Dear spmers
John Asburner answered some my questions a few weeks ago about how coreg
works - ie/ based on joint histogram between two image volumes.
I think the following questions may help clarify things for me as I am
still confused.
I am still unclear how mutual information coregistration deals with
an epi volume that only has a partial brain and a full T1 image volume.
a-Does the coreg program ignore the regions somehow in the partial brain
volume as being out of the intersection of where the 2 brains best fit?
b- Is the problem with coreg's problem with epi distortion in part due to
geometric distortion with large enough intensities that have coherent
information so it tries to fit this info in with the T1 brain?
Thanks a lot,
Sincerely,
Jeff
Jeffrey Lorberbaum, MD
Assistant Professor of Psychiatry
Penn State University- College of Medicine
Hershey, PA
On Wed, 10
Jan 2007 [log in to unmask] wrote:
> Thanks for the responses John, Daniel, and Marko
>
>
> This helps and John, I read through your other responses to yesterday's
> e-mails
> John.
>
> My questions 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
>>
>>
>
>
>
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