Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
by Park, James 27 Oct '20

27 Oct '20

External Email - Use Caution Hello, My name is James Park, and I had a question regarding some issues with Freesurfer. We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others. Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server). I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location. I was wondering if there is any workaround for this issue? This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551. Thank you for your help in advance. Sincerely, James Park Research Specialist Dpt. of Neurosurgery, Emory james.kunwoo.park(a)emory.edu<mailto:james.kunwoo.park@emory.edu> 732-589-4215 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Tracula: Calculation of MD values from other eigenvectors
by Chong, Catherine (Cat), Ph.D. 27 Oct '20

27 Oct '20

External Email - Use Caution Dear Tracula Experts, We are trying to address a question from a reviewer who is wondering why we included all of the average diffusion parameters in our model ( i.e. FA, MD,FA, RD, and AD) for distinguishing two groups of patients . The reviewer comments that MD values are calculated from AD and RD henceforth, including of all of the three parameters ( AD, RD, and MD) might have biased our analysis. I understand the reviewer’s concern that MD is calculated from adding all three eigenvalues/3, but I am uncertain about the relationship between the eigenvalues and the calculation of ‘average’ parameters for a given fibertract. I am looking forward to your guidance, With kind Regards, Catherine

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Re: [Freesurfer] Exited with errors, segmentation fault
by Hoopes, Andrew 27 Oct '20

27 Oct '20

Hi Julia, This is a small bug that's been fixed in the 7.1.1 patch release. I would recommend updating freesurfer versions (there will be no differences in recon-all results). Best, Andrew On 10/13/20, 8:44 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Julia Lam" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of julia.lam(a)mau.se> wrote: External Email - Use Caution Hi, In one of 56 volumes, recon-all exited with errors (segmentation fault). I tried to rerun but received the same result. How can this be solved? I’ve attached the recon-all.log and recon-all.error. I am looking forward to your reply. Kind regards, Julia Lam

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Postdoctoral Fellowship
by Didenur Sahin 27 Oct '20

27 Oct '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800 -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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NIH funded postdoctoral position
by Ron Killiany 27 Oct '20

27 Oct '20

External Email - Use Caution Hi everyone, We have been fortunate to obtain funding for a postdoctoral position. A brief description is enclosed. Please feel free to pass this along to anyone who might be interested. --ron -- Ronald J. Killiany, Ph.D. Center for Biomedical Imaging Departments of Anatomy & Neurobiology, Neurology, Radiology and Environmental Health Boston University School of Medicine and Boston University School of Public Health 700 Albany Street, W701 Boston, Massachusetts 02118 *phone: 617-358-8276* fax: 617-638-4922

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Re: [Freesurfer] freeview Core Dumped Error after upgrade in ubuntu
by fsbuild 27 Oct '20

27 Oct '20

External Email - Use Caution Hello Antonin, I’ve found a few posts that seem to indicate you can upgrade as well as downgrade the kernel (and its dependent packages) by editing the /etc/apt/sources.list to point to the Ubuntu distribution you want (and then running update, upgrade, dist-upgrade commands)..   Not sure what the previous Ubuntu distribution name was for you, but this post, https://sypalo.com/how-to-upgrade-ubuntu, lists the distributions as, 18.04 - bionic 18.10 - cosmic 19.04 - disco 19.10 - eoan 20.04 - focal 20.10 - groovy While that post gives the example of *upgrading*, this post gives the example of *downgrading*, https://linuxconfig.org/how-to-downgrade-ubuntu-linux-system-to-its-previous-version, but I think they are essentially doing the same thing, i.e. it’s a function of the distribution name listed in /etc/apt/sources.list. Note that even if you are downgrading the kernel, as far as the apt package manager is concerned you still have to run the various “upgrade” commands to change the distribution to a different one even if it is older. - R. On Oct 26, 2020, at 11:00, Rovai Antonin <Antonin.Rovai(a)erasme.ulb.ac.be> wrote:       External Email - Use Caution        Dear experts,I use to have a perfectly working freesurfer installation on my Ubuntu18.04 LTS machine, until that doomsday where I installed updates asrecommended by ubuntu itself.Now, each time I run freeview, I get the following error:Aborted (core dumped)I reinstalled freesurfer from scratch, fixing nothing.I think Ubuntu did a kernel upgrade; now I have a uname -r output =5.4.0-52-genericI think it used to be 49 instead of 52 before the upgrade, but I am notsure.Do you know of any patch fixing this, by any chance?Thanks for your lightsAntonin RovaiHôpital Erasme - ULBCliniques universitaires de BruxellesRoute de Lennik 808 - B - 1070 BruxellesS www.erasme.ulb.ac.beDisclaimer : http://www.erasme.ulb.ac.be/email-disclaimer_______________________________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tracula error: run list is longer than subject list
by Shanika Jayakody 26 Oct '20

26 Oct '20

External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about. I wonder if anyone can help me figure out a solution. Many thanks Oshadi

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segmentHA on Human Connectome Project
by AmirHussein Abdolalizadeh 26 Oct '20

26 Oct '20

External Email - Use Caution Hi, I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions: 1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline ( https://github.com/Washington-University/HCPpipelines) 2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject. 3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9). I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required. Bests, Amir

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Traculina availability
by Ngoh Zhen Ming 26 Oct '20

26 Oct '20

External Email - Use Caution Good Morning! I understand that the stable release of TRACULInA will be included in the next version of freesurfer. Is there an estimate of when that will be? Or if there are any versions that are currently openly available for trial? Thank you and look forward to hearing back! Zhen Ming, NGOH This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

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freeview Core Dumped Error after upgrade in ubuntu
by Rovai Antonin 26 Oct '20

26 Oct '20

External Email - Use Caution Dear experts, I use to have a perfectly working freesurfer installation on my Ubuntu 18.04 LTS machine, until that doomsday where I installed updates as recommended by ubuntu itself. Now, each time I run freeview, I get the following error: Aborted (core dumped) I reinstalled freesurfer from scratch, fixing nothing. I think Ubuntu did a kernel upgrade; now I have a uname -r output = 5.4.0-52-generic I think it used to be 49 instead of 52 before the upgrade, but I am not sure. Do you know of any patch fixing this, by any chance? Thanks for your lights Antonin Rovai Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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Freesurfer October 2020