Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

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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how to build a monkey parcellation
by 乔易成 18 Jul '22

18 Jul '22

External Email - Use Caution Hello ! I want to build a parcellation(for example,lh.**.gcs) used on monkey brains.I used mris_sample_parc to sample individual atlas onto its pial surface,then used mris_ca_train to get a gcs out of eight subjects. Then, I used mris_ca_label to apply the new gcs onto every surface.However,the new gcs cannot work on subjects that are not used in the training step.Thanks for help!

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Interpretation of intergroup comparisons
by Adriana Cannizzaro 17 Jul '22

17 Jul '22

External Email - Use Caution Hello Freesurfers, We performed a whole-brain analysis using general linear model analysis with FreeSurfer mri_glmfit for neuropsychiatric symptoms (i.e: depression, etc) to assess their effect on brain’s cortical volume, thickness and area between groups (controls vs mild cognitive impairment, control vs Alzheimer, Alzheimer vs mild cognitive impairment).The severity score (level is either 1,2 or 3) of the neuropsychiatric symptoms was included as fixed factors, while MRI parameters (cortical volume, thickness and areas) were regarded as dependent variables. Thus, these are two sets of results for group_x_var : For reference : CN= Control group MCI= Mild cognitive impairment group AD: Alzheimer group NPIDSEV: Depression severity Contrast ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot Explanation g2v1_CN_AD_NPIDSEV.area.lh.fwhm10_group-x-var_neg is there a difference between the group VARiable slopes? contrast 0 0 1 -1. t-test with Group1>Group2 being positive. Note: this is an interaction between group and VARiable 1 -2.0763 158049 2847.57 -19.8 -63.8 12.5 0.0077 0.0066 0.0088 3957 -5537.87 cuneus 2 -2.4711 147091 2469.14 -35.3 -51.9 35 0.0205 0.0187 0.0223 5579 -7317.77 inferiorparietal g2v1_AD_MCI_NPIDSEV.volume.rh.fwhm10_group-x-var_pos is there a difference between the group VARiable slopes? contrast 0 0 1 -1. t-test with Group1>Group2 being positive. Note: this is an interaction between group and VARiable 1 2.2852 91120 1748.47 63.7 -39.7 -4.3 0.0054 0.0045 0.0063 3263 4658.91 middletemporal We would like to have more information on the interpretation of these results. Specifically, we would like to know how to interpret the sign of the max coefficient in relation to the difference between the groups on the severity of depression/NPIDSEV and on the volume/area/thickness of the region of interest. Our interpretation for the first result for example was that the difference between the CN and MCI slopes is negative as depression severity increases, however this does not indicate the direction of the slopes regarding the area of the cuneus or the parietal inferior region. Is this correct? Thank you very much for your help, Adriana Cannizzaro

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Re: [Freesurfer] Rookie question
by Addison, Reuben 17 Jul '22

17 Jul '22

I have a rookie question regarding free surfer after going through the excellent course on youtube First time I know the free surfer does the reconstruction on the anatomical scan (eg., T1t1_mprage_sag_p2_iso.nii) I see 3 other files in my data that were never used in the tutorials (SpinEchoFieldMap_AP/PA.nii, AHead_Scout_32ch-head-coil.nii, Phoenix_Document.nii). I am wondering when they were needed. I read about them just never saw them used. Thanks, Reuben N. Addison Postdoctoral Fellow Brain Recovery Lab MGH Institute of Health Professions<https://www.mghihp.edu/> Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129 p. 225-439-5354 | raddison(a)mghihp.edu<mailto:raddison@mghihp.edu>

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Problem with labels
by Alberto Del Cerro Leon 17 Jul '22

17 Jul '22

External Email - Use Caution Hello Freesurfer Team, I am trying to use a ROI to create a label into fsaverage. Once I registered my ROI to the fsaverage space I performed a mri_vol2surf and mri_cor2label to obtain a label of the ROI on the fsaverage surface. However, this label has several holes and irregularities. I know how to edit manually with tksurfer but, is there a method to fill the holes and smooth the borders of the label automatically?

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recon-all finished without error but no results
by Zixuan Lin 17 Jul '22

17 Jul '22

External Email - Use Caution Hello! I am trying to run recon-all but it only converted the original image to .mgz and finished without error. I checked all other folders and it's empty. Attached please find the recon-all.log. The command line I used is recon-all -i hc01.nii -s hc01 -sd /home/zlin/Documents/MDD_CVR/control Could you please help me check what happens here? Thanks a lot, Zixuan.

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FW: recon-all error on brain with abnormality
by Gumenyuk, Valentina 17 Jul '22

17 Jul '22

External Email - Use Caution Dear Freesurfer team, I was trying to run recon - all of the brain ( see below) with large hemorrhage in the right hemisphere. Recon all finished with the an error ( log is attached) . Please advise what can be done to complete the recon all on this type of the brain abnormality. Thank you , Valia [cid:image001.png@01D89616.87353E10] The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Freesurfer July 2022