Dear Steven, John and others
I think the dicom converter in SPM does an excellent job, and when it
comes to orientation I have seen nothing like it. I would actually
argue that the people who are to blame are the ones who think that
each slice needs its own DICOM file.
Best
Torben
Den 31/03/2009 kl. 15.17 skrev Steven Liu:
> Dear John:
>
> I used SPM_DICOM_essential also in SPM8b, but it does not help.
> The problem here is that when you try to convert too many fMRI DICOM
> files, for example,
> if you have 300 volumes, each with 50 slices, you will have 15000
> DICOM files
> to convert into Analyze, then spm_dicom_convert will fail due to
> memory
> problem. Even if it does not fail, it will take very very long
> time to complete
> such a converting. I think, this is a big bug since SPM2, SPM5 or
> SPM8b
> has not resolved this problem. SPM has to make a C+++ version for
> this function
> or totally change the way of coding and processing in the next
> version of SPM.
> At now, we can use the latest version of MRIConvert or MRICron (each
> of the two
> software packages has a command-line exe file for you to run at a
> batch mode
> without through a GUI) to convert big fMRI DICOM files.
> But for a few number of DICOM files, spm_dicom_convert works
> excellently
> becasue it takes care the origin much more accurately than any other
> software.
>
> Steven
>
> Steven
>
>
>
>
> On Tue, Mar 31, 2009 at 7:35 AM, John Ashburner <[log in to unmask]
> > wrote:
> The memory problems were occuring because all the header info was
> stored from
> all the DICOM files, so that it could be sorted into different
> volumes. A
> more recent version of the converter only saves the essential fields
> in
> memory. This is available in SPM8b, but also may (not entirely
> sure) be
> included among the recent updates for SPM5.
>
> Best regards,
> -John
>
> On Tuesday 31 March 2009 03:52, Michael T Rubens wrote:
> > try dicominfo instead of spm_dicom_headers (I think you need Image
> > Processing Toolbox).
> > Michael
> >
> > 2009/3/30 Steven Liu <[log in to unmask]>
> >
> > > I used to have the same problem when I converted more than 280
> volumes,
> > > each of
> > > which had more than 40 slices. And it is very slow to use
> > > SPM_DICOM_Convert to
> > > convert fMRI DICOM files to Analyze. It is ok if you use it to
> convert a
> > > few number of DICOM
> > > files, such as Structural DICOM files. You may use MRIConvert
> to convert
> > > functional
> > > DICOM when you have too many files.
> > >
> > >
> > > Steven
> > >
> > >
> > >
> > > 2009/3/30 ±«Ãô <[log in to unmask]>
> > >
> > > Hi,
> > >
> > >> Excuse me for a beginner's question. I am trying to convert the
> original
> > >> dicom files to the format that can be recognized by SPM5. So I
> tried
> > >> using
> > >> spm_dicom_convert and spm_dicom_headers. However, the
> following error
> > >>
> > >> messages appeared:
> > >> >> spm_dicom_headers('003_0001');
> > >>
> > >> ??? Error using ==> fread
> > >> Out of memory. Type HELP MEMORY for your options.
> > >>
> > >> Error in ==> spm_dicom_headers>decode_csa2 at 508
> > >> t(i).item(j).val = fread(fp,len,'*char')';
> > >>
> > >> Error in ==> spm_dicom_headers>decode_csa at 425
> > >> t = decode_csa2(fp,lim);
> > >>
> > >> Error in ==> spm_dicom_headers>read_dicom at 100
> > >> dat = decode_csa(fp,tag.length);
> > >>
> > >> Error in ==> spm_dicom_headers>readdicomfile at 66
> > >> ret = read_dicom(fp, 'il',dict);
> > >>
> > >> Error in ==> spm_dicom_headers at 25
> > >> tmp = readdicomfile(P(i,:),dict);
> > >>
> > >> %% Here, '003_0001' is a dicom file. I am using SPM5 on Matlab
> R2007b
> > >> with 1G RAM
> > >>
> > >>
> > >> Thanks!
>
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