Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
by Yi Leng Fung 02 Feb '19

02 Feb '19

External Email - Use Caution Dear FreeSurfer Developers, I ran -recon-all -all on my subjects with the aim of examining the gray volumes of the ex vivo entorhinal and perirhinal cortex. Prior to extracting the gray volume numbers of the entorhinal and perirhinal cortex from ?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and perirhinal cortex on the ?h.BA.thresh.annot on Freeview. However, I noted that their locations on the annot file did not correspond to the locations indicated by ?h.entorhinal.thresh.label and ?h.perirhinal.thresh.label. I have also loaded the annot files and label files from the fully recon-ed subject named "bert" on Freeview and observed the same mismatch in the labeling. I am curious why this might be the case. For your reference, I have uploaded a few screenshots from Freeview, on "bert", to demonstrate the label names in the annot file, both with and without the outline of the label files. I have searched the archive and have not been able to find any similar queries on this, hence it would be of tremendous help if someone could clarify this observation. If it is of interest, I am running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04. Thank you for your assistance and I look forward to hearing from you. Best regards, *Yi-Leng*

1 0

Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 01 Feb '19

01 Feb '19

External Email - Use Caution Hello Rodrigo, Please use capital -C and not lowercase -c to tell the tar command what directory to untar the files into; you used -C the first time when the file could not be found, but on the subsequent commands you changed it to -c  - R. tar -C /eeg/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar..gz Rodrigo Montenegro at 13:42 2/01/2019         External Email - Use Caution        Hey! I have not received any feedback from that… Not sure if the mail was lost?...  Any help would be appreciated! Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: Rodrigo Montenegro [mailto:rmontenegro11@gmail.com] Sent: 30 January 2019 20:39 To: 'Freesurfer support list' <freesurfer(a)nmr.mgh.harvard.edu> Cc: 'rodrigo.montenegro(a)ndcn.ox.ac.uk' <rodrigo.montenegro(a)ndcn.ox.ac.uk> Subject: RE: [Freesurfer] Trouble Installing FreeSurfer {Disarmed} Importance: High Hi R, Thanks for the quick response. I have but still couldn’t go through the process. I have also read your e-mail but I have no idea what you refer to in your second e-mail. This is what I have got:  Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of fsbuild Sent: 28 January 2019 23:17 To: freesurfer(a)nmr.mgh.harvard.edu Cc: rodrigo.montenegro(a)ndcn.ox.ac.uk Subject: Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}         External Email - Use Caution        … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R._______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Postdoctoral position in Eating Disorders at UCSD
by Grethe, Amanda 01 Feb '19

01 Feb '19

External Email - Use Caution Research Postdoctoral Fellowship at UC San Diego’s Eating Disorders Center for Treatment and Research The University of California, San Diego Eating Disorders Center for Treatment and Research is an international leader in research on the neurobiology of eating disorders and related problems. We have IOP and day treatment programs for adults, adolescents, and children with eating disorders, as well as a medical stabilization unit in conjunction with Rady Children’s Hospital. UCSD EDC’s programs are growing quickly, and we are currently accepting applications for postdoctoral fellows. Current eating disorder treatments are of limited efficacy. New insight into neurobiological mechanisms that contribute to symptoms is supporting development of more effective interventions. The UCSD program is unique in that it has faculty and staff who focus on combining research into neurobiology with treatment development. This is an exciting opportunity for individuals to learn about brain and behavior and apply this knowledge to new treatment approaches. We also encourage applications from candidates who come from backgrounds outside of eating disorders, particularly anxiety, substance use, trauma, or pediatrics, and we have a strong preference for candidates who have experience or interest in functional neuroimaging. Many of our postdocs stay on in permanent staff or faculty positions. Research Postdoctoral Position Research postdoctoral fellow: to specialize in studying mechanisms underlying eating disorder symptoms and psychopathology (e.g., incentive processing, reinforcement learning, interoception). Experience and interest in neuroimaging (functional MRI, structural MRI) and neurocognitive assessment is preferred, as we have a strong neuroimaging program conducting research on the neurobiology of ED. The position will entail immersion in MR image analysis using one or more software tools, including AFNI, FSL, SPM, FreeSurfer, and R. Imaging sessions will take place at UCSD’s Center for Functional MRI, which is equipped with two research-dedicated GE 3T short-bore scanners. Experience with other experimental methodologies is also welcome. The ideal candidate would be a research-oriented person with a goal of an independent research career focused on cognition, brain functioning, and treatment development to translate research findings to improved clinical care of individuals with an eating disorder. Many of our research postdocs write training grants and transition to permanent staff or faculty positions. Appointment length is up to 2 years and is based upon the UC post-doctoral scholar salary scale. The position is available the summer of 2019, and applications will be accepted until the position is filled. Required qualifications • PhD in Clinical Psychology or related area • Experience in neurocognitive assessment preferred • Experience in neuroimaging or similar methods preferred • Preference for strong background and training in cognitive neuroscience and statistics • Established track record of publications To apply for this position, please email a cover letter, CV, and three references to Christina Wierenga, PhD (cwierenga(a)ucsd.edu<mailto:cwierenga@ucsd.edu>) and Amanda Bischoff-Grethe, PhD (agrethe(a)ucsd.edu<mailto:agrethe@ucsd.edu>). ---- Amanda Bischoff-Grethe Associate Adjunct Professor University of California, San Diego 9500 Gilman Drive MC 0738 La Jolla, CA 92093-0738 Tel: 858-246-0604 Fax: 858-246-0556

