If you have two binary masks, you can use mri_mask to compute the voxels that overlap in both

On 09/27/2017 01:48 PM, Yagmur Ozdemir 19 wrote:

Hello Dr. Greve,

Sorry for the late response; I thought my initial description was enough.

As far as I understand, the fMRI version of this code would automatically define an ROI based on cluster-extent based tresholding of functional data that contains the significant regions. Then loads a selected anatomical ROI(like a label) for comparison with this functional area, and I am not entirely sure how this comparison works but at the end outputs, I guess, an estimation of this area and produces an anatomical+functional "label." The anatomical label it uses comes from Freesurfer and I found this code in a website related to Martinos center (https://martinos.org/mne/stable/index.html) so I wanted to take my chances for asking about it here. I am basically looking for a way to define ROIs automatically in freesurfer.

Best, Idil ________________________________________ 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: Tuesday, September 26, 2017 12:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] generating automatic functional label

Hi Idil, I'm not going to plow through someone else's code:) If you want to summarize what it does, I might be able to figure out if we have something that does it.

On 09/25/2017 03:21 PM, Yagmur Ozdemir 19 wrote:

...

Hello FreeSurfer developers,

This is a piece of code I came across for producing a functional label with using time course estimates from MEG/EEG data, for freesurfer use. I am wondering if something similar is available to estimate a functional label/region from fMRI data with similar tresholding.

https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.ht...

Best, Idil

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