Try to load the label on RhFFA_sphere.nii.gz in tkmedit to make sure they line up. And what space is your binary mask in? It needs to be in anatomical space to use with a label. It's a little crazy, but you can map it to anatomical space if you need to.
Emily Ward wrote: > Hi Doug, > > I've been running: > > mri_cor2label --c s105/rois/RhFFA_sphere.nii.gz --id 1 --l > s105/labels/RhFFA_sphere.label > > to generate my label from my nifiti file. And then putting it through: > > func2roi-sess -sesslabel RhFFA_sphere -s s105 -roidef > RhFFA_8rad_sphere -analysis repetitionAnalysis > > and viewing it like this: > > tkmedit-sess -s s105 -a repetitionAnalysis -c RhFFA_sphere -map mask -fthresh > .5 > > When I compare the label mask to the nifiti file, the label appears > much more inferior than the nifti file and has holes in it. Since this > is a sphere, it has a pre-specified number of voxels comprising it, > but when I run roisummary-sess, the number of voxels varies from > person to person. > > I just want an average beta value for all the voxels in the sphere for > the conditions in my analysis. Is there something I'm missing? > > Thank you, > > Emily > > > > > > > > > > > > On Wed, Feb 9, 2011 at 11:18 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > >> You have to make it work with func2roi-sess. One way to do this is to create >> a label file then use the -labelfile option to func2roi-sess. You can create >> a label from a binary mask with mri_cor2label. Spec "--id 1" >> >> doug >> >> Emily Ward wrote: >> >>> Hello, >>> >>> I am trying to get a summary of beta value activation for a hand-drawn >>> binary mask. This mask is a sphere, so it does not correspond to a >>> particular anatomical label or functional contrast. Is there any way >>> to apply roisummary-sess to this type fo binary mask (in nii or mgz >>> format)? If not, can I specify my mask as an roi so that the >>> roisummary-sess function will work? Or is there another command I >>> should be using to get a summary of beta values for a particular mask? >>> >>> Thank you, >>> >>> Emily >>> _______________________________________________ >>> 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 >> >> >> >> 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 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
