Hi,
I am trying to paint the functional significance map onto the surface generated from the antomical (monkey brain). What I am doing now is using the following command:
" tksurfer ${tmp_subj} ${hemi} ${cut_surface} -overlay /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii -overlay-reg ${reg_dir}/register.dat "
the "sig.256.reg.nii" is the significance map and "register.dat" is the transformation matrix.
It looks like that the commands are doing fine, I see the signicance map on inflated surfaces. However, I also see other tutorial that used mri_vol2surf to display the significance map. I wonder whether or not our method is not as good as mri_vol2surf.
I am asking this question also because we are creating ROIs from the surfaces. Now our ROIs (labels) are only corresponding to a very tight layer of voxels surrounding the white matter. Shall I use mri_label2vol to include all the graymatter voxels surrounding the label?
Any suggestions would be very helpful.
Yang
Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. You can also control the depth of projection with mri_vol2surf (eg, sample half way between the white and pial surfaces).
doug
Yang Liu wrote:
Hi,
I am trying to paint the functional significance map onto the surface generated from the antomical (monkey brain). What I am doing now is using the following command:
" tksurfer ${tmp_subj} ${hemi} ${cut_surface} -overlay /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii -overlay-reg ${reg_dir}/register.dat "
the "sig.256.reg.nii" is the significance map and "register.dat" is the transformation matrix.
It looks like that the commands are doing fine, I see the signicance map on inflated surfaces. However, I also see other tutorial that used mri_vol2surf to display the significance map. I wonder whether or not our method is not as good as mri_vol2surf.
I am asking this question also because we are creating ROIs from the surfaces. Now our ROIs (labels) are only corresponding to a very tight layer of voxels surrounding the white matter. Shall I use mri_label2vol to include all the graymatter voxels surrounding the label?
Any suggestions would be very helpful.
Yang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the quick reply. What the standard procedure to get a volume ROI from a surfaced defined ROI?
My solution is to create a label by filling a region in a closed path. Then is the next step to use mri_label2vol?
Yang
On Mon, Apr 18, 2011 at 1:15 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. You can also control the depth of projection with mri_vol2surf (eg, sample half way between the white and pial surfaces).
doug
Yang Liu wrote:
Hi,
I am trying to paint the functional significance map onto the surface generated from the antomical (monkey brain). What I am doing now is using the following command:
" tksurfer ${tmp_subj} ${hemi} ${cut_surface} -overlay /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii -overlay-reg ${reg_dir}/register.dat "
the "sig.256.reg.nii" is the significance map and "register.dat" is the transformation matrix.
It looks like that the commands are doing fine, I see the signicance map on inflated surfaces. However, I also see other tutorial that used mri_vol2surf to display the significance map. I wonder whether or not our method is not as good as mri_vol2surf.
I am asking this question also because we are creating ROIs from the surfaces. Now our ROIs (labels) are only corresponding to a very tight layer of voxels surrounding the white matter. Shall I use mri_label2vol to include all the graymatter voxels surrounding the label?
Any suggestions would be very helpful.
Yang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
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.
yes, that works. You'll probably want to fill the ribbon using the --proj option (something like --proj frac 0 1 .1)
doug
Yang Liu wrote:
Hi Doug,
Thanks for the quick reply. What the standard procedure to get a volume ROI from a surfaced defined ROI?
My solution is to create a label by filling a region in a closed path. Then is the next step to use mri_label2vol?
Yang
On Mon, Apr 18, 2011 at 1:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. You can also control the depth of projection with mri_vol2surf (eg, sample half way between the white and pial surfaces). doug Yang Liu wrote: Hi, I am trying to paint the functional significance map onto the surface generated from the antomical (monkey brain). What I am doing now is using the following command: " tksurfer ${tmp_subj} ${hemi} ${cut_surface} -overlay /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii -overlay-reg ${reg_dir}/register.dat " the "sig.256.reg.nii" is the significance map and "register.dat" is the transformation matrix. It looks like that the commands are doing fine, I see the signicance map on inflated surfaces. However, I also see other tutorial that used mri_vol2surf to display the significance map. I wonder whether or not our method is not as good as mri_vol2surf. I am asking this question also because we are creating ROIs from the surfaces. Now our ROIs (labels) are only corresponding to a very tight layer of voxels surrounding the white matter. Shall I use mri_label2vol to include all the graymatter voxels surrounding the label? Any suggestions would be very helpful. Yang ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.
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