You can map the ROIs into fsaverage space as binary masks, then average them together, then binarize the average (you'd have to pick the threshold). You cannot give mri-glmfit mutliple labels, but you can merge the labels together (mri_merge_labels)
On 08/04/2017 03:13 PM, Sadie Marvel wrote:
Sorry, I meant that I would somehow want to merge all of these masks together into one. Not changing the values in the masks, but somehow combining them. Also, with the mri_glmfit --label flag, is it possible to have multiple labels listed (like one label per subject)? Sort of like a frame mask where we we want to take into account every subject's individual ROI label.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, August 3, 2017 4:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI labeling?
what do you mean by an average of the mask? Such an average would not be binary.
On 08/03/2017 04:30 PM, Sadie Marvel wrote:
And what if I wanted to compute just one ROI mask (for each region) that is an average of all the subjects individual ROI masks? ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, August 3, 2017 4:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI labeling?
If you are just going to use them as a mask for mri_glmfit, then you can just pass it as --mask or --label, no need to map it back to the individual (which you could do with mri_surf2surf)
On 08/03/2017 04:08 PM, Sadie Marvel wrote:
Hi again Freesurfers,
I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each subject's individual surface before creating labels for these ROIs, and if so, what would the registration file be to register the fsaverage space back to each subject's space? The goal of this is to be able to run mri_glmfit on just the spaces within these labels. Is there a better method? Also, each subject will have a different number of labels considering that not every ROI was present on every subject. will this be a problem when running glmfit?
​Thanks
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer