External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
Oh boy, a w file! What if you give it the extension .mgz?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 5:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
External Email - Use Caution
Alas, it works!! And it is converted to an overlay, so Ruopeng please disregard my earlier question. Thank you so much for all your invaluable advice, Bruce.
My final question is for Doug, related to converting a FWHM of 3 mm to # iterations of nearest neighbour for ‘mris_spherical_average -prior.’ In the attached image, I used 9 iterations but I am not sure if this is what would be recommended.
Thank you all!
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: May 20, 2021 7:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] blurring average label files
Oh boy, a w file! What if you give it the extension .mgz?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 5:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
Hi Kristi,
I think the color scale bar only sync with overlays, not labels. I will change that.
Best Ruopeng
On May 20, 2021, at 3:22 PM, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: May 20, 2021 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Subject: Re: [Freesurfer] blurring average label files
External Email - Use Caution
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce -
Kristi Drudik -
Wang, Ruopeng