mri_binarize and mri_segstats will work on any mgh or nii files. Note
that because something is an mgh or nii file does not mean it is volume
or surface based. Eg, if you
mri_convert lh.thickness lh.thickness.nii.gz
you will have a nifti file with number of columns = number of vertices,
1 row, and 1 column. So it looks like a volume in that it has columns,
row, and slices, but the underlying data is interpreted as a
surface-based map

On 5/22/19 12:33 PM, Barletta, Valeria wrote:
>
> That is a great solution, thank you!
>
>
> How exactly can I apply this whole thing to .mgh surface-based files?
>
> I cannot convert them to .nii and I think mri_binarize and
> mri_segstats work only on volumes.
>
>
> Thanks,
>
> Vale
>
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Wednesday, May 22, 2019 10:47:19 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] question on surface analysis
>
>
> On 5/22/2019 10:19 AM, Barletta, Valeria wrote:
>>
>> Dear Freesurfer,
>>
>> I have a surface file containing values of a cortical myelination
>> index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)
>>
>>
>> What I need to do is:
>>
>> - Masking the surface filewith the lesion mask, to create a new
>> lesion mask that contains the myelination index values from
>> rh.MS075_CME.mgh;
>>
> Try
> mri_mask rh.MS075_CME.mgh rh.surf_CL03.mgh rh.MS075_CME.mask.mgh
>>
>> - Assess the percentage (or also the absolute number) of vertices
>> that are under a certain threshold of myelination
>> index values whithin the new lesion mask.
>>
> You can use mri_binarize to create a mask of the myelination map (use
> --min and --max to spec the range), then use mri_segstats inputing the
> binarized mask with --seg and using --id 1. In the output summary file
> (--sum sumfile), the "number of voxels" will be the number of
> vertices; this could be modified to give the surface area instead.
>>
>>
>> What is the best way to do this?
>>
>>
>> Thank you,
>>
>> Vale
>>
>>
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>
>
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