Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

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]

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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

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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

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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

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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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Postdoctoral position open at the University of Geneva
by federica ribaldi 17 May '21

17 May '21

External Email - Use Caution Dear Freesurfer users, Prof Garibotto’s group, Laboratory of Neuroimaging and Innovative Molecular Tracers ( https://secure-web.cisco.com/1f690DlehlIiGMbMNMyi9vyUen43cL9dNElX6oldhDASYv…) University of Geneva, Switzerland has an open postdoctoral position to contribute to the scientific research in the field of Alzheimer’s Disease (AD) and cognitive disorders, focusing on clinical and neuroimaging analyses (mainly PET and MRI) combined with genetic and biofluids data to define and model disease characterization and progression. More information about our group, the call and application link can be found here: https://secure-web.cisco.com/1POXw5qHPPSUhfiRwFc3DD62M6qjUjqrAu1zkbeJ3GIvI2… Feel free to distribute this announcement to potentially interested people. Best, Valentina Garibotto

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Sulcus represented in wm.mgz filled in lh.white
by Dierker, Donna 17 May '21

17 May '21

External Email - Use Caution Hi freesurfer experts, I have some cases where sulci near the occipital pole are reflected in the wm.mgz, but are filled in the white surface. Attached is a capture showing the sulcus near the image center, where the crosshairs are located. Might the topology fixer have filled in this sulcus, to reduce topological errors? This was generated using recon-all -all, freesurfer 6.0, ubuntu 18.04.3. Thanks, Donna ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Overlay of MGH clusters on Broadmann atlas
by Romanella,Sara (BIDMC - Wilkinson - Neurology SF) 16 May '21

16 May '21

Hi FreeSurfer community, I have a cluster.mgh file (along with the .annot and .summary) resulting from correlation analysis of cortical thickness in a group of patients. I can open it as overlay in freeview but I was wondering if there was any chance to overlay it to a Broadmann atlas (hopefully in freeview) so I can visually show the overlap of the clusters with the BA areas. I cannot seem to find a Broadmann atlas in fsaverage to open in freeview. Also I was wondering, if I want to convert .mgh and open it on Connectome Workbench what extension do you think I should use (e.g., .gii). Should I use mri_convert or mris_convert? I am not sure if .mgh should be converted as a surface. Thank you so much for your help! Sara ? Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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How to use atlas AAL3 label on Freesurfer?
by Diógenes Bispo 15 May '21

15 May '21

External Email - Use Caution Hi Freesurfer team I would like to know how I convert an AAL3 atlas label to the standard Freesurfer space. In addition, I would like to extract volume and cortical thickness from the subjects in this region of interest. I am using Freesurfer version 7.1.1. Atlas AAL3 (https://secure-web.cisco.com/1tq7UWlhNLqqLMlQ1A0WbA7mUYazrixorG3fe8eaD1j3rn…) Thanks. Diógenes diogenesdiego(a)gmail.com

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Freesurfer May 2021