Bruce Fischl wrote:
> Hi George,
>
> I'll leave this for Doug. I think the more standard stream is to use
> mri_vol2surf to sample your fMRI volume onto the surface. It has
> explicit parameters that control how you sample, but again once you've
> sampled it you can display it on *any* surface and it will look the
> same (white, pial, inflated, etc...)
>
> cheers,
> Bruce
>
>
> On Tue, 5 Feb 2008, George He wrote:
>
>> Hi Bruce,
>> Thanks for your reply. The command I used to visualize is:
>> tksurfer SUBJID rh inflated -overlay
>> allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz
>> \
>> -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \
>> -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot
>> what is the option to make the overlay displayed, say, on the pial
>> surface,
>> or on the face that is at the middle of the pial and the white surface?
>> (I don't see a sampling option in tksurfer help.)
>> George
>>
>>
>> On Feb 5, 2008 3:17 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi George,
>>>
>>> there are two different questions here: (1) what anatomical boundary
>>> does
>>> each surface represent, and (2) how do you sample functional data onto
>>> the surface. For (1) the pial surface is indeed the boundary between
>>> gray
>>> matter and CSF, but for (2) once you choose a sampling strategy
>>> (anywhere
>>> from gray/white out to pial) the fMRI data can be displayed on any
>>> of the
>>> surfaces simply as a visualization. Is that clear?
>>>
>>> Bruce
>>>
>>>
>>> On Tue, 5 Feb 2008, George He wrote:
>>>
>>>> Hi freesurfer experts,
>>>> It seems to me the pial surface should be the surface of gray matter,
>>>
>>> but
>>>
>>>> when I overlay functional activations on it, it seems to be surface of
>>>
>>> white
>>>
>>>> matter.
>>>> The reason I think so is that when I load the same activation in both
>>>> tksurfer and tkmedit,
>>>> if I click on an activated area (or any point) on the pial surface in
>>>> tksurfer, save it, and load it in tkmedit, the point will land on the
>>>> yellow/green lines while the tksurfer and tkmedit show the same
>>>
>>> talairach
>>>
>>>> coordinate for the point.
>>>> If I click on a point that is on the red line in tkmedit, save it, and
>>>
>>> load
>>>
>>>> it in tksurfer, they (tkmedit and tksurfer) show different talairach
>>>> coordinates for the points.
>>>> Question: what is the truth and what should I expect?
>>>> Thanks,
>>>> George
>>>>
>>>
>>