 |
 |
Hi again, Thank you for your response. We do not have a pair of SE-EPI b0s (in opposite directions) so I guess I can only use eddy without topup. yes, or as I said, with a “traditional” fieldmap if you have one. If your version of eddy recognises the --field switch it means that you can. Just be aware that with a traditional fieldmap you have to register the field to the first volume in your diffusion data set yourself, and that isn’t alway trivial. Jesper Best, Mahmoud On Thu, Apr 27, 2017 at 1:59 PM, Jesper Andersson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Mahmoud, you don’t need opposing PE for the dwi:s. As long as you have at least a pair of SE-EPI (i.e. b0:s) you can run topup on those and feed that into eddy together with your single PE dwi:s. Even if you don’t have a SE-EPI pair you can still run eddy without the topup output. In that case eddy will still correct for eddy currents, subject movement and outliers, but the susceptibility distortions will not be corrected. I cannot remember of the current release allows you to feed a “traditional” fieldmap into eddy. If not it will be part of a soon to be released “patch” of eddy. Jesper On 21 Apr 2017, at 06:10, Mahmoud <[log in to unmask]<mailto:[log in to unmask]>> wrote: Thanks Matt! Is it also possible to use topup+eddy when there is no opposite PE for DWI? if yes, could you point out how? Thank you, Mahmoud On Fri, Apr 21, 2017 at 9:26 AM, Matt Glasser <[log in to unmask]<mailto:[log in to unmask]>> wrote: As long as the whole brain is covered you can still use them. Fugue can be used for this purpose and there are multiple postings in the archives detailing the commands. Peace, Matt. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Mahmoud <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Friday, April 21, 2017 at 7:59 AM To: <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] DWI susceptibility correction using B0 GRE field map Hello All, In thePNC dataset ( DOI: 10.1016/j.neuroimage.2013.07.064<https://doi-org.proxy.library.emory.edu/10.1016/j.neuroimage.2013.07.064>) the B0 field maps have been collected primarily for fMRI and with different slice thickness and matrix size (in-plane resolution) than DWI. I wonder under what condition we can use the B0 field maps to correct susceptibility distortion of DWI. Can someone please say what are the appropriate steps? Thank you! Mahmoud