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FSL  June 2007

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Subject:

Fugue within Feat

From:

Bradley Buchsbaum <[log in to unmask]>

Reply-To:

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

Date:

Wed, 20 Jun 2007 10:14:50 -0700

Content-Type:

text/plain

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text/plain (38 lines)

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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