Thanks, Andreas. That's a good point. I didn't think of that. So in the
ApplyXFM_gui, I should use str2diff.mat as the transformation matrix with
anat as the reference volume and just enter fdt_paths as the input volume,
right? Thanks for the input!
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library
To: [log in to unmask]
Sent: 1/2/2006 12:58 PM
Subject: [FSL] AW: [FSL] AW: [FSL] Calculating FA after probabilistic
tractograp hy
Hi,
why don't you want to proceed the other way around, i.e. transform the
mask into diffusion space by the inverse of diff2str.mat)? If you
transform the FA map, the interpolation may alter your FA values whereas
getting a binary mask in diffusion space should be straight forward.
Cheers-
Andreas
________________________________
Von: FSL - FMRIB's Software Library im Auftrag von Kristen Lindgren
Gesendet: Mo 02.01.2006 17:58
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] Calculating FA after probabilistic
tractograp hy
Hello. I have a quick follow-up question to your instructions on how to
calculate FA from probabilistic tractography. In previous e-mails, I
was
told to use the following commands to get this information:
avwmaths_32R pathway -thr <threshold> -bin -mul dti_FA FAmask
avwstats FAmask -M
However, I just realized that my masks for probabilistic tractography
(mode=twomasks_symm) were in anatomical space and not diffusion space;
therefore, I had to apply the diff2str.mat transform during probtrack.
Does this mean that I need to apply the diff2str.mat transform to dti_FA
before using the above commands? If so, are these the selections I
would
make?
Transformation matrix = diff2str.mat
Input volume = dti_FA
Reference Volume = anat (T1 image that was used for registration), based
on
existing volume
Thanks for your help. Hope you had a great holiday!
Kristen
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