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-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 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-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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