You need to make a transformation matrix that describes the transformation
from standard to diffusion space. Probably the best way to do that is to
coregister your DTI b0 to standard space:
flirt -in <b0File> -ref <standardFile> -omat <diff2standard.mat> -out
<b0File2StandardFile>
Then verify that your coregistration was good by loading the
<b0File2StandardFile> on top of the <standardFile> in FSLView.
Then invert the matrix so you have one that does the transformation you
want:
convert_xfm -omat <standard2diff.mat> -inverse <diff2standard.mat>
Then you can apply the transformation matrix to your ROI, as you describe
below.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of David Roalf
Sent: Monday, August 13, 2007 5:43 PM
To: [log in to unmask]
Subject: [FSL] Coverting Standard Mask back to native space
I would like to take a mask created in standard (MNI) space and transform it
to native space using a b0 (DTI) image (NIFTI_gz file format). The FSL FAQ
recommends using the following to covert a mask from one space to another:
>> flirt -in standard_mask -ref highres -applyxfm -init
standard2highres.mat -datatype float -out highres_mask
then:
avwmaths highres_mask -thr 0.5 -bin highres_mask
I have tried this command and I am prompted with the error: Could not open
matrix file standard2highres.mat (and sure enough I don't have the tool in
my usr/fsl/local/bin folder, but I do have std2imgcoord). So I am unsure if
I simply do not have this correct tool or if I am doing something
incorrectly. I am running FSL 3.3 via Cygwin.
D. Roalf
Oregon Health Science University
Portland OR
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