Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Start a nNew thread

I have a question for "Segmentation of thalamic nuclei."
by Gwang-Won Kim 21 Jun '19

21 Jun '19

2 1

Registration of image volumes
by Shrabani Ghosh 21 Jun '19

21 Jun '19

External Email - Use Caution Hi freesurfer, I want to do registration on two image volumes nifti file. What are the commands I have to use to do the registration? Shrabani Ghosh

2 13

Re: [Freesurfer] Problem with installation test
by fsbuild 21 Jun '19

21 Jun '19

External Email - Use Caution Hello Shrabani, It looks like you do not have tcsh installed on your machine to run recon-all which is a tcsh script, If you are using RedHat/CentOS linux, $ sudo yum install tcsh Fedora linux $ sudo dnf install tcsh Ubuntu/debian linux, $ sudo apt-get install tcsh I would also probably install csh the same way as well. - R. On Jun 19, 2019, at 20:49, Shrabani Ghosh <srbn.ghosh99(a)gmail.com> wrote:        External Email - Use Caution        Hi  freesurfer, I am following the installation test as suggested (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and am currently stuck at example 2. When I ran recon-all, I got the output: "bash: /home/sghos003/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory"Any suggestions? Thank you.. Shrabani Ghosh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
by David S Lee 20 Jun '19

20 Jun '19

External Email - Use Caution Hello FreeSurfer Experts, I wanted to re-post this question (posted June 4th), yet did not receive your guidance: I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version. - 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but in the volumetric output, there are values for the regions. - 2 subjects' medical nuclei masks are located in the Putamen region (more superior/detached from the rest of the amygdala). I found the exact same inquiry RE: AAA region posted on April 30, 2019, but I did not see any response. What would be your recommended course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions? Thank you for your time, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

2 1

neuroimaging pre-registration template
by Remi gau 20 Jun '19

20 Jun '19

External Email - Use Caution Dear neuroimagers, We are organizing a hackathon<https://docs.google.com/document/d/1fckBKZEv_Jh0hJ6oVdYuK21krhZtnH0uhwcHp0j…> to develop a tool to help researchers creating a pre-registration / registered-report for neuroimaging experiments. The hackathon is embedded in the upcoming meeting of the Society for Improving Psychological Science<https://www.improvingpsych.org/SIPS2019/> in Rotterdam, NL, July 7-9. We are thus interested in the challenges that people face when preregistering their studies. If you have pre-registered (or currently are pre-registering) one of your neuroimaging study, please take 5 minutes to fill in this survey<https://docs.google.com/forms/d/e/1FAIpQLSe9IAMFThhpPday_tHvkh1dTGCqjcdKpeb…> and give us any feedback you can. Thank you for your time! Johannes Algermissen, David Mehler, Remi Gau, Stephan Heunis

1 0

Change colorbar font color in Freeview
by Saskia Helbling 20 Jun '19

20 Jun '19

External Email - Use Caution Hi all, I changed the background color in Freeview to white and now want to change the font color of the colorbar to black for better visibility. Any ideas on how to do this? Many thanks in advance, Saskia

1 0

problem with reconstruction
by Barletta, Valeria 20 Jun '19

20 Jun '19

Dear Freesurfers, I am having issues with a reconstruction which is giving me giant defects that I cannot correct (see screenshots). I tried to work on the wm and also to use the command recon-all -subject NIMMS02_2year_recon -T2 T2SPACE.nii.gz -T2pial -autorecon3 ... to correct using T2 images. Nothing worked. This never happened to me except this time. Any suggestions? Thank you a lot, Vale

2 2

Parcellation to FS surface annotation
by Williamson, Brady 19 Jun '19

19 Jun '19

External Email - Use Caution Hello, I am trying to convert parcellations in MNI space (BrainNetome and Craddock 200) to a surface annotation file in fsaverage space. I have seen several posts that seem to talk about steps that may be applicable but none of them are very efficient. Is there an easy/direct way to do this conversion? It seems like I am missing something really obvious, like a one line command, that would do the trick. Thank you for any assistance, Brady

2 1

Problem with installation test
by Shrabani Ghosh 19 Jun '19

19 Jun '19

External Email - Use Caution Hi freesurfer, I am following the installation test as suggested ( https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and am currently stuck at example 2. When I ran recon-all, I got the output: "bash: /home/sghos003/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory" Any suggestions? Thank you. Shrabani Ghosh

1 0

Re: [Freesurfer] Longitudinal Masking and FDR
by Hua, Jessica 19 Jun '19

19 Jun '19

External Email - Use Caution Dear Kersten, Thank you so much for your help! 1. As recommended, I masked my analyses using the label. 2. And that would be great if you could take a look at it when you have time. In the mean time, I will continue to try to figure out how to modify the FDR2 script. Best, Jessica Hua

1 0

← Newer
1
...
4
5
6
7
8
9
10
...
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 2019