I am not sure the below message went through as I did not get a confirmation
from this am so I am resending. Sorry if this is duplicate
Thanks for the responses John, Daniel, and Marko
This helps and John, I read through your other responses to yesterday's
e-mails
John.
To sort out what to do next, my questions now are how does mutual information
coregistration work? I know that it
is heavily based on shape (right?) but I can't quite understand how it works
from the spm5 manual or its references.
How does the coreg process handle epi distortion / signal dropout between T1
and BOLD-fMRI where there is info in one image and not in another
How does the coreg differ from just coaligning two binary masks (is there
segmentation in the routine)?
If I wanted to normalize using the strucural, why couldn't I just use reorient
to match up the first epi image volume with a skull-stripped structural
acquired with the same exact dimensions a few minutes earlier and then use a
skull-stripped structural to get normalization parameters.
This way I would avoid the problem of epi artifacts with coregistration. Does
this logic sound faulty?
Somehow I have to make sure that the epi distortion won't interfere
with either
aligning the t1 to epi or the normalization process, correct?
Thanks a lot,
Sincerely
Jeff
Jeffrey P. Lorberbaum, MD
Assitant Professor of Psychiatry
Penn State Herhsey Medical Center
Quoting "Ashburner John (PSYCHOLOGY)" <[log in to unmask]>:
>
>
> (1) Is there a way to get rid of epi distortion post-processing without
> a field map
>
> It would be nice if there was a method for doing this in SPM, but I'm
> afraid there isn't.
>
> (2) Am I stuck with spatially normalizing the epi images to the epi
> template
> using some masking of distorted regions?
>
> No, but I would suggest you check out one of the emails I sent to the
> list yesterday.
>
> (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 expect (b) to work much better than (a), but if you are using
> SPM5, then the Segment button should do a reasonable job. You could
> also try spatial normalization via segmentation of your EPI data. I
> don't know how well this is likely to work though.
>
>
> (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))
>
> I'm afraid not.
>
>
> Best regards,
> -John
>
>
----- End forwarded message -----
----- End forwarded message -----
|