> Hello I emailed a couple of days having trouble with DICOM import. I am
> trying to go on and see if I can pre-process our data - with no success.
> Thinking that our DICOM data was somehow not being able to be read, I tried
> some of the sample data sets provided by the web site.
There are many versions of DICOM around, and many of them are based on
extensions to the existing standard (which requires thousands of pages of
very tedious documentation). If you have a versin that the converter can't
deal with, then I'd be happy to take a look at some examples of your DICOM to
see if there is a simple fix for the conversion. My bits of code have to
deal with the original data, so if there are problems with the NIFTI or
ANALYZE format, then the effects generally show up in these routines.
> Starting with
> 'Display' - we tested with *.nii and it is displayed no problem - if we try
> to 'Realign' and Load the *.nii does not show up on the file selector
> window.
I have no idea why this would happen - unless the filter panel contains one of
the old style filters. If this is the case, then change it back to the
default ".*".
> Using the provided *.img files does not show up when trying to
> load them to 'Realign.' Moreover we can't display them (*.img) and get the
> following error.
The files not showing up could relate to the filter thing. I'm not sure about
the error message, but make sure you have a readable
C:\AndrewP\data\test\img\sM03953_0005_0007.hdr file. Try a copy/paste of the
following to see what happens:
dir C:\AndrewP\data\test\img\sM03953_0005_0007.hdr
> I am using SPM5 with no updates (because if we use with
> updates_826 we get an error with selecting realign from the dropdown and
> with updates_958 SPM won't even start up.) We are using MATLAB 6.5 for
> Windows 2000 (about to use 7.1) and wondering how much of this is a MATLAB
> problem, a SPM software problem, or our inability to use the right updates
> with our version of MATLAB. If anyone could be of assitance that would be
> great! I apologize for submitting such a rudimentary question/problem.
I really would suggest installing the updates. We are not very motivated to
spend time diagnosing or fixing problems in old software, whereas we are much
more likely to come up with fixes for any problems in the latest version.
Generally, the later versions also have more of the old bugs fixed.
The latest problem that has been encountered relates to MATLAB 6.5, which not
so many of us developers are using any more. See Rik Henson's recent emails
to the list. The local testers in the FIL are generally not updating their
versions as frequently as they could be (they have some nice TortoiseSVN
things that they could use to make this very easy), so SPM doesn't receive as
much in-house testing as it once did.
Best regards,
-John
> --------------------------
> Running "Display Image"
> ??? Error using ==> spm_vol (subfunc)
> C:\AndrewP\data\test\img\sM03953_0005_0007.img: Unknown file format.
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_vol.m (subfunc1)
> On line 83 ==> v = subfunc(P(i,:));
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_vol.m (subfunc2)
> On line 71 ==> V = subfunc1(P);
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_vol.m
> On line 57 ==> V = subfunc2(P);
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_image.m
> On line 305 ==> if ischar(P), P = spm_vol(P); end;
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_config_display.m (dispim)
> On line 97 ==> spm_image('init',job.data{1});
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m (run_struct1)
> On line 1474 ==> feval(prog,val);
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m (run_struct1)
> On line 1482 ==> run_struct1(c.val{i});
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m (run_struct1)
> On line 1482 ==> run_struct1(c.val{i});
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m (run_job)
> On line 417 ==> run_struct1(c);
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m (serial)
> On line 2039 ==> run_job(jobs);
>
> Error in ==> C:\MATLAB6p5\spm5\spm5\spm_jobman.m
> On line 70 ==> serial(varargin{2:nargin});
>
> ??? Error while evaluating uicontrol Callback.
>
> --------------------------
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