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Because of the magnitude image...the first two rows look weired. But if I understood you correctly I can use this image and run the FUGUE analysis in FSL without doing any additional analysis on these images, right? Thanks for your comments, Julia On Fri, 8 Jul 2011 15:22:42 -0500 Matt Glasser <[log in to unmask]> wrote > It is better to keep communications on the FSL list. The standard Siemens > field maps sequence is gre_field_mapping, which is a gradient echo-based > sequence. The images you sent seemed fine to me, I'm not sure why you think > they are distorted. > > Peace, > > Matt. > > -----Original Message----- > From: Julia Foecker [mailto:[log in to unmask]] > Sent: Friday, July 08, 2011 3:18 PM > To: Matt Glasser > Subject: Re: [FSL] Unwarping with FUGUE > > Siemens Trio 3T MRI; > > MPRAGE sequence (TE=30, flip angle 90, Echo spacing: 0.7)... > Does this answer your question? > > > Julia > > > On Fri, 8 Jul 2011 15:06:06 -0500 Matt Glasser <[log in to unmask]> wrote > > > What scanner did you acquire this on, and what sequence did you use? > > > > Peace, > > > > Matt. > > > > -----Original Message----- > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > > Of Julia Foecker > > Sent: Friday, July 08, 2011 2:55 PM > > To: [log in to unmask] > > Subject: [FSL] Unwarping with FUGUE > > > > Hi, > > > > I would like to do the unwarping with FUGUE. I have the two images, a > > Fieldmap > > and the Magnitude image. > > > > FLS says: The fieldmaps required by FUGUE must be in undistorted > > coordinates. > > That is, the field map should not have any geometric distortion in it (or > > negligible amounts) as can be obtained from a spin-echo sequence, or > > gradient-echo sequences if the echo time is sufficiently small. The > > distortion > > present in a sequence can readily be seen in the absolute (or magnitude) > > image > > and normally manifests itself as a depression or extension of the inferior > > frontal lobes (when the scans are acquired axially - it is different for > > other > > acquisition planes). > > > > Actually, as seen from the magnitude image, there are geometric > distortions, > > in > > my fieldmap...however I do not know how to correct them. Is it still > > possible to > > correct them? > > And if so, how can I do this? Probably it would be easier if you can see > the > > image. Is there a possibility to send the image (in a word dok or pdf)? > > > > Thanks so much, > > Julia