Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

question about mri_segment_hypothalamic_subunits
by fsbuild 11 Oct '20

11 Oct '20

External Email - Use Caution Hello Victor, If you used the 7.1.1 installer package, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/…, then it should have installed /Applications/freesurfer/7..1.1 for you.  I believe the same is true for the 7.1.0 installer, i.e., /Applications/freesurfer/7.1.0, and similarly for the 7.0.0 installer.  We set it up that way so the distributions would be separate.  This allows people to switch among/compare the distributions by setting FRESURFER_HOME differently, e.g.,  $ export FREESURFER_HOME=/Applications/freesurfer/7.1.1or$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0etc….. then source’ing the shell setup script for either sh or csh, e.g., for sh$ source $FREESURFER_HOME/SetUpFreeSurfer.sh The installer packages create an uninstall script under each distribution, e.g.,  /Applications/freesurfer/{7.1.1, 7..1.0, 7.0.0}/uninstall.sh.  So if you wanted to start with a clean install you could try running the uninstaller script(s), and then re-install using the .pkg files, e.g.,  to run the 7.1.1 installer, $ sudo /Applications/freesurfer/7.1.1/uninstall.sh  - R. On Oct 8, 2020, at 18:13, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:Hi Victor,I highly recommend that you keep both installations separate.Cheers,/Eugenio  Juan Eugenio IglesiasSenior research fellowCMIC (UCL), MGH (HMS) and CSAIL (MIT)http://www.jeiglesias.com    From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edu>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Thursday, October 8, 2020 at 17:54To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] question about mri_segment_hypothalamic_subunits Hi all,  I installed the most recent dev version of FS7.1, and copied its files over the old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and receive an error:  error: freesurfer has not properly been sourced I am using mac os Catalina 10.15.6. How can I fix this? Victor ZengBeth Israel Deaconess Medical CenterKeshavan Lab-- 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._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer 5.3.0 recon-all error
by Michele Valotti 09 Oct '20

09 Oct '20

External Email - Use Caution I am using freesurfer 5.3.0 (unfortunately this is the version I have to use) and I am encountering an error in the process. I have attached the recon-all.log file. Any pointers to identify the error would be very helpful, Thank you, Michele

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seed point on the CC and Pons
by Jie Zhao 09 Oct '20

09 Oct '20

External Email - Use Caution Hello Freesurfer Experts I am trying to set the correct seed point to cutting the corpus callosum and pons for a macaque subject. It is aimed to remove the brainstem and cerebellum, right? My command line is : recon-all -s monkey2 -autorecon2-inflate1 -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80 The output result is sucessed without errors, but the wm.mgz still include the brainstem and cerebellum in my freeview. I am wondering whether my coordinate used above command is correct ? It is from the Cursor on the right of wm in attached pictures. I know here need talairach coordinate and which one on the Cursor is correct ?Sorry for my ignorance. Any suggestions will be appreciated! Kind Regards Jie

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Seed region in anatomical data for resting state fMRI data
by Kim, Gwang-Won 09 Oct '20

09 Oct '20

Hi there, I obtained a seed region (left superior frontal)from anatomical data to process resting state fMRI data as follows: fcseed-sess -o lh.SFC.dat -segid 1028 -s session -fsd rest. I wonder if what the seed region is the left superior frontal was correct. Question1: Can I display the lh.SFC.dat as MR image (anatomical image) using Freeview? I'd like to obtain ROI region as a seed region from anatomical data to process resting state fMRI data. Question2: How do I make the seed region if I use 8-mm radius spheres centered on a MNI coordinate [x=20, y=20, z=20] as the seed region. Thanks, Gwang-Won

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TODAY: IronTract Challenge webinar and live demo!
by Yendiki, Anastasia 09 Oct '20

09 Oct '20

Dear FreeSurfers - Join us today at 12pm EDT / 6pm CET for the IronTract Challenge webinar/happy hour! Learn about this effort to assess tractography methods objectively and get up to speed on how to participate by the deadline of November 8. The webinar will include demos on how to submit your results to the challenge and how to share your challenge code on the QMENTA platform. Register here for zoom link to the webinar: https://us02web.zoom.us/webinar/register/WN_OVGWn3SIRF2qw_8Ujks-Hg See you soon! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://scholar.harvard.edu/a-y

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A basic question: What does aparc, wmparc, aseg mean?
by Zhiyuan Yu 09 Oct '20

09 Oct '20

External Email - Use Caution Hi All, I have seen aparc, wmparc, aseg frequently but I do not know what they represent. Could anyone explain them for me? Thanks, Zhiyuan

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Re: [Freesurfer] question about mri_segment_hypothalamic_subunits
by Iglesias Gonzalez, Juan E. 08 Oct '20

08 Oct '20

Hi Victor, I highly recommend that you keep both installations separate. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng(a)bidmc.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, October 8, 2020 at 17:54 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] question about mri_segment_hypothalamic_subunits Hi all, I installed the most recent dev version of FS7.1, and copied its files over the old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and receive an error: error: freesurfer has not properly been sourced I am using mac os Catalina 10.15.6. How can I fix this? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ 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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question about mri_segment_hypothalamic_subunits
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 08 Oct '20

08 Oct '20

?Hi all, I installed the most recent dev version of FS7.1, and copied its files over the old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and receive an error: error: freesurfer has not properly been sourced I am using mac os Catalina 10.15.6. How can I fix this? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ 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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Postdoc Positions at University of Pennsylvania
by Tisdall, Dylan 08 Oct '20

08 Oct '20

External Email - Use Caution Hi all, I'm recruiting postdoc follows for a couple of NIH-funded projects at the University of Pennsylvania. Projects include 1) development of motion-resilient methods for pediatric neuroimaging, and 2) ex-vivo/in-vivo 7T neuroimaging and analysis methods to find biomarkers for specific neurodegenerative diseases. Please see the job ads: http://www.dylantisdall.com/2020_pediatric_postdoc_ad.pdf http://www.dylantisdall.com/2020_ftdc_postdoc_ad.pdf and reach out to me if you have questions or would like to apply. Thanks, Dylan --- Dylan Tisdall, PhD Research Assistant Professor Department of Radiology Perelman School of Medicine University of Pennsylvania Room D406 Richards Medical Labs 3700 Hamilton Walk Philadelphia, PA 19104

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Matlab Matlab Runtime issue
by Wei Shao 08 Oct '20

08 Oct '20

External Email - Use Caution Hello, Freesurfer team My name is Wei Shao, FS user, I have a few questions regarding the Matlab package and the hippocampal subfield function with FS. I have followed the instruction from the website to install Matlab, sue the fs_install_mcr R2014b (Oct 01, 2020 14:41:05) Exiting with status 0 (Oct 01, 2020 14:41:05) End - Successful. Finished MCR v84 (R2014b) already exists in /usr/local/freesurfer/7.1.0-1 do you want to reinstall? [y/n] exiting without install *However*, when I try to use the hippocampal seg command: *segmentHA_T1.sh, it gives me this error* ERROR: cannot find Matlab 2014b runtime in location: /usr/local/freesurfer/7.1.0-1/MCRv84 The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b. To do so, please run the following commands (you might need root permissions): LINUX: cd /usr/local/freesurfer/7.1.0-1 curl " https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime2014b.tar.gz" tar xvf runtime2014b.tar.gz Even after I did this as the following, it still gave me the same response when I tried segmentHA_T1.sh. Could you tell me how to fix this? Thanks! Best, Wei

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Freesurfer October 2020