Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Recon All
by Amar Shukla 21 Jul '22

21 Jul '22

External Email - Use Caution Dear Sir, I am a PhD scholar using the freesurfer tool to conduct my research work. I tested the recon all method in the Free Surfer, and it was effective with the data set that was used by me. What are the exact default parameters for the different processes of recon all that were used in motion correction, intensity normalization, etc?. It would be really helpful if you could provide me with the link or the article where it is explained clearly, this will help me to get through these processes in more depth and in a more constructive manner. Although the Free Surfer website has an FAQ regarding this process, there are no clear explanations about what the default parameters are during recon all. -- With Regards, Amar Shukla PHD Scholar UPES

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Screenshots in Freeview within a container
by Garikoitz Lerma-Usabiaga 21 Jul '22

21 Jul '22

External Email - Use Caution Hi! Is there any way to write freeview screenshots when running Freeview as part of a Docker container? thanks! Gari

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Re: [Freesurfer] volume group analysis
by Douglas N. Greve 21 Jul '22

21 Jul '22

The sig.table.dat has the sig values in it (ie, -log10(p)*sign). The gamma.table.dat will have the contrast values. These are NOT percentages but have the units of the input y table. On 7/20/2022 9:18 AM, Carolina Ferreira wrote: > External Email - Use Caution > > Hi, I'm using the asegstats table to run a group analysis and it worked. However I’m not sure what file contains the results. Is it the sig.table.dat? Are the numbers in there the percentage difference between the groups? > > Thank you > Carolina

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Cortical Parcellation stats
by Mohanad Arafe 21 Jul '22

21 Jul '22

External Email - Use Caution Hello, I am attempting to measure the gray matter volume (mm^3) of the insula. After getting all of my labels, I performed the following operations to merge the insula labels before computing the stats: mri_annotation2label --subject progr_120544 --hemi lh --outdir ./location mri_annotation2label --subject progr_120544 --hemi rh --outdir ./location mri_mergelabels -i lh.insula.label -i rh.insula.label -o insula >From here, I'd like to get the volume of the insula for the entire brain and not just in a specific hemisphere. When I looked at the mris_anatomical_stats command, it requires one to specify which hemisphere does the label contain to. However, the mri_mergelabels command merges both hemispheres. I am not sure where to go from here and seek advice. Thank you, Mohanad

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Pial surface edits question
by Grass, Diana 21 Jul '22

21 Jul '22

Good afternoon, I am working on the pial surface edits for this subject, and I found an overlap of the surfaces. I am attaching a picture for your reference. The point I am referring to is the one marked with the red cross at the bottom and center of the brain. What would you suggest doing in this case? Thanks in advance for your help. Best, Diana Grass PhD Student | Medical Engineering and Medical Physics Brain and Cognitive Sciences Harvard-MIT Health Sciences and Technology dgrass(a)mit.edu<mailto:ct24@mit.edu> | dgrass(a)mgh.harvard.edu | 973 816 6751 <tel:832.603.9175>

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VM password request
by Hannes Ruge 21 Jul '22

21 Jul '22

External Email - Use Caution Hi, I am trying to unzip the VM image. Could you please send the current passwort. And two additional questions: 1. are there plans to provide a docker v7.3 image in the near future? 2. are there plans to include freesurfer's subcortical segmentation capabilites (e.g. thalamus) into fmriprep? Thanks Hannes

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Re: [Freesurfer] Operating systems
by fsbuild 20 Jul '22

