Here is a good thread on the subject
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;JtaMhg;20090727085433%2B0
100
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Dan Golding
Sent: Friday, May 07, 2010 6:09 AM
To: [log in to unmask]
Subject: Re: [FSL] Trouble reapplying flirt matrix
Hi Mark
-applyxfm is not appropriate for what I'm trying to do. The only reason I'm
trying to reapply the flirt xfm to t1 data is to fully understand the
conventions are coordinates etc that flirt uses.
I did my best to look through the past threads on the forum, I went as far
back as September. The closet I found to what you've described is
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;R%2FM5pQ;20090930081157%2
B0100 which doesn't really explain it.
Please could you either point me in the direction of the thread you were
referring to, or somewhere where I can better understand the flirt
conventions.
Also, I read in another post that flirt uses the first voxel's corner as a
center of rotation. I find that when I do it that way I get a blank image
out, but if I take the image midpoint as the center of rotation I get a
complete brain image, but not transformed quite correctly.
Any help on how I can manually apply the .mat file generated by FLIRT will
be greatly appreciated.
Thanks
Dan
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