fname is the name of the file you want to load for every subject (the label
file name in your case). Subject 1 is the FS id of the first subject you want
to load (followed by subject 2, ...)
cheers
Bruce
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kristi Drudik
<kristina.dru...@mail.mcgill.ca>
Sent: Friday, February 26, 2021 11:02 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution
External Email - Use Caution
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
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce
Sent: February 25, 2021 11:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcal probability maps
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>
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Kristi Drudik
Sent: Thursday, February 25, 2021 9:59 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
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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
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: February 23, 2021 8:09 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
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
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Kristi Drudik
Sent: Tuesday, February 23, 2021 2:30 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
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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
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Douglas N. Greve
Sent: February 23, 2021 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution
Hi Doug,
The sulci are .label format because they were painted directly on the surface
using FreeSurfer 7.1.
Best,
Kristi
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Douglas N. Greve
Sent: February 19, 2021 10:16 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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:
External Email - Use Caution
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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