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 greve@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
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