In principle, there is a new form of multi-slice DICOM, which could be used.
I don't think it is yet supported by all scanner manufacturers, and it would
require some modifications to SPM so that it could deal with it. This
approach is likely to be the future though.
Best regards,
-John
On Tuesday 31 March 2009 16:24, Steven Liu wrote:
> Dear Torben:
>
> You are right, if each slice has its own DICOM file, there will be
> too many DICOM files for a long fMRI series and then we will have
> problem when using SPM_DICOM_Convert, that is it! But this is the
> way how the scanner works and it generates the DICOM files, each file for
> each slice, right?. So, can we set up the scanner so that it generates
> DICOM
> files in the way: each file for each volume? I really do not think that
> it is very necessary
> to generate each DICOM file for each slice.
>
> Steven
>
>
>
> 2009/3/31 Torben Ellegaard Lund <[log in to unmask]>
>
> > 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!
|
