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SPM  March 2009

SPM March 2009

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Subject:

Re: spm_dicom_headers, OUT OF MEMORY?

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Tue, 31 Mar 2009 20:47:36 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (320 lines)

That's correct, but we do eventually hope to support multi-slice. I'm not
really sure why you were getting the out of memory problem though.

Best regards,
-John

On Tuesday 31 March 2009 20:17, 鲍敏 wrote:
> 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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