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-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
> <gr...@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-boun...@nmr.mgh.harvard.edu 
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
>> <gr...@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.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg&m=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ&s=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M&e=
>> --
>> 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: 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg&m=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ&s=dNTiTZM2k4H_ZFSLvXIpaHUFlf2j9OsxSfiZbdVVy1Y&e=
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: 
>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg&m=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ&s=-MNH1l23vgFGiXhqvaJyfT33Qag5-ddnxlYIHUU99W0&e=
>>
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>> Freesurfer mailing list
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
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>> HelpLine at
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>>
>>
> --
> 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: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg&m=aMym90RXPTRXUjS44fWDifC3lOBmvpC_rC-M7He_Z1k&s=8tEPQ3dGqFz_yFHfi3eLzBFZeLVSlnzJ29N9tWAiLxg&e=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg&m=aMym90RXPTRXUjS44fWDifC3lOBmvpC_rC-M7He_Z1k&s=Dx8USv0Xlng8Xa5wVfJEiTv7vhPY1SgdlPTeoBTIjR4&e=
>
> _______________________________________________
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>
>
> The information in this e-mail is intended only for the person to whom it is
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
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>

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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