Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

Long_stats_slopes
by AJ 21 May '21

21 May '21

External Email - Use Caution Hi, Is there any way to run long_stats_slopes on the aseg.stats file on the total thalamic structure instead of separately as right and left. Many thanks. AJ

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Re: [Freesurfer] blurring average label files
by Kristi Drudik 20 May '21

20 May '21

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(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer(a)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-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 1:29 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Kristi Drudik <kristina.drudik(a)mail.mcgill.ca<mailto: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(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer(a)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-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 12:48 PM To: Freesurfer support list <freesurfer(a)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(a)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

3 9

Issue Pertinent To Freesurfer Usage
by Noyan Jawed 20 May '21

20 May '21

External Email - Use Caution Dear Freesurfer, I have downloaded the application but I am unable to run it. Can you please help me in resolving this issue? Regards, Noyan Jawed

2 2

Re: [Freesurfer] blurring average label files
by Kristi Drudik 20 May '21

20 May '21

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(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer(a)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-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 12:48 PM To: Freesurfer support list <freesurfer(a)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(a)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

2 1

blurring average label files
by Kristi Drudik 20 May '21

20 May '21

External Email - Use Caution 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

2 2

MEXFile error in thalamic nuclei segmentation script
by Hall, Thomas Edwin (teh1m) 19 May '21

19 May '21

External Email - Use Caution Freesurfer support, I have installed freesurfer on a Linux (centos 7.7) machine and used ' fs_install_mcr R2014b' to install the Matlab MCR. It runs 'segmentThalamicNuclei bert' successfully on that machine. I tarred up that installation and copied it to a Linux VM (centos 7.6), untarred it, and tried to run the same test but get the error show in the following screenshot. Both machines have gcc 4.8.5 installed. Do you know what is causing this error? The Linux VM does not have internet access so I could not use fs_install_mcr on that machine. Thanks, Ed Hall [cid:f8bd5c95-d297-4b58-914d-30502a04b3ba]

2 1

FreeSurfer error when running Hippocampal Subfields
by Joana Collet i Fàbregas 19 May '21

19 May '21

External Email - Use Caution Good morning, I am a Biomedical Engineering Student at Universitat de Barcelona and I am creating a python script that has a Watchdog which detects new patients in a specific folder, and we want it to run FS and Hippocampal Subfields. The FS runs properly, but when the script arrives to the Hippocampal Subfields command, it breaks. When using the FreeSurfer's Hippocampal Subfields from a python script after running FS recon-all right before, the processing is not performed due to the error shown in the attatched file. However, when running the Hippocampal Subfields from the terminal it does work. We have even tried to create a watchdog only for the Hippocampal Subfields, and when we move a folder obtained after running FS to a specific folder, it also runs properly. It is only when it is concatenated with FS that it does not work. We have contacted MathWorks Support, but they told us to reach you. The Matlab versions we have are Matlab_R2020a and Matlab_R2014b. Thanks a lot, Joana Collet

4 5

Freeview Update using MAC
by Erika Nolan 19 May '21

19 May '21

External Email - Use Caution Good afternoon, I downloaded Freesurfer 7.1.1 and am trying to open HCP .gii files in Freeview. I tried updating Freeview (https://secure-web.cisco.com/1veSBR5ECpngEulfhl0eWcwLxUmMQ4QR1JG2qWSdPD48G1…) using the instructions for MacOS but it fails: Mac 1. Go into your $FREESURFER_HOME and create a backup of your existing freeview app (this may require sudo access): cd $FREESURFER_HOME cp Freeview.app Freeview-backup.app 2. Download the dev, standalone freeview tarball from here<https://secure-web.cisco.com/1-rTW8L4qktbL8zcQ8YGBhA2846k3Po3bbKwIzxjkbPFAK…> 3. Untar freeview within your $FREESURFER_HOME (this may require sudo): cd $FREESURFER_HOME tar -xzvf /path/to/freesurfer-darwin-macOS_HighSierra-dev-freeview.tar.gz 4. IMPORTANT: If you are replacing freeview in a freesurfer release LESS than 7.0, then you must also remove the line "source $FREESURFER_HOME/sources.csh" from the $FREESURFER_HOME/bin/freeview script The tar file that downloads is " freesurfer-darwin-macOS-dev-freeview.tar" is this file correct? My Mac is a MacOS Sierra (not HighSierra), version 10.12.6. Is it possible for me to get a file that is compatible with my Mac? Thank you for your help!!! Erika

3 4

SUIT cerebellum parcellations
by Erik O'Hanlon 19 May '21

19 May '21

External Email - Use Caution Dear FS Experts, Just wondering if it's possible to use the SUIT labels in the LUT to obtain cerebellar quantification measures and also to make masks for tractography specific to each area? Thanks in advance Erik

1 0

C.Thickness: Statistical analyses with three groups
by Steve Petersen 19 May '21

19 May '21

External Email - Use Caution Dear Freesurfer experts, My goal is to compare the cortical thickness between three groups. For that purpose, I performed whole brain analysis with a F-contrast to evaluate a group effect. Since the F-test was significant, I performed pairwise comparisons to evaluate the direction of these differences. However, I noticed that some brain areas that are significant in one pairwise comparison (that are consistent with our hypothesis) were not significant in the F-test. I am a bit lost about how to proceed in this situation, can I report significant results in the pairwise comparison that were not previously significant in the F-contrast or do I need to perform the pairwise comparisons by applying a mask to the brain areas where there were significant results in the F-test? Apologies for asking this simple question, I am a beginner in statistical analysis with MRI data. Thank you very much for your help. Best regards,

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