From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce
Sent: February 26, 2021 12:14 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcal probability maps

 

Hi Bruce,

 

Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.

 

Best,

Kristi 

 

 

Sorry, it doesn’t have the greatest help 😊

 

mris_spherical_average

usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>

where which is one of

            coords

            label

            vals

            curv

            area

 

so something like

 

mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>

 

 

 

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Hi Bruce,

 

Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?

 

Best,

Kristi 

 

 

Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?

 

Cheers

Bruce

 

 

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Hi Doug,

 

That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).

 

Best,

Kristi 

 

 

what do you mean by painted? Do you mean you drew them on there using FreeView?

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Hi Doug,

 

The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.

 

Best,

Kristi 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: February 19, 2021 10:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulcal probability maps

 

What format is your sulcus in?

On 2/16/2021 2:38 PM, Kristi Drudik wrote:

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Good afternoon,

 

I hope this email finds you well.

I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). 

To obtain these probability maps, I:

1. Painted the sulcus of interest on the surface by creating a .label file.
2. Registered this .label file to fsaverage (mri_label2label)
3. Converted the .label file to vol (mri_label2vol)
4. Converted it to a surface file (mri_vol2surf)
5. Concatenated the data to create an average (mri_concat --mean)
6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)

Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?

Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?

Thank you very much for your time and help. Please let me know if you have any questions.

Best,
Kristi   

 

                                                                

Kristi Drudik 

Ph.D. Student, Clinical Psychology

 

Montreal Neurological Institute 

McGill University 

Montreal, Canada 

 

 

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