Hi Jeff,
> This ventricular activity occurs within some subjects and at a group level
> (n=40). Within-subjects, the spatial normalization comparing the mean epi
> normalized image to the epi template looks generally good to my eye using check
> reg and surfing at different points in the brain although though the images are
> obviously blurry.
If you do a check_reg on the normalized, non-smoothed images, do they
line up ok? With this group size, one or two normalizations gone astray
may do a lot of harm.
> (1) Is there a way to get rid of epi distortion post-processing without a field
> map
You can account for epi*movement disortions with realign and unwarp, but
as the epi-distortions themselves are due to the acquisition mode this
will be more difficult. I am not aware of an approach allowing this
without referring to a measured fieldmap.
> (2) Am I stuck with spatially normalizing the epi images to the epi template
> using some masking of distorted regions?
I don't think so:
> (2) Should I co-register structural and epi images to each other even though
> there is epi distortion in the OFC and spatially normalize:
> (a) the structural to the structural template
> or
> (b) gray matter template to gray matter template
I would go with the latter option: if you segment the T1 (which I
presume you have) and coregister the gm to a mean epi, the distortions
should not influence the results too much as coregistration is a global
matching only (your voxel size may be a problem, though). I tend to use
the epi as the target so that they are not moved around too much but you
can also do it the other way around and take all other epis with you
(coregister only, not reslice).
> (3) Is there a way to mask out distorted areas in coregistration (if I were to
> coregister structural and functional images) and then do #2))
See above. I have never looked into masking for coregistration as no
regional matching is done so I don't even know if the option exists.
Best,
Marko
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
=====================================================================
|