Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30083 discussions

Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found
by Alvarado,Luis R 01 Nov '21

01 Nov '21

External Email - Use Caution Hi all, I ran into issues running binaries like mri_aparc2aseg, mri_vol2vol, etc. on 7.1.2 $ mri_vol2vol mri_vol2vol: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by mri_vol2vol) The issue is resolved when I switch back to 7.1.1. I am running Ubuntu 18.04.5 LTS. any help will be appreciated. Luis R. Alvarado Graduate Student Fellow Department of Anatomical Sciences and Neurobiology University of Louisville Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.
by Sherin Sugathan 31 Oct '21

31 Oct '21

External Email - Use Caution Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use*FreeSurfer Longitudinal*to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting: |+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+ | FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue? Thanks in advance Reshma

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Magnetization Transfer Images and recon-all
by Marlene Tahedl 31 Oct '21

31 Oct '21

External Email - Use Caution Hi! I have a couple of Magnetization Transfer MR images from a group of patients which I would like to analyze using the FreeSurfer pipeline. However, when applying "recon-all" to those images, the algorithm stops after just a few minutes. Although it says "finished without error", no images have been produced. Is there a way to apply recon-all to MT, maybe some conversion to make the MT images look more like a T1? Thanks! Marlene.

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Re: [Freesurfer] A question regarding a Freeview command
by Douglas N. Greve 31 Oct '21

31 Oct '21

I don't think there is anything specific for the --table option, but everything else is the same. On 10/24/2021 4:31 PM, Alvarado,Luis R wrote: > > External Email - Use Caution > > Hi Douglas, > > I was wondering if there are any “--table option” specific tutorial > for the mri_glmfit function. I am trying to decide wheatear to export > my ROI results to R or use the mri_glmfit function. > > Best, > > Luis >

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results visualization
by Marina Fernández 29 Oct '21

29 Oct '21

External Email - Use Caution Dear experts, Do you know what are the steps to follow to visualize a surface-map of freesurfer results in Caret? Thank you very much in advance. Best regards, Marina

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Re: [Freesurfer] developer password
by fsbuild 29 Oct '21

29 Oct '21

External Email - Use Caution Sure - sending password and upgrade instructions to your private email shortly. - R. On Oct 29, 2021, at 13:55, Eli Bulger <esbulger(a)cmu.edu> wrote:        External Email - Use Caution        Hello,I am hoping to use Freesurfer on Windows 10. I have tried to use VirtualBox, but it requires a developer password. I have seen many emails on this mailing list where the password is provided through email. Is it possible to have a copy sent to this email? Thank you,_______________________Eli BulgerPh.D. Student, Biomedical EngineeringCarnegie Mellon University_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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developer password
by Eli Bulger 29 Oct '21

29 Oct '21

External Email - Use Caution Hello, I am hoping to use Freesurfer on Windows 10. I have tried to use VirtualBox, but it requires a developer password. I have seen many emails on this mailing list where the password is provided through email. Is it possible to have a copy sent to this email? Thank you, _______________________ Eli Bulger Ph.D. Student, Biomedical Engineering Carnegie Mellon University

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Postdoctoral Position – Pediatric Neuroimage Analysis and Deep Learning
by Gang Li 28 Oct '21

28 Oct '21

External Email - Use Caution A postdoctoral research associate position is available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current research focuses on the development of advanced image processing and deep learning techniques for pediatric neuroimaging data for better understanding the dynamic development of brain structure, function and connectivity in health and disease during the prenatal and early postnatal stages. The successful candidate will support our efforts in advancing pediatric neuroimaging analysis technologies (e.g., reconstruction, parcellation, registration, prediction, modeling, harmonization, etc.). We are seeking highly motivated individuals who have extensive research experience in medical image analysis and deep learning and demonstrated academic excellence, including publications in first-class journals or conferences. The candidate should have a Ph.D. (or equivalent) in Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, Neuroscience, or related fields. Good command of programming tools including Python, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis (https://secure-web.cisco.com/13Nk5BnjS6JPAxxwIm0Lhc3q1raGx4_OpDQ-XY13280OPg…) The University of North Carolina at Chapel Hill is an equal opportunity and affirmative action employer. We strongly encourage applications from diverse backgrounds. Interested candidates should email a cover letter and a resume to Dr. Gang Li (gang_li(a)med.unc.edu)

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Local GI MRI_segstats error
by COLLEEN PLETCHER 28 Oct '21

28 Oct '21

External Email - Use Caution Hello, I am trying to run mri_segstats for local GI indices. I am getting a file not found error for /tmp/mri_segstats.tmp.sub-1007_ses_01/.lh.176.ctab I did not get an error message when running the recon-all -localGI command and I am using freesurfer version 7.1.1. Any advice would be appreciated! Thanks, Colleen

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Re: [Freesurfer] freeview segmentation fault: 11 on MacOS 10.15.7
by fsbuild 28 Oct '21

28 Oct '21

External Email - Use Caution Hello Emmanuel, You could try the suggestions in this post from last month, https://secure-web.cisco.com/1H6jl_CDKnKsqkQWb-ixQ370LPSa0jmM_IIgqtrwqvBfOr… It’s not formatted too well through the mail list archive, so I will try and send it to your private email separately. - R. On Oct 28, 2021, at 10:36, Emmanuel Guizar Rosales <emmanuel.guizarrosales(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Team,I installed Freesurfer freesurfer-darwin-macOS-7.1.1-20200811-8b40551 and tried to view surface files in freeview. However, if I try to open surface files in freeview, it crashes.Note: I can open the Freeview.app, but as soon as I try to load a surface file, it crashes. If I try to start freeview from the terminal after runningexport FREESURFER_HOME=path/to/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.shfreeviewthe app won’t even start and return the following error in the terminal:/Applications/freesurfer/7..1.1/bin/freeview: line 2:  1202 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"Attached you will find the full problem report:Every help would be much appreciated!Best wishes,Emmanuel*

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