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 file with 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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

It worked perfectly, thank you!!

________________________________ 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 1:22:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question on surface analysis

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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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