RhFFA_sphere.label when loaded on functional data seems to correspond to RhFFA_sphere.nii.gz when loaded on anatomical data. When the label is just loaded on the nii.gz file, they seem to overlap, but if they are both overlaid on an anatomical image, the label is far superior to the nii.gz mask.
At this point, I am going to load nifit mask and the beta.nii file that corresponds to a particular analysis into matlab and calculate the average beta value for a particular ROI that way. There's a less guessing and I have better control over what I'm calculating. Thanks though! On Wed, Feb 9, 2011 at 1:54 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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
