What software was used to reconstruct the surface?
With freesurfer, there is an offset between the orig.mgz and the surface. And
depending on many factors, you might have to flip/rotate the surface to be in
the same orientation as the volume (or bring the volume to the surface).
See this thread:
http://www.mail-archive.com/caret-users%40brainvis.wustl.edu/msg02081.html
Also see the "Check Alignment between Normalized Volume and Surface" section
here:
http://brainvis.wustl.edu/help/pals_volume_normalization/spm5_normalization_pals.html
Examining the surface contour overlaid on the volum in volume view All is often
very enlightening.
On Aug 11, 2015, at 4:42 AM, j...@nbrc.ac.in wrote:
>>
> yes, ours is an individual s surface reconstruction, and so we checked the
> registration in spm8( using anatomical image used for reconstruction and
> the functional image volumes used for mapping), where the volumes are
> coregistered properly, but shows anomaly in caret.
>
> thank you
>
>
>
> This almost always is because the functional volume is not
>> stereotactically registered to the anatomical volume used to generate the
>> fiducial surface. Is this an atlas surface (e.g., one of the PALS mean
>> midthickness surfaces), or is it an individual's surface reconstruction?
>> If atlas, this could happen if you were trying to map SPM functional data
>> to the AFNI mid thickness surface, for example, because there are
>> noticeable differences between those stereotaxic spaces.
>>
>> If individual, make sure the functional volume is in register with the
>> anatomical volume used to generate the surface.
>>
>>
>> On Aug 10, 2015, at 1:40 AM, j...@nbrc.ac.in wrote:
>>
>>> Hi,
>>> when i map the functional data onto caret fiducial surface, it appears
>>> that the mapping is shifted in rostrocaudal axis, caudally, by about 2
>>> -3 mm. anyone has idea what could be possibly wrong here?
>>> thanks,
>>> john
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>>
>>
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>>
>
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