Ed,
We are also registering our datasets to the average 152_T1 (using flirt) and then
bringing them back into AFNI. Currently I have a script which brings these analyze
datasets back into AFNI, in MNI space.
First, we have a 1x1x1 mprage anatomy, converted to analyze, and registered with
flirt:
registering T1 (mprage) TO MNI avg152T1, output a matrix
applying matrix to T1, keep FOV of MNIavg152 space, but 1x1x1 resolution( use -
applyisoxfm 1)
Here is the to3d command line to do this:
to3d -prefix "subj"_T1_MNI_reg -session "path" -anat -view tlrc -xFOV 90L-92R -
yFOV 126P-92A -zSLAB 71.5I-109.5S -orient LPI "path" $subj"_T1_MNI_reg.hdr
Analyze volumes in MNI space are oriented as LPI, and thus need to be read into
AFNI that way. The offsets above are set to put a 1x1x1 dataset that has been
registered to the 152_T1 into AFNI, the origin set at the MNI origin of 90L 126P 72I
This is from the MNI colin27 dataset (one subject anatomy MNI 1x1x1) 90L 126P 72I
The FOVs for MNI space appear to be:
182x, 218y, 182z
Keep in mind that we are still playing around with this, but so far, it seems to work
fine. As an AFNI user, you already know that AFNI supports Talairach space, not
MNI space. So basically, we are dealing with the same issues; i.e, how to get
Brodmann areas, etc, out of a dataset in MNI space. I suppose many people have
grapled with the same issue, and I know that Matthew Brett has done some work in
that regard. I'd be interested to know what strategy you settle on. I am also
wondering how SPM users deal with this issue...
Tim Souza
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