Oh boy, a w file! What if you give it the extension .mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kristi Drudik
Sent: Thursday, May 20, 2021 7:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] blurring average label files
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Hi Bruce,
The output file from -priori saves as a .w which does not load as a label onto
fsaverage lh.pial (see attachment). Also, if I try to load this .w file as a
surface, freeview crashes. This is why I thought I should be looking at the
overall output of mris_spherical_average with -prior flagged.
Ruopeng – do you have an ETA as to when the color scale bar will be updated to
work for labels as well? i.e., would you recommend I wait for an update or
attempt to convert this averaged label to an overlay?
Thank you all!
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: May 20, 2021 5:08 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
Did you load the output file from -prior (not the overall output of
mris_spherical_average)? Also, 9 is a pretty small amount of smoothing.
Probably like a fwhm of 1-2 mm or something
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 3:53 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
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Hi all,
Bruce – please notice that the maps do not change no matter the number of
iterations I apply. Why would this be?
Ruopeng – any advice on how to display the colour bar according to the heat map
of the average label would be great
Doug – any advice on how to convert a FWHM of 3 mm to # iterations of nearest
neighbour for this specific command would be great
Thank you all for your time and advice.
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: May 20, 2021 3:22 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
I defer to Ruopeng for the 2nd question. And for the first Doug knows the exact
formula to go from iterations of nearest neighbor smoothing to fwhm. It goes as
the sqrt, so fwhm ~ sqrt(niters) I believe.
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 3:18 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
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Hi Bruce,
Thank you! Regarding the number of iterations for this command, what type of
smoothing does this command execute? My experience is with mris_fwhm which
applies one pass with a Gaussian smoothing kernel of 3mm diameter. So I am
wondering, what smoothing does mris_spherical_average perform and how many
iterations I should be aiming for?
Also, in addition to the “heat scale” pull-down menu, is there a way to display
this heat scale with a colour bar with the min and max levels? When I click
colour bar in the toolbar, it doesn’t not sync with the heat scale (see
attachment).
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: May 20, 2021 2:15 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
Almost. -prior takes two parameters. The second is the file name to write the
results to.
In freeview near the label panel there is a “color” pull down menu. You can
change that from solid color to heat scale
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 2:04 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
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Hi Bruce,
Thank you very much! Apologies for my simple questions but just to clarify:
In Freeview, where do I select to show the p-vals instead of the binary level?
Also, how would the entire command be listed with the required flags? Would it
be something along the lines of
mris_spherical_average -prior <iterations> -o fsaverage <which> <fname> <hemi>
<spherical surf> <subjects…> outputname
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 1:35 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
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<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 1:29 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Kristi Drudik
<kristina.dru...@mail.mcgill.ca<mailto:kristina.dru...@mail.mcgill.ca>>
Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
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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
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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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