"Nguyen, Thang Q" wrote:

Hello all,

I have a few questions that bassically address atlas maps in freesurfer. I understand that the freesurfer average atlas uses a customized manually traced atlas.

1. Are the subjects aligned to any canonical map when running an

mri_glm analysis?

They are aligned to the target subject (arg of --trgsubject). This is usually average7 ( a rep of the icosahedron).

2. If we have an fmri analysis through SPM, how can we ensure that

the fmri atlas and the freesurfer atlas are aligned properly?

Much of this is in the help for tkregister2 (see tkregister2 --help). Register the individual's functional to the individual's structural to create a register.dat. Then resample your activation map for each individual to the individual's surface, then run mris_glm. Note that this will not work if you've performed a non-linear registration and resampling from the individual's functional space to talairach space. Note that there's not really an fmri atlas involved. You register to the anatomical, then resample onto the surface, then mris_glm performs the intersubject registration.

3. Can we align the parcellation map to the MNI map and reparcellate

the subject?

Not sure what you mean here.

doug

Thanks for all of your help,

Thang

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