Yes to your first question.
Regarding your second question: do the brain structures line up properly, or
are there displacements? If the brain structures line up properly you can
safely ignore any effects on the image rim.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Anastasia A Ford
Sent: Thursday, January 08, 2009 12:49 PM
To: [log in to unmask]
Subject: Re: [FSL] T1 to b-zero registration for tractography
Matt,
Thank you for your reply.
I am not sure I understand your suggestion entirely. You say that I should
first register my T1 to the MNI 2 mm using FNIRT and then use applywarp to
the original T1 using MNI 1 mm template as reference and the transform that
I got from FNIRT for the 2 mm MNI?
Also, I tried registering eroded FA to cropped FOV T1 using the
configuration that Jesper has provided and The FA image still seems to be
stretched beyond the volume of the T1. I attached a screen shot of the
images, where the red/yellow underlay is the eroded FA registered to T1 and
T1 is the overlay. You mentioned previously that if FLIRT does not work (if
FA is stretched beyond the borders of T1), then my data must have some sort
of non-linear distortions that could be handled by FNIRT. If the fnirted FA
is still stretched does that suggest that the distortion is too drastic for
FNIRT? How would this distortion be manifested?
Thank you,
Anastasia
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