Dear Michael,
Thanks for your reply. We've got a Siemens Skyra, running VD11, and we converted our
data using dcm2nii (April 2011 version).
Any idea what might have gone wrong?
Best wishes,
Priscila
Hello Priscila,
Was your diffusion data obtained by any chance on a VB17 platform using
the CMRR MB sequence with the polarity inverted via the check box on the
Sequence/Special tab? If so, it has recently come to light that a bug
exists with the VB17 version such that the reported diffusion directions
are inverted between the blip-up, blip-down acquisitions, even though the
actual directions were not.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 4/29/13 9:09 AM, "Jesper Andersson" <[log in to unmask]> wrote:
>Dear Priscila,
>
>> Hello. I have been asked to analyse a set of diffusion data and to do
>>so I have been following the topup steps on the fsl website. I have come
>>to the stage of "applytopup" and I am unsure about ordering of the data
>>and the corresponding acqparams.txt file. I have been told that the data
>>were acquired in 2 series, the first with blip down (A->P) and the
>>second blip up (P->A), phase encoding was in the y-direction. Is this
>>the correct way to interpret this?
>>
>> My acqparams.txt file looks like this:
>> 0 -1 0 0.065
>> 0 1 0 0.065
>>
>
>You should use the same acqparams.txt file for applytopup as was used for
>topup. The data should be organised such that all volumes in a file
>pertains to the same row in acqparams.txt.
>
>I think that this page
>https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplyto
>pup
>explains it reasonably well.
>
>
>> I also wondered whether having .bvec files with opposite sign (+/-)
>>indicates that the data has not been collected using identical
>>protocols. I understand that the numbers stored in the 2 .bvec files
>>associated with each series correspond to the x, y and z components for
>>each diffusion direction, but when I look at the values they differ in
>>sign between the 2 series.....
>>
>
>It does indeed sound as if your diffusion vectors are different for the
>two acquisitions. If you don't want do run eddy, i.e. if you rely on some
>other tools for movement and eddy current correction, that is not a
>problem. The diffusion signal is expected to be identical for v and -v
>(where v is a diffusion vector) so there is no problem with pooling the
>data and using either of the bvec files.
>
>However, if you want to run eddy that is NOT a good situation. What you
>want for eddy to work is data with the same/similar diffusion signal but
>different distortions. This can be achieved by sign-swapping either the
>phase-encode direction or the diffusion-gradient direction. BUT if you
>swap both you have effectively swapped the distortions twice leading to
>similar/identical distortions in the two images and then there is no
>differential signal to drive the correction.
>
>Jesper
>
>
>> e.g. file1.bvec
>>
>> 0 0.99999934 0 0.3456666666
>> ........
>> 0 ........
>> ........
>> 0 ........
>>
>> e.g. file2.bvec
>>
>> 0 -0.9999956 0 -0.3456670000 <- same magnitude, different sign
>> ........
>> 0 ........
>> ........
>> 0 ........
>>
>> According to the applytopup help page, once I have used it I will be
>>left with a single set of images, but which bvec file should I use?
>>
>>
>> I would really appreciate your input on this.
>>
>> Thanks in advance,
>>
>> Priscila
>>