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

-- 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/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.

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 greve@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 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

-- 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/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 greve@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