On Feb 6, 2008 2:07 PM, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

George He wrote:
Hi,
suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up?

In theory, just the stuff in the middle, though usually the voxel size is so big that it gets both surfs. You can also use --interp trilinear to interpolate. You can also use --projfrac-avg to average across the ribbon.

what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ?

It will sample outside of the brain.

doug

Thanks,
George

On Feb 6, 2008 1:33 PM, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

Yea, tksurfer does not allow you to control the sampling distance. To do
this, use mri_vol2surf

doug

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
>>>>
>>>
>>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting