Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

External 3D View Issue
by Harriet Cornwell 18 Jun '21

18 Jun '21

External Email - Use Caution Hello, We thought we had finished manually editing a T1 scan and so opened it in the external 3D view to perform final checks and it looks incredibly messy (see attached screenshot). Are you able to advise whether this is an issue? If so, is it possible to fix it and, if it can be fixed, how we should go about doing so? Also, do you have any idea what might have caused this to happen? Thank you in advance! Harriet Cornwell

2 1

Problem with Anatomicts in Freesurfer
by Yuqian Chen 17 Jun '21

17 Jun '21

External Email - Use Caution Dear Sir or Madam, Hope you are doing well! Thank you very much for your contribution to the freesurfer software which offers great help to research in the neuroimaging area. However, I met a problem when using it and I hope you can help me with it. The freesurfer version I use is freesurfer-linux-centos7_x86_64-7.1.1.tar.gz. I hope to implement AnatomiCuts with my own data which is tractography data (.vtk) reconstructed from HCP dataset with ukf tractography method. When I tried to run the dmri_AnatomiCuts command (the complete command is: dmri_AnatomiCuts -s wmparc.nii.gz -f 100307_ukf_pp.vtk -c 100 -n 14 -e 50 -o output -d s), the following messages appears: ups ups ups ups ups ups ... queue emplace 3894 queue emplace 0 It seems that the algorithm is running. But it just stays here and I cannot get the final results even with input data of only 100 fibers divided into 2 clusters. I am really confused what is going on here. Are there any special requirements for the input data? Your help will be greatly appreciated. Regards, Yuqian

1 0

matching .label file from left to right hemisphere using a group template (fsaverage6)
by Xiaoxuan Yan 17 Jun '21

17 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to define the anatomically homotopic vertices between the left and right hemispheres on the fsaverage6 template. To do this, I am planning to map a .label file from the left hemisphere to the right hemisphere. I intend to follow the instructions on this wiki page https://secure-web.cisco.com/1dNutup50lUjZBRwKC0jge2QUROar1Y3UGcZEu3ZCD5VUF… to do it. However, at step 1.2, when I try to use surfreg to perform surface registration from fsaverage6 to fsaverage_sym with the command surfreg --s fsaverage6 --t fsaverage_sym --lh surfreg --s fsaverage6 --t fsaverage_sym --lh —xhemi I encountered an error “canot find norm”. I reckon that this occurs since I am using the fsaverage6 template which does not have a corresponding norm.gz file. May I know if there is any way to get around this issue? Best wishes Matilda

1 0

Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years
by Alexandru Hanganu 16 Jun '21

16 Jun '21

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and neuropsychiatric evolution in Parkinson’s disease using multi-modal MRI imaging techniques and machine learning.* The project is funded by the Canadian Institutes of Health Research (CIHR) . It involves longitudinal analyses of cortical thickness, tractography and BOLD resting-state fMRI analyses and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and predictors of Mild Behavior Impairment (MBI) in Parkinson’s disease in collaboration with Dr. Zahinoor Ismail who has led the development of the MBI-checklist. The project will make use of an existing longitudinal study containing structural, diffusion weighted imaging and functional MRI, neuropsychological and behavioural assessment, and genotyping at three time points. The PCAN lab has been a pioneer in using different neuroimaging techniques to study the origins and evolution of cognitive more recently neuropsychiatric deficits in Parkinson’s disease with the ultimate goal of early prediction of dementia in the disease. Other interests include the function and application of neuromodulation techniques such as transcranial magnetic stimulation, Transcranial direct stimulation and low intensity focused ultrasound. The PCAN Lab is located in the Healthy Brain Aging labs of the Hotchkiss Brain Institute part the Foothills Campus of the University of Calgary. The Foothills campus is home to the Seaman Family MR Research Centre which host a General Electric 3T research dedicated MRI scanner. Requirements of the position include a PhD in Neuroscience, biomedical engineering, biomedical sciences, or Psychology with experience in the analysis of one or multiple MRI neuroimaging techniques such as cortical thickness/volumetry (e.g. *Freesurfer, FSL*), functional connectivity (e.g. *PPI, ICA, graph theory*), diffusion weighted imaging (e.g. *Dipy, MRTrix, FSL*). Some fluency in computer programming (e.g. *Linux, Unix, MATLAB, or Python)* is also required as well as the ability to write scientific peer-reviewed manuscripts. Please send applications (Cover letter, CV, and the name of 2 references including current supervisor) to Oury Monchi: oury.monchi(a)ucalgary.ca

1 1

Tracula Anlsysis
by A.R. Sekar 16 Jun '21

16 Jun '21

External Email - Use Caution Hello Experts, I am using Tracula to analyse the white matter tracts of the cerebellum. I saw that the atlas has the Middle cerebellar peduncle<https://secure-web.cisco.com/1RU8MdA4Yds_PepNEq52WWjK8jWdz6oYfoTgR9zPaeseQL…>, does it also have the other 2 major white matter tracts of the cerebellum: inferior (ICP), and superior cerebellar peduncles (SCP)? If not how can I go about using tracula for the analysis of these white matter tracts? Thanks for your help! Regards, Akila

2 1

mri_mcsim error when building Monte Carlo on fsaverage5
by Øystein Sørensen 16 Jun '21

16 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to build my own Z Monte Carlo on fsaverage5, as described on the BuildYourOwnMonteCarlo tutorial (https://secure-web.cisco.com/1uikaYhiWSF4KzsQTXjySqLmwrS4IRC0PJ5sIbxRfHQXCe…) but I get a segmentation fault. As a reproducible example, the following command tries to compute 10 replications at FWHM=15 and save it in a subdirectory fsaverage5 of my current directory. $ mri_mcsim --o ./fsaverage5 --base mc-z --surface fsaverage5 lh --nreps 10 --fwhm 15 Issuing this command leads to a segmentation fault. The full output is in the attachment (mri_mcsim_error.txt), and here are the last lines before the error happens: Loading /Applications/freesurfer/7.1.1/subjects/fsaverage5/surf/lh.white group_avg_surface_area 84969.3 group_avg_vtxarea_loaded 1 Loading label file cortex Loading /Applications/freesurfer/7.1.1/subjects/fsaverage5/label/lh.cortex.label Segmentation fault: 11 Adding the «--debug» option gives no additional information. If I add the “—no-label” option, it works. However, I need those labels for later use in mri_glmfit-sim so that does not solve the issue. Using fsaverage6 instead works fine: “$ mri_mcsim --o ./fsaverage6 --base mc-z --surface fsaverage6 lh --nreps 10 --fwhm 15” gives no error messages. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1 2) Platform: macOS Big Sur 11.4 PS! I’m also aware that permutation testing is in general recommended rather than Z Monte Carlo simulations, but in this particular application the dataset is so large that permutation testing is likely not a viable option, due to computing constraints. Best regards, Øystein Sørensen, PhD Associate Professor in Statistics Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo http://secure-web.cisco.com/1WEu63aU9x0YgcndrjS1ZoT7n-mRQdI0c2tfDzloh2yF1pU…

1 0

Re: [Freesurfer] TRACULA trac-all cores/threads
by Drucker, Daniel 16 Jun '21

16 Jun '21

> Hi Daniel - Can you track down which command does this? I suspect that it's something in the pre- or post-processing, because I haven't added multi-threading to the main TRACULA executables (yet). trac-all calls trac-preproc calls eddy_openmp Daniel

2 1

Re: [Freesurfer] Error in freeview
by fsbuild 15 Jun '21

15 Jun '21

External Email - Use Caution Hello Swati, Please check you have you setup the freesurfer environment by setting the environment variable FREESURFER_HOME to where the freesurfer distribution is installed followed by source’ing either the bash or csh setup script.   You can see the commands for that here, https://secure-web.cisco.com/1pWXNrTwcNFgC7ksSikz4u20fb7za4hxJ3a… The freeview binary expects to live under <freesurfer_installation_directory>/bin with the libraries it needs under the parallel subdirectory <freesurfer_installation_directory/lib.  Otherwise it may not find libraries like the one you listed which should be under <freesurfer_installation_directory/lib/vtk - R. On Jun 15, 2021, at 13:48, Swati Banerjee <swati.banerjee29(a)gmail.com> wrote:        External Email - Use Caution        Dear I am getting an error using the freeview. Please help me to resolve this issue.freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directoryWith regards,Swati--    -_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Error in freeview
by Swati Banerjee 15 Jun '21

15 Jun '21

External Email - Use Caution Dear I am getting an error using the freeview. Please help me to resolve this issue. freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory With regards, Swati -- -

1 0

Job Opening at CUMC/NYSPI: Scanning RA Position
by Chrisanthopoulos, Marika (NYSPI) 15 Jun '21

15 Jun '21

External Email - Use Caution Hello all, The Clinic for Aging, Anxiety, and Mood Disorders (CAAM) at the New York State Psychiatric Institute/Columbia Medical Center is currently interviewing to hire a Scanning (MRI) Research Technician. Please view the job description and submit your application through this link<https://secure-web.cisco.com/1FLIsp1bq-6rAoLTU9CMzclsVcu_Zim13NYcs2HcA11QrB…> if you are interested in applying. Thank you, Marika Chrisanthopoulos Program Manager Clinic for Aging, Anxiety, and Mood Disorders (CAAM) Neurobiology and Therapeutics of Aging New York State Psychiatric Institute Columbia University Medical Center P: 646-774-8697 F: 646-774-8693

1 0

← Newer
1
...
5
6
7
8
9
10
11
...
14
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2021