Hi Kristi
You can change the display in freeview to show the p-vals instead of just the
binary label. Actually you can blur and write the output in
mris_spherical_average (undocumented) with:
mris_spherical_average -prior <# of iterative averages> <file name to write
blurred pattern to>
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kristi Drudik
Sent: Thursday, May 20, 2021 1:29 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Kristi Drudik <kristina.dru...@mail.mcgill.ca>
Subject: Re: [Freesurfer] blurring average label files
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Hi Bruce,
In that case, how would I tell the command “mris_spherical_average” to blur the
output? Also, how can I display the probability values in a colour scale?
Thank you very much!
Best,
Kristi
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, May 20, 2021 at 12:57 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
Hi Kristi
I don’t think it does any blurring unless you tell it to. The output should
reflect the actual alignment of those labels
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: Thursday, May 20, 2021 12:48 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution
Hi again!
On second thought, we are wondering if this averaged .label file was already
blurred during the mris_spherical_average command. If this is the case, do you
know what smoothing has been done and by how much? We are interested in seeing
the probability of each vertex after the average of the labels.
Thank you as always for all of your help!!
Best,
Kristi
From: Kristi Drudik
Sent: May 19, 2021 6:42 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: blurring average label files
Hello Freesurfer group,
I am using the command ‘mris_spherical_average’ to map and average a series of
label files onto fsaverage (I have created the label files manually by drawing
directly on subject surfaces in FreeView). This has allowed me to create a
surface probability map, where each vertex on the FreeSurfer fsaverage surface
is represented from 0% to 100% as belonging to my sulcus of interest (see
screenshot ‘.label’).
I would like to blur the data and load this blurred average as an overlay onto
the fsaverage pial. However, when I run ‘mri_label2vol’ followed by
‘mris_fwhm’, I lose the probability map and the average label is turned into
one large label (see screenshot ‘overlay’, where most of the map has 99%
overlap).
Would there be a way to blur this averaged label (obtained from
mris_spherical_average) with a similar command to ‘mris_fwhm’ but for label
files?
Let me know if you have any questions regarding the procedure. Very much
looking forward to your response and thank you for all your time!
Best,
Kristi
Kristi Drudik
Montreal Neurological Institute
McGill University
Montreal, Canada
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