It's an empirical relationship based on the number of iterations
needed to get a delta function to look like a gaussian of a certain
FWHM. You can still specify the number of iterations with --nsmooth. See
the --help.
doug
On 8/5/10 5:34 PM, Xinian Zuo wrote:
> 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
>>
>>
>
>
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