There is sometimes an issue with DICOM sorters with those magnitude images.
Probably that is what is going on, and it doesn't have anything to do with
the images themselves.
Peace,
Matt.
-----Original Message-----
From: Julia Foecker [mailto:[log in to unmask]]
Sent: Friday, July 08, 2011 3:33 PM
To: FSL - FMRIB's Software Library
Cc: Matt Glasser
Subject: Re: [FSL] Unwarping with FUGUE
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
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