The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is your tkmedit command? doug
On 04/05/2012 06:04 AM, René Besseling wrote:
Hi Doug,
I'm using tksurfer to visualize the surface maps; this looks OK for both the original map overlaid on fsaverage and the mapped surface (generated using mri_surf2surf) overlaid on subj01. The mapping from surface to cortical ribbon also works well for fsaverage but goes haywire for subj01, see pics in attachment.
I noticed that mri_surf2vol gives different results when using different --template volumes. Why is that? I assumed that the --template image essentially provides the range of voxel coordinates to which the surface values can be mapped. In other words: when providing a template with a bigger field of view, I'd expect the center of the resulting output to look the same as the output generating when using a small FOV template. Does it matter whether you write your output as .mgz or .nii?
Best regards,
Rene
On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
How are you visualizing the results? Can you send a pic? You should be using tkmedit. doug On 04/04/2012 09:59 AM, René Besseling wrote: > Dear Freesurfer users, > > I've been trying to map a Qdec contrast sig.mgh to the native volume > of a subject using mri_surf2surf (to get from Qdec fsaverage surface > to native surface) and mri_surf2vol (to map from native surface to > native volume cortical ribbon). However, the last step goes wrong: I > get a nii with the same range of values as were in the surface, but > the nonzero voxels are scattered all over, so I guess there is > something wrong with the surface-to-voxel coordinate mapping. Below is > my code, any ideas on what goes wrong? > > Best regards, > > Rene > > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh > > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon > --identity sub01 --template subj01/mri/orig.mgz --o > sig_2subj01_volumetric.nii > > > _______________________________________________ > 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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Hi Doug,
Sorry, missed your reply. I assumed the --identity argument was used for looking up the surface-to-volume mapping somewhere in the predefined folder structure of this subject. Anyhow, my last command was
mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii
so I guess no transformation is needed since the surface is already in the proper space (that of subj01).
About my tkmedit command: I'm not using that. I usually visualize my results in Matlab, for the pics I send I used Freeview and tksurfer (so commands such as "mrview T1.mgz" and "tksurfer fsaverage lh inflated")
Best regards,
René
2012/4/5 Douglas N Greve greve@nmr.mgh.harvard.edu
The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is your tkmedit command? doug
On 04/05/2012 06:04 AM, René Besseling wrote:
Hi Doug,
I'm using tksurfer to visualize the surface maps; this looks OK for both the original map overlaid on fsaverage and the mapped surface (generated using mri_surf2surf) overlaid on subj01. The mapping from surface to cortical ribbon also works well for fsaverage but goes haywire for subj01, see pics in attachment.
I noticed that mri_surf2vol gives different results when using different --template volumes. Why is that? I assumed that the --template image essentially provides the range of voxel coordinates to which the surface values can be mapped. In other words: when providing a template with a bigger field of view, I'd expect the center of the resulting output to look the same as the output generating when using a small FOV template. Does it matter whether you write your output as .mgz or .nii?
Best regards,
Rene
On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
How are you visualizing the results? Can you send a pic? You should be using tkmedit. doug
On 04/04/2012 09:59 AM, René Besseling wrote:
Dear Freesurfer users,
I've been trying to map a Qdec contrast sig.mgh to the native volume of a subject using mri_surf2surf (to get from Qdec fsaverage surface to native surface) and mri_surf2vol (to map from native surface to native volume cortical ribbon). However, the last step goes wrong: I get a nii with the same range of values as were in the surface, but the nonzero voxels are scattered all over, so I guess there is something wrong with the surface-to-voxel coordinate mapping.
Below is
my code, any ideas on what goes wrong?
Best regards,
Rene
mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh
mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii
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-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Try loading it in tkmedit, something like:
tkmedit sub01 orig.mgz -overlay sig_2subj01_volumetric.nii
doug
On 04/12/2012 03:46 AM, René Besseling wrote:
Hi Doug, Sorry, missed your reply. I assumed the --identity argument was used for looking up the surface-to-volume mapping somewhere in the predefined folder structure of this subject. Anyhow, my last command was mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii so I guess no transformation is needed since the surface is already in the proper space (that of subj01). About my tkmedit command: I'm not using that. I usually visualize my results in Matlab, for the pics I send I used Freeview and tksurfer (so commands such as "mrview T1.mgz" and "tksurfer fsaverage lh inflated") Best regards, René
2012/4/5 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is your tkmedit command? doug On 04/05/2012 06:04 AM, René Besseling wrote: Hi Doug, I'm using tksurfer to visualize the surface maps; this looks OK for both the original map overlaid on fsaverage and the mapped surface (generated using mri_surf2surf) overlaid on subj01. The mapping from surface to cortical ribbon also works well for fsaverage but goes haywire for subj01, see pics in attachment. I noticed that mri_surf2vol gives different results when using different --template volumes. Why is that? I assumed that the --template image essentially provides the range of voxel coordinates to which the surface values can be mapped. In other words: when providing a template with a bigger field of view, I'd expect the center of the resulting output to look the same as the output generating when using a small FOV template. Does it matter whether you write your output as .mgz or .nii? Best regards, Rene On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: How are you visualizing the results? Can you send a pic? You should be using tkmedit. doug On 04/04/2012 09:59 AM, René Besseling wrote: > Dear Freesurfer users, > > I've been trying to map a Qdec contrast sig.mgh to the native volume > of a subject using mri_surf2surf (to get from Qdec fsaverage surface > to native surface) and mri_surf2vol (to map from native surface to > native volume cortical ribbon). However, the last step goes wrong: I > get a nii with the same range of values as were in the surface, but > the nonzero voxels are scattered all over, so I guess there is > something wrong with the surface-to-voxel coordinate mapping. Below is > my code, any ideas on what goes wrong? > > Best regards, > > Rene > > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh > > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon > --identity sub01 --template subj01/mri/orig.mgz --o > sig_2subj01_volumetric.nii > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- 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>
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Douglas N Greve -
René Besseling