Hello Irene,
> I have solucionated the DICOM import probelm with a script in Matlab.
It would seem that the errors you report argue otherwise...
> After doing 'Slice timing ' process in SPM8 , Matlab told me that my TR
> is 0.4 but it is 3.Anyway, I can cotinue processing the data.
Yes, but if spm assumes a wrong TR when doing slice timing, this will of
course effectively result in data corruption.
> In the nex step, REalign:Estimate & Reslice appears the following error
> an I can`t continue the data processing:
> "There is not enough overlap in the images to obtains a solution.
> Offending image:
> Users/......../as21476-0004-0001-00002-01.img
> Please check that your header information is OK. The Check Reg utility
> will show you the initial alignment between the images, which must be
> within about 4 cm about 15 degrees in order for SPM to find the optimal
> solution.
> *¿Any idea?*
Yes, you could try what spm suggests in the error message: use check reg
to see how far away the images are from each other. If you are looking
at consecutive fMRI images, then they should be fairly close to each
other - close enough, at least, to get them realigned, which is, as spm
states, about 4cm and 15 degrees. Not even the kids I scan move that
much :) so if this error appears, likely something is still wrong with
your data conversion routine, or you selected images from different
series, sessions, modalities, or subjects.
Hope this helps,
Marko
>
> > Date: Thu, 29 Mar 2012 15:41:11 +0100
> > From: [log in to unmask]
> > Subject: Re: [SPM] SPM8 Warning
> > To: [log in to unmask]
> >
> > That's a tricky one. I included all the solutions for the various
> > problem data I've encountered in the SPM DICOM conversion code. This
> > seems to be new one.
> >
> > When you do encounter problems with DICOM conversion, it may be worth
> > letting the mailing list know what sort of scanner the data came from.
> > Each manufacturer uses their own modifications to DICOM.
> >
> > Best regards,
> > -John
> >
> > On 29 March 2012 00:09, irene lerin labrada <[log in to unmask]> wrote:
> > > Hi!!!
> > >
> > > The problem is that ,after doing DICOM Import in SPM8, we only have the
> > > first slices of each volume(1,9,17,25...etc) so we are missing a lot of
> > > information to continue prepocessing the data. ¿Any solution?
> > >
> > > Thanks!!
> > >
> > >> Date: Wed, 28 Mar 2012 17:56:47 +0100
> > >> From: [log in to unmask]
> > >> Subject: Re: [SPM] SPM8 Warning
> > >> To: [log in to unmask]
> > >
> > >>
> > >> Normally, there are a series of numbers in the DICOM headers that can
> > >> be used to determine which DICOM files should be put together into the
> > >> same 3D volume. Some manufacturers (or sequence programmers - I'm not
> > >> really sure) don't set these fields in the header. Therefore, the
> > >> conversion routine needs to make an educated guess (which I think it
> > >> probably does quite well) about which DICOMs should be slices in which
> > >> NIfTI file.
> > >>
> > >> The message is only a warning that things may have gone wrong. I hope
> > >> that in most instances, all should be OK - but I can never be 100%
> > >> sure. I would suggest checking with your MR sequence developers to
> > >> see if the ordering of the slices into volumes makes sense, given the
> > >> information in the DICOM headers.
> > >>
> > >> Best regards,
> > >> -John
> > >>
> > >> On 28 March 2012 16:40, irene lerin labrada <[log in to unmask]> wrote:
> > >> >
> > >> > Hi!
> > >> >
> > >> > I am working with SPM8 and fMRI for my thesis.
> > >> > When I start the preprocessing of the data, in the fisrt step (DICOM
> > >> > Import)
> > >> > appears the following warning and i can't continue processing
> the data:
> > >> >
> > >> >
> > >> > " The AcquisitionNumber counter does not appear to be chanching from
> > >> > one
> > >> > volumen to another. Another possible explanation is that the
> same DICOM
> > >> > Slices are used multiple items. The conversation is having to
> guess how
> > >> > slices should be arrangeg into volumes "
> > >> >
> > >> > ¿Anyone had had the same problem?
> > >> > I have checked the headers and all of them are allright.
> > >> >
> > >> > Thanks!
> > >> >
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
____________________________________________________
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