could do to get this to work? Is
>> there something special we have to set to get it to run happily in text mode?
>>
>> Thanks very much,
>>
>> Jon Freedlander, MA.Cand.
>> Research Program Assistant II
>> Johns Hopkins University
>> School of Medicine
>> Department of Neurology
>>
>>
>
--
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Dept. of Psychiatry
University of Cambridge
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