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FSL  June 2012

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Subject:

Re: bvec/bval file error

From:

Michael Harms <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 22 Jun 2012 20:57:33 -0500

Content-Type:

text/plain

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text/plain (128 lines)

I'm not at all surprised that DICOM conversion software might need some
tweaks in the face of a new software platform (VD vs. VB).  MRIConvert
and dcm2nii should give the same results, so it is good that you are
comparing the two.  And the really important thing is that the bvecs for
oblique acquisitions need to be rotated.  If you want details for a way
to test this behavior, see the Word document that we put together at
Item 8 of Sample Datasets at
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

cheers,
-MH

On Fri, 2012-06-22 at 23:51 +0000, Joanne Lin wrote:
> Thanks Matt, Andreas and Michael for your advice - that's very helpful, I'll be sure to get in touch with Chris Rorden.
> 
> I'm just unsure as to a) why dcm2nii worked fine on all the previous datasets but not this one and b) why MRIConvert had no trouble.  But perhaps that's a question for Chris Rorden too.
> 
> Thanks again!!
> Jo
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Michael Harms [[log in to unmask]]
> Sent: Saturday, 23 June 2012 12:55 a.m.
> To: [log in to unmask]
> Subject: Re: [FSL] bvec/bval file error
> 
> The 0's in the bvecs are obviously a problem which the beta version will
> hopefully fix.  But the intent for both dcm2nii and MRIConvert, worked
> out for the Siemens VB platform, is that they rotate the bvecs from
> oblique acquisitions into the imaging axes.  There is a flag in dcm2nii
> that controls this behavior, and if you pay attention to its output it
> should be clear whether the bvecs have been rotated or not.
> 
> cheers,
> -MH
> 
> On Fri, 2012-06-22 at 00:41 -0500, Matt Glasser wrote:
> > For the Skyra I think you need to get a beta version from Chris
> > Rorden, the author of dcm2nii (who is not affiliated with fMRIB/FSL).
> > If your data still has a problem, I’m sure he would be happy to have
> > your data to figure out the fix.
> >
> >
> >
> > Peace,
> >
> >
> > Matt.
> >
> >
> >
> >
> > ______________________________________________________________________
> >
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> > Behalf Of Joanne Lin
> > Sent: Friday, June 22, 2012 12:26 AM
> > To: [log in to unmask]
> > Subject: [FSL] bvec/bval file error
> >
> >
> >
> >
> > Hi experts,
> >
> >
> >
> > I have a question about bval/bvec files derived from Siemens Skyra
> > images (VD11 I think?).
> >
> >
> >
> > I was happily using dcm2nii for all of our images and it was working
> > fine; however, it seemed go funny with today’s participant.
> >
> >
> >
> > The bval file looked normal (0 1500 1500…etc) until about two thirds
> > of the way through, where it gave me -1 -1 -1…until the end (from
> > about number 36-64)
> >
> >
> >
> > Similarly with the bvec file, it was normal for the first part, then
> > gave me a whole bunch of zeros from 37-64.
> >
> >
> >
> > The actual diffusion images look fine though.
> >
> >
> >
> > I put the same DICOM files through MRIConvert, just to see, and it did
> > not give me -1s or 0s at all but I noticed the first part of the bvecs
> > were not the same.  I have read through some posts about bvec files
> > from different conversion tools, and from my very broad understanding
> > (please correct me if I’m wrong!) it’s something to do rotating bvecs
> > for oblique acquisitions, but I still am not sure whether to stick
> > with dcm2nii or MRIConvert.
> >
> >
> >
> > What could have happened to my bvals/bvecs in dcm2nii today?  And why
> > would they behave so differently in MRIConvert?
> >
> >
> >
> > If I go ahead and use the ‘good’ bvals/bvecs from MRIConvert for this
> > participant, I assume that I should use the MRIConverted bvals/bvecs
> > for every participant – is that right?
> >
> >
> >
> > Any advice would be fantastical :-)!
> >
> >
> >
> > Cheers,
> > Jo
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >

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