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
>
>
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
|