Can you run the following? mri_surf2vol --mkmask --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o surf-mask.nii tkmedit sub01 orig.mgz -overlay surf-mask.nii -fthresh .5
this should just create a mask of the rh surface in the volume. If this fails, then there's something wrong with the subject data. doug On 04/17/2012 03:43 AM, René Besseling wrote: > That gives the same scattered appearance as before, see attachment. So > I guess it's not a viewer issue. Maybe something to do with missing > header information of the original T1 scan? > By the way: strange that the overlay contains so many zeros; one would > expect (transparent) NaNs... > > Best regards, > > Rene > > > On Thu, Apr 12, 2012 at 7:38 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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>> > <mailto: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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel: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>> <tel: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> > <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> > <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>> > <mailto: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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer