Hello,
I have two quick question:
1. in group analysis, example_func is the same for all copes right? It
is actually bg_image that is created by merging
/reg_standard/reg/highres images and then thresholding and averaging
them. And /reg_standard/reg/highres image is basically the "original
highres" (in subject space) image transformed into standard space?
2. If using non-corrected thresholding in post-stats (group analysis),
feat does not calculate any tal coordinates (the cluster coordinates).
How could we get tal coordinates for non-zero voxels in thresh_zstat if
non-corrected thresholding is used? I have come up with one method and
would like to know whether it is correct? Is there a simpler method?
to get tal coordinates for non-zero voxels in thresh_zstat image (for
group ananlysis):
1. dump the indices for nonzero voxels (afni tool):
3dmaskdump -mask thresh_zstat.hdr -o output.txt thresh_zstat.hdr
2. remove the 4th column from output.txt (output.txt has 4 columns -
3 indices and 4th is the z value);
3. use img2talcoord
img2talcoord -tal mni_standard -img example_func -xfm identity.mat
-vox -flirt output.txt > tal_coords.txt
where mni_standard is the standard brain used (fsl mni brain);
example_func is from the same cope directory as thresh_zstat
identity.mat is used since thresh_zstat is already is standard
space
and it is assumed that afni indexes voxels in the same way fsl does.
Thank you!
zrinka
Zrinka Bilusic-Vezmar
UCLA Brain Mapping
660 Charles Young Drive South
Los Angeles, CA 90095
310-794-5060
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www.brainmapping.org
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