Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Start a nNew thread

white and gray matter masks
by John Anderson 10 Aug '16

10 Aug '16

2 1

New way of installing and running Freesurfer - containers
by Chris Filo Gorgolewski 09 Aug '16

09 Aug '16

Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies). Features: - Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42474.html> ) - understands BIDS <http://bids.neuroimaging.io/> formatted datasets - performs recon-all on all subjects - allows you to run each subject independently (and potentially in parallel) - automatically performs longitudinal analysis when multiple sessions are detected - creates custom group level template for your study - can be easily converted to a Singularity <http://singularity.lbl.gov/> image using docker2singularity <https://github.com/chrisfilo/docker2singularity> tool and run on your local HPC/cluster You can find more information here: https://github.com/BIDS-Apps/freesurfer Please let me know what do you think! Best, Chris

2 2

Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 09 Aug '16

09 Aug '16

Postdoctoral research associate positions are 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 focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, 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. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu) For more information, please visit: http://www.unc.edu/~gangl/contact.html.

1 0

Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 09 Aug '16

09 Aug '16

1 0

Error running hippocampal segmentation with FS6
by Lauri Tuominen 09 Aug '16

09 Aug '16

Dear freesurfers, I tried running hippocampal segmentation using the Dev version 6 on launchpad. I get the following error message: I ran the recon-all command yesterday and it worked fine. Cheers! Lauri Tuominen INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160805 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160809 INFO: SUBJECTS_DIR is /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6 -rw-rw-r-- 1 ljt22 dinahgp 490999 Aug 9 09:26 /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.log Linux compute-0-57 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux `/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/recon-all' -> `/autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) left Tue Aug 9 13:11:58 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz left T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: application is running on a locale different from the original platform locale. Error using segmentSubjectT1_autoEstimateAlveusML Too many input arguments. MATLAB:TooManyInputs Warning: Unable to open display 'localhost:48.0'. You will not be able to display graphics on the screen. #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) right Tue Aug 9 13:12:06 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz right T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threa/pbs/ljt22/pbsjob_59.o12129908

1 0

hippocampus question
by Jasmin Alves 09 Aug '16

09 Aug '16

Dear Freesurfer, I have noticed that the subcortical grey matter volume output for the hippocampus differs slightly from other segmentation methods, I was wondering if this is due to what subfields of the hippocampus are included in the segmentation. I was curious which subfields Freesurfer includes as regional boundaries for the hippocampus. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

2 2

Average Hippocampal Subfield Maps
by Jessica Sevick 09 Aug '16

09 Aug '16

Hello, I am wondering if it is possible to make average .mgz for the hippocampal subfields for a set of control images? Thanks, Jessica Sevick T: 403.944.8652 C: 587.576.6666

1 0

Linking surface and volume coordinates in Freeview
by Isabelle Deschamps 09 Aug '16

09 Aug '16

Dear Freesurfer experts, In May 2016, one of the high priority on the Freeview Development board was to "Link the surfaces together (i.e. when you click on a vertex in the inflated surface, it should go to that vertex on the white and pial) & show identical vertex information in the Voxel Info panel. When clicking on a point on the 2D surface, automatically move the cursor in the 3D view to the closest point on the surface to that point in the volume." I couldn't find any information about whether this priority has been addressed yet or not. Would it be possible to have an update? Thank you in advance for the information, Isabelle

1 0

Re: [Freesurfer] resample structural ROI in functional space?
by Kami Koldewyn 09 Aug '16

09 Aug '16

Never mind - for some inexplicable reason, I did not consider using mri_convert, which works splendidly for doing this. Sorry for posting when tired and before thoroughly exploring my options. -kami From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Kami Koldewyn <k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, 8 August 2016 19:33 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] resample structural ROI in functional space? Hi All, I have a set of ROIs that were created in structural space, currently saved as volume masks. I would like to transform these into functional space, re-sampled to the functional resolution. Can anyone suggest a good way to do this? -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

1 0

Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 08 Aug '16

08 Aug '16

1 0

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