1 0

Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 01 Feb '19

01 Feb '19

External Email - Use Caution … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R. On , at 18:11  1/28/2019, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Rodrigo,Did you download the tar file freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz from this page, and attempt to follow the steps below ?https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallIf you do not have permission to untar (write files) into /usr/local, you could try using another path. But usually if the tar command has a problem it will echo some error/text to the terminal, e.g., "Permission denied", or say there was an error.If the command simply returns to the prompt than it should have succeeded, e.g., success with "$" bash shell prompt.$ tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$Please try and point out the step that does not work for you.- R.On , at 17:47  1/28/2019, Rodrigo Montenegro <rmontenegro11(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I’m a Medicine student at Oxford University and I have just registered to FreeSurfer. I just went through the registration process so I'm very new to FreeSurfer but have only run to problems so far and would like to ask for your help: 1.       I have register with FreeSurferWiki but can’t login: it gives me one of the following errors:i.                      “Error 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache serve”.ii.                   Or that it is an “Invalid username or password” (not sure if  2.       More importantly I have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to install FreeSurfer but the being totally new to Linux I have not had success to install it:i.                     I’m not sure if at all the files are unzipped from the .gz file.ii.                   And I have been unable to create the Bash files to define the environment for it. 3.        Finally, I notice that you do have an installation for Virtual Disk Image but the download for it (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu…) is a gz file not a .vdi file as it should be (see picture below): <image002.jpg> So either way I wasn’t able to get through with the installation and any help is appreciated. Could you please provide some advice? Many thanks, Rodrigo Montenegro+44(0)7503070807 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 3

Freesurfer Recon-all error
by Jones, Kevin 01 Feb '19

01 Feb '19

3 5

Pb testing the FreeSurfer Installation
by Lise_A 01 Feb '19

01 Feb '19

External Email - Use Caution Dear Sir or Madam, I've just installed the last version of FreeSurfer for Linux ( freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin…>), but I got some troubles testing it: When trying to follow Example 2 ( https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download) I get a "syntax error message": lise.aujoulat@ICM-COHEN-LF001 ~ $ *export SUBJECTS_DIR=/home/lise.aujoulat/Bureau/SUBJECTS_DATA* lise.aujoulat@ICM-COHEN-LF001 ~ $ * bash recon-all -i sample-001.nii.gz -s bert -all/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: erreur de syntaxe près du symbole inattendu « ( »/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: `set inputargs = ($argv);'* You can find a screen shot attached to this email. It seems that no one encountered this problem so far. I had installed the macOS version some months ago on my personal computer and encountered no problem at that time. How could I fix this? Thanks for your help, Lise -- Lise AUJOULAT MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France. Phone number: + 33 6 87 97 30 32 Mail: aujoulat.lise(a)gmail.com / lise.aujoulat(a)etu.upmc.fr

3 4

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 February 2019