Hi John,
I am the guy who first posted the message. Actually, the single dicom file that
I want to convert includes 16 slices at the same time point. I think it is a multi-
slice DICOM. So it seems SPM cannot handle this format currently?
Cheers,
Min
>-----原始邮件-----
> 发件人: "John Ashburner" <[log in to unmask]>
> 发送时间: 2009-04-01 02:48:50
> 收件人: [log in to unmask]
> 抄送:
> 主题: Re: [SPM] spm_dicom_headers, OUT OF MEMORY?
> 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 鲍敏 <[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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