Hi Volkmar and SPM
Thanks. It turns out that recompiling the binaries fixed the problem. Nothing special needed, just
make / make install. There were no other obvious problems with the binaries but perhaps the mex
calls had changed in subtle ways. In any case spm5 seems to work fine with R2006b at this point,
although i have not tested all functionality.
Darren
==============Original message text===============
On Thu, 08 Feb 2007 1:09:43 pm CST Volkmar Glauche wrote:
Hi Darren & other list members,
I did not even dare trying Matlab 2006b yet (still working on R14SP2/3),
but there are a number of incompatibilities that may come into play. SPM5
has not been updated to work around most of them. I would guess this has
something to do with the way SPM5 digests DICOM headers in
spm_dicom_headers.m. There are a lot of fread(...) calls, reading the
DICOM header byte for byte (or char for char). This may be a reason for
misinterpreting numbers, since the meaning of fread(...,'char') has
changed in MATLAB 2006b.
If ever possible, I would recommend to stick to MATLAB R14SP2/3 for
SPM5.
Volkmar
On Thu, 8 Feb 2007, d gitelman wrote:
> Hi
>
> I am trying to import DICOM files but running into an error. I am running
> spm5 with all patches/updates, Matlab 2006b, on a workstation with red hat
> enterprise linux 4. The error listed below does not occur when the same
> dataset is imported on either a windows machine (matlab 2006, same spm5) or
> a linux machine running RH linux 8 and Matlab R14+.
>
> The error appears to be related to the exe file- mat2file- but it is unclear
> how to fix it. The error is one that mat2file is producing and not Matlab
> per se. Has anyone seen a similar error?
>
> thanks
> darren
>
>
> Running "DICOM Import"
>
> Changing directory to: /usr/local/freesurfer/subjects/etT1/
> ??? Subscripted assignment dimension mismatch (2).
> Error in ==> file_array.subsasgn>subfun at 125
> mat2file(sobj,dat,va{:});
> Error in ==> file_array.subsasgn at 63
> subfun(sobj,double(dat),args{:});
> Error in ==> nifti.subsasgn>fun at 74
> val = subsasgn(obj.dat,subs(2:end),val);
> Error in ==> nifti.subsasgn at 20
> obji = fun(obji,subs,val);
> Error in ==> spm_dicom_convert>write_volume at 589
> N.dat(:,:,i) = plane;
> Error in ==> spm_dicom_convert>convert_standard at 208
> write_volume(hdr{i},root_dir,format);
> Error in ==> spm_dicom_convert at 44
> convert_standard(standard,root_dir,format);
> Error in ==> spm_config_dicom>convert_dicom at 96
> spm_dicom_convert(hdr,'all',job.root);
> Error in ==> spm_jobman>run_struct1 at 1474
> feval(prog,val);
> Error in ==> spm_jobman>run_struct1 at 1482
> run_struct1(c.val{i});
> Error in ==> spm_jobman>run_struct1 at 1482
> run_struct1(c.val{i});
> Error in ==> spm_jobman>run_job at 417
> run_struct1(c);
> Error in ==> spm_jobman>serial at 2039
> run_job(jobs);
> Error in ==> spm_jobman at 70
> serial(varargin{2:nargin});
>
> ??? Error using ==> spm_jobman('serial','','jobs.util.dicom');
> Subscripted assignment dimension mismatch (2).
> ??? Error while evaluating uicontrol Callback
>
>
--
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/===========End of original message text===========
--------------------------------
Darren R. Gitelman, M.D.
Department of Neurology
710 N. Lake Shore Dr. #1122
Chicago, IL 60611
Voice: (312) 908-8614
Fax: (312) 908-5073
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