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.
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.
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 greve@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 greve@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
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 greve@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 greve@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
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 greve@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 greve@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 greve@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 greve@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
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 greve@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 greve@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 greve@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 greve@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
Thank you very much, Doug!
On Fri, Aug 6, 2010 at 9:24 AM, Douglas Greve greve@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 greve@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 greve@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 greve@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 greve@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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Xinian Zuo