Nice to know the gold standard, now going with the mri_vol2surf :)
One more question: As for the overlay surface smoothing option, in
tksurfer gui, I can set it by following ' tools -> surface -> smooth
overlay -> number of steps', or give an value to option ' --surf-fwhm
' in the command. What is the relationship between the two?
xinian
On Thu, Aug 5, 2010 at 2:13 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
> I'm not entirely sure how tksurfer is sampling from the volume to the
> surface. mri_vol2surf is the gold standard, so use that.
>
> doug
>
> Xinian Zuo wrote:
>>
>> Hey Doug,
>>
>> Following your suggestions, I ran the command below:
>>
>> mri_vol2surf --mov data.nii.gz --reg
>> ${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
>> ./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
>> --projfrac 0 --interp nearest
>>
>> but, seems the values in rh.test.vol2surf.mgh is different (little
>> higher) from what I got from tksurfer gui by saving overlay surface.
>> any thoughts?
>>
>> Thanks!
>>
>> On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> mri_vol2surf is the right command. Have you looked at the help for it?
>>> You
>>> can get it by running
>>>
>>> mri_vol2surf --help
>>>
>>> I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation.
>>> You can load the result directly into tksurfer to see if it looks the
>>> same.
>>>
>>> doug
>>>
>>>
>>> Xinian Zuo wrote:
>>>
>>>>
>>>> Dear surfers,
>>>>
>>>> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
>>>> surface in the way:
>>>>
>>>> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>>>>
>>>> , then save surface overlay as a mgh file. My question is, how can I
>>>> get the identical mgh data by using a command line without launching
>>>> the tksurfer gui? I found there is a command mri_vol2surf, but not
>>>> sure about these default settings in tksurfer gui. Really appreciate
>>>> it if some know and like to give your suggestions.
>>>>
>>>>
>>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>>
>>>
>>
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
--
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2485
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