Dear Brad,
Most of the steps in the Fugue section of Feat are involved
with getting the registration between the EPI and fieldmap
right. For instance, the sigloss mask is only used to assist
in this registration process - it does not enter into the
actual undistortion itself. Hence, if you simply want to
apply the undistortion without registration then you should
have got good results with a simple Fugue call. If this was
not the case then there must be something else that needs
fixing.
As to the registration being off - that sounds quite dramatic.
It might indicate some other problem with the images. Can you
upload an example set of images (distorted EPI, fieldmap,
FM_2_EM.mat, undistorted EPI, etc) to our upload site?
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
(and don't forget to send us the reference number)
It would be very useful for us to see what is happening, and
hopefully there is a simple answer to why you are having
problems with both approaches.
All the best,
Mark
On 20 Jun 2007, at 18:14, Bradley Buchsbaum wrote:
> Hi,
>
> After playing around with Predlude and Fugue using the online
> documentation (and having only a little success) I decided to try
> using the Feat front-end. This produced much better results, probably
> because Feat does a number of things that are not discussed in the
> tutorial (e.g. masking with "sigloss", etc.). While the unwarping
> works much better within Feat there
> is still some disagreement between the anatomical images and the
> unwarped epis. One issue has to do with the alignment of the field
> map to the distorted EPI, which produces the transformation matrix
> FM_2_EF.mat. In our case the phasemap images are acquired just before
> the EPI sequence, so we expect these images to already be well
> aligned. But FM_2_EF.mat has a z-shift parameter of -12.0092, which is
> an implausible shift (this is a general problem we have using
> automated registration algorithms with our 4T epi data). Indeed, if I
> rerun FUGUE using the unregistered fieldmap, the results improve
> dramatically.
>
> I guess the answer is that I need to create my own script without the
> fieldmap-to-epi registration step, but the Feat script is quite
> elaborate and I'd like to avoid this.
>
> any suggestions?
>
> regards,
>
> Brad Buchsbaum
>
>
>
>
> --
> Bradley R. Buchsbaum
> Helen Wills Neuroscience Institute
> 210 Barker Hall, UC Berkeley
> phone: 510-642-2839
> email: [log in to unmask]
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