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FSL  August 2018

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Subject:

Re: AP-PA field maps to correct EPI distortion in DTI?

From:

"Glasser, Matthew" <[log in to unmask]>

Reply-To:

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

Date:

Wed, 8 Aug 2018 00:27:09 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (53 lines)

How about giving the details of your diffusion data and your field maps.
If they cover the same FOV, it should be possible if you have SE EPI
images with reversed phase encoding directions to compute the field with
topup (and then properly scale it in Hz).  Alternatively if you have
standard field maps and compute the field, those should work too.

Matt.

On 8/7/18, 12:13 PM, "FSL - FMRIB's Software Library on behalf of Josh
Robinson" <[log in to unmask] on behalf of [log in to unmask]>
wrote:

>FSL experts,
>
>We are trying to figure out if we can use EPI field maps collected for
>functional data to correct EPI distortions on DW data after running eddy,
>with the end goal of doing probabilistic tractography.
>
>Our DTI acquisition included one b0 at the beginning, along with 30 DW
>volumes, acquired A > P, no blip-up blip-down, thus running top up is not
>an option. We collected AP & PA fieldmaps intended for functional data,
>followed by 25 minutes of functional data collection, before collecting
>DTI scans for each participant, and we want to use these field maps to
>correct our diffusion data as well if possible. We used a Siemens scanner
>for our acquisition.
>
>Our MR physicist has advised against doing this, saying these field maps
>would introduce artifacts into our DTI analysis, but after reading other
>posts on the forum we think this would be a viable option? Our basic
>understanding is that after running eddy we could use
>fsl_prepare_fieldmap to prepare a magnitude image from the fieldmaps and
>register it to the b0 of our diffusion data, which would then be applied
>to the DW images. Would this be accurate?
>
>Any guidance would be greatly appreciated.
>
>Thank you,
>
>Josh
>
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