Thank you very much, Doug!
On Fri, Aug 6, 2010 at 9:24 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
> 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
>>>
>>>
>>
>>
>
>
--
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
