Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

DTI scan process steps for single and multiple shells
by Zeng, Qi 15 Oct '20

15 Oct '20

External Email - Use Caution Hi Freesurfer experts, Are the steps for processing DTI scan the same for single and multiple shells? for example, both via -prep, -bedp, -path. Thank you so much! Best, Qi

2 1

Openings for Postdoc and PhD positions @UConn Brainlens
by Jieyin Feng 15 Oct '20

15 Oct '20

External Email - Use Caution Hi all, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab:* https://www.brainlens.org/employment *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry, and Director of the Brain Imaging Research Center at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT, NIH T32 ). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

1 0

Openings for Postdoc and PhD positions @UConn Brainlens {Disarmed}
by Jieyin Feng 15 Oct '20

15 Oct '20

External Email - Use Caution Hi all, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment <https://www.brainlens.org/employment>* *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://psych.uconn.edu/person/fumiko-hoeft/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>), and Director of the Brain Imaging Research Center (https://birc.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn (https://www.brainlens.org <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT https://slac.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>, NIH T32 https://cncct.research.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

1 0

Re: [Freesurfer] tk applications failing to launch on VM (Windows)
by fsbuild 14 Oct '20

14 Oct '20

External Email - Use Caution Hello Chris, I think tksurfer has been deprecated as newer versions of freeview can be used instead.  A search thru the freesurfer support mail list for tksurfer brings up several posts including these, [Instead of tksurfer] you can also use tkmeditfv and tksurferfv. They take the tkmedit/tksurfer arguments but run freeview. Freeview does support surface-based ROI drawing. There is a Path/Custom Fill tool button on the left pane. Once it is checked, you should see a bunch of tool buttons similar to what tksurfer had for ROI drawing.  Are you saying that a new install of the VM on your Mac OS machine did not work, as in the Ubuntu OS did not come up in the VM window?   It would be good to know what version of Mac OS you are running.  I would also try and use the latest version of Virtualbox to run on the Mac.   Many people have Macs where they retain having everything on one partition as the machines come out of the box, i.e., they don’t re-partition the disk into multiple partitions to keep a separate/clean boot partition.  So depending upon the size of the built in drive/SSD and what is already occupying space there, I have seen some people run out of space on that single partition after installing the VM.   I would check that you have ~40G of space free on your boot partition if that is where the VM also lives. - R. On Oct 14, 2020, at 11:05, Mcnorgan, Christopher <cpmcnorg(a)buffalo.edu> wrote:        External Email - Use Caution        Hi,I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I’ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads). Both of the students report that the tk applications (tkmedit and I think also tksurfer) fail to launch. At the command line, they run the command, and nothing really happens.One student provided a bit more information:I don't know if this helps, but I ran tksurfer and actually got an error that read out, ' TCL_init failed: Cannot find a usable init.tcl.  This probably means that Tcl wasn't installed properly.  TK_init failed: invalid command name "tcl_find/library” ‘Unfortunately I could not provide any help at all because when I attempt to run the VM on virtualbox on my mac, following the directions at https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_macThe OS fails to boot, and I only see a series of messages about recovering a journaled filesystem before the VM halts.Most of their learning has involved the CLI so it hasn’t been a huge impediment, but we’re about to run the GLM, and will require these resources to visualize.Thanks,Chris/*********************************************** Chris McNorgan* Assistant Professor* Department of Psychology* University at Buffalo, * The State University of New York* http://ccnlab.buffalo.edu/* Office: 716.645.0236* Lab: 716.645.0222**********************************************/_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Password
by fsbuild 14 Oct '20

14 Oct '20

External Email - Use Caution Hello Satya, I will send the password to your email directly. - R. On Oct 14, 2020, at 15:49, Satya Kothapalli <satya.au(a)gmail.com> wrote:        External Email - Use Caution        Hi,  I wanted to try out FreeSurfer and  followed the install guide from https://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-09-10). However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtual machine should just boot  up to Desktop without requiring a password. Is there a default password I am supposed to use? <image.png> Thank you,Regards,Satya. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Password
by Satya Kothapalli 14 Oct '20

14 Oct '20

External Email - Use Caution Hi, I wanted to try out FreeSurfer and followed the install guide from https://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-09-10). However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password. Is there a default password I am supposed to use? [image: image.png] Thank you, Regards, Satya.

1 0

tk applications failing to launch on VM (Windows)
by Mcnorgan, Christopher 14 Oct '20

14 Oct '20

External Email - Use Caution Hi, I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I’ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads) Both of the students report that the tk applications (tkmedit and I think also tksurfer) fail to launch. At the command line, they run the command, and nothing really happens. One student provided a bit more information: I don't know if this helps, but I ran tksurfer and actually got an error that read out, ' TCL_init failed: Cannot find a usable init.tcl. This probably means that Tcl wasn't installed properly. TK_init failed: invalid command name "tcl_find/library” ‘ Unfortunately I could not provide any help at all because when I attempt to run the VM on virtualbox on my mac, following the directions at https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_mac The OS fails to boot, and I only see a series of messages about recovering a journaled filesystem before the VM halts. Most of their learning has involved the CLI so it hasn’t been a huge impediment, but we’re about to run the GLM, and will require these resources to visualize. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

1 0

Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed}
by Jieyin Feng 13 Oct '20

13 Oct '20

External Email - Use Caution Hi All, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment <https://www.brainlens.org/employment>* *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://psych.uconn.edu/person/fumiko-hoeft/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>), and Director of the Brain Imaging Research Center (https://birc.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn (https://www.brainlens.org <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT https://slac.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>, NIH T32 https://cncct.research.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

1 0

error trac all prep
by Camerino, I.L. (Ileana) 13 Oct '20

13 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command: #!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached thank you in advance Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

2 1

Open the .annotation file with Notepad is garbled
by 1248742467 13 Oct '20

13 Oct '20

External Email - Use Caution Hello, FreeSurfer Why is it garbled when I open the .annotation file with Notepad? Is there any solution?  Looking forward to your reply

2 1

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