20 Jul '22

External Email - Use Caution Hello Andrew, I interpret the note on the freesurfer download page, When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). - to indicate some users may not be eager to switch to running Freesurfer on a different OS, or switch to a newer version of Freesurfer right away, e.g., built with different compilers, since it could change their analysis and/or ability to reproduce their results.   I would try to ensure such users have an option to continue to use the current OS and freesurfer version they have already used in their work. I believe the XSEDE cluster supports freesurfer running on both CentOS7 and CentOS8, https://secure-web.cisco.com/1GZkovhGWetTjyuKEvCub14Ijpzsusc0…  The IT infrastructure group supporting freesurfer has no plans I know of to migrate away from CentOS and some people are running CentOS8 stream. Most of the inquiries I see about using Freesurfer pertain to running freesurfer on CentOS/RedHat linux, Ubuntu linux, and other linux OS’s whereby the currently available freesurfer builds and .rpm .deb installer packages are compatible with theOS.  Apart from making use of the existing interoperability among the RedHat, Ubuntu, Debian, Fedora, SUSIE, etc. linux (and scientific) OS derivatives, I’m not aware of any plans to develop or test freesurfer on specific linux OS’s like the ones you mentioned. - R. On Jul 20, 2022, at 12:31, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com> wrote:        External Email - Use Caution        Hi FS development team,We are about to install an OS on one of our servers. We are trying to figure out what OS to use.  I see that FS 7.3 now is compiled for Ubuntu 20.0. Which is great. Will you mainly be supporting just Ubuntu in the future. Most supercomputers run Redhat which worked great when you compiled with CentOS. I was wondering if you are going to consider either rocky or almalinux. Both are distributions that came out of the ashes of centos which is why I ask. Aaron Tanenbaum_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Operating systems
by Aaron Tanenbaum 20 Jul '22

20 Jul '22

External Email - Use Caution Hi FS development team, We are about to install an OS on one of our servers. We are trying to figure out what OS to use. I see that FS 7.3 now is compiled for Ubuntu 20.0. Which is great. Will you mainly be supporting just Ubuntu in the future. Most supercomputers run Redhat which worked great when you compiled with CentOS. I was wondering if you are going to consider either rocky or almalinux. Both are distributions that came out of the ashes of centos which is why I ask. Aaron Tanenbaum

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Jobs at Northwestern’s Alzheimer’s Disease Center
by Adam Martersteck 20 Jul '22

20 Jul '22

External Email - Use Caution *Apologies for cross-posting listservs* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease <http://secure-web.cisco.com/1os8bjA2GGuqsqLRdnOyst5hgeqVHhHK23L0gkUDEg90RCl…> is seeking a research data analyst and research study assistant. Northwestern’s Mesulam Center is 1 of 33 NIA-funded Alzheimer’s Disease Research Centers, and home to the SuperAging Project and studies of atypical dementia syndromes. We are located on Chicago’s downtown campus, nestled between the Magnificent Mile and the city's beautiful lakefront. Prior experience with Alzheimer's disease is *not a requirement*. The primary responsibilities of the two positions are to use analytical, statistical, and programming skills to help collect, curate, analyze, and interpret biomedical data, including neuroimaging and biomarker derivatives. Both roles will work alongside PhD investigators to develop data-driven solutions and answer scientific questions about aging, Alzheimer’s disease, and related dementia syndromes. Successful candidates for the two positions will have proportional prior experience and education: (1) The research data analyst will have a MS or PhD, and/or several years’ experience in data science, computer science, biomedical engineering, or neuroscience. (2) The research study assistant should have a BA or BS and be interested in learning the fundamentals of neuroimaging, from data collection to analysis. Apply online: For the Research Data Analyst Associate position <https://secure-web.cisco.com/1PFgc4rrfnmIjp1zwwdmU41IfrJXRNft07y-F8-PLVAyp4…> (MS, PhD, or years of experience) For the Research Study Assistant position <https://secure-web.cisco.com/1xJCiZZXB5CJMqC_9HOhbuER7ZRIeV4HGEI0CeGE4ENBmg…> (BA, BS, less prior experience) *Adam Martersteck, PhD* Assistant Professor Northwestern University Feinberg School of Medicine, Department of Radiology Mesulam Center for Cognitive Neurology and Alzheimer's Disease 300 E. Superior Street, Tarry 8-729, Chicago IL 60611 312-503-5632 (office) | amartersteck(a)northwestern.edu

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Error connecting Ubuntu 18 to X-server Xming
by Maite Larzabal Alaba 19 Jul '22

19 Jul '22

External Email - Use Caution Dear Freesurfer community: I've been trying so hard to install your Freesurfer software on my computer. I followed all the instructions (of windows subsystem for Linux install and setup by WSL). I finally get writing the code but at the last steps ($freeview and then changing the Xming hosts file from the windows side to contain my IP address) still don't work. It still not connecting to display but it detect the IP. Please could you help me? I'll attach a photo of the final steps that I'm referring (those at your web https://secure-web.cisco.com/1WV7Cdioq6kj3slC7muFCJEaztv3vP3PVEC9wjnYKOWbs_…) Thank you very much and i hope you will be able to answer soon, Maite

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