Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Tkmedit gui download
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 01 Apr '20

01 Apr '20

Hi all, I am still trying to adapt to working from home, and I am forced to work with incredibly slow download speeds. I am trying to download FS6.0 for mac for the sole purpose of using tkmedit, rather than the entire toolbox, just so I can edit brains (I anticipate downloading FS6.0 for mac in my house would take like 36 hours). Can someone provide me a link to download just the necessary codes for tkmedit in macs? I would greatly appreciate this. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Is it possible to "fill in" the region delimited by an ROI label?
by Mohammad Rashid 01 Apr '20

01 Apr '20

External Email - Use Caution Hi all, I'm able to load in a yellow outline for the entorhinal region by loading a file named ?h.entorhinal_exvivo.label as a volume. (I first load in a brain image such as brain.mgz, and then display the outline on top of it.) Is it possible to get a solid highlight of the entorhinal region in this manner, as opposed to just an outline of the region? (Strangely enough, if I load ?h.entorhinal_exvivo.label as a label on an surface file, such as ?h.inflated, then the entorhinal region is seen filled in with a yellow color on the 3D surface. This is the effect I want, except on a 2D volume.) Any help is greatly appreciated, Mohammad

2 4

Tutorial Data Error Message
by Batra, Vinita R. 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Team, When I run the test_commands.sh.15 I get the following error message as shown below. dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom Reason: image not found Abort Abort dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom Reason: image not found Saving session... ...copying shared history... ...saving history...truncating history files... ...completed. Please help me with this. Thank you Vinita Batra

2 1

Re: [Freesurfer] Tutorial Data Error Message
by fsbuild 01 Apr '20

01 Apr '20

External Email - Use Caution Hello Vinita, Try installing the X software from the Xquartz  distribution, https://www.xquartz.org/ - just download and install. - R. On Apr 1, 2020, at 15:27, Batra, Vinita R. <vbatra(a)lsuhsc.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Team, When I run the test_commands.sh.15I get the following error message as shown below. dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib  Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom  Reason: image not foundAbortAbortdyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib  Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom  Reason: image not foundSaving session......copying shared history......saving history...truncating history files......completed.  Please help me with this. Thank you Vinita Batra_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Setup & Configuration Error
by Hossein Shooli 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Development Team, I have just install the FreeSurfer (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) on my mac Catalina OS (10.15.2). The installation path was set as default (/Application/freesurfer). Then, in the Setup & Configuration step I have faced some troubles that I'm in need to fix it. In this step the first line " $> export FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ". an error occurred as below: Hosseins-MacBook-Pro:~ dhs$ > export FREESURFER_HOME=/Applications/freesurfer Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory Hosseins-MacBook-Pro:~ dhs$ I have done this steps using bash shell but the results was the same as following: bash-3.2$ chsh -s /bin/sh Changing shell for dhs. Password for dhs: bash-3.2$ > export FREESURFER_HOME=/Applications/freesurfer/ bash-3.2$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer//SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer//SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory bash-3.2$ I have checked the mail archives but there no answer to my problem. Please help me to solve the issue and setup freesurfer successfully. Bests regard Hossein [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/01/20, 12:44:24 PM

2 2

Recon-all exited with errors
by Wang, Lily 01 Apr '20

01 Apr '20

Hi All, I have a subject whose T1 quality is quite good but reconstruction exited with errors so I am not sure what the issue could be. Attached is the recon-all.log. Could it be that the subject is very old and has a lot of degeneration? Thank you, Lily

3 5

Color map - color bar
by Adam Rytina 01 Apr '20

01 Apr '20

External Email - Use Caution Hello all, I did the post-processing on brain images in Freesurfer. I changed the color coding to display where MR signals values are higher or lower. I need to add the color bar onto the image in order to easily identify what "blue" or "red" color means. Please, in which program is it possible to change the color map and to add the color bar as well? I tried to implement it in ITK-SNAP but the option of adding the color bar is not implemented there. Thanks a lot Regards Adam

2 1

Re: [Freesurfer] Setup & Configuration Error (Mac OS Catalina)
by fsbuild 01 Apr '20

01 Apr '20

External Email - Use Caution Hello Hossein, Not sure what you have set for your shell in terminal, but the default shell in Mac OS 10.15 is no longer bash but zsh instead. So first try running the bash shell, $ bash … then try again to do … $ export FREESURFER_HOME=/Applications/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On Apr 1, 2020, at 02:35, Hossein Shooli <h.shooly(a)gmail.com> wrote:return: can only `return' from a function or sourced script

1 0

Setup & Configuration Error
by Hossein Shooli 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Development Team, I have just install the FreeSurfer (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) on my mac Catalina OS (10.15.2). The installation path was set as default (/Application/freesurfer). Then, in the Setup & Configuration step I have faced some troubles that I'm in need to fix it. In this step the first line " $> export FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ". an error occurred as below: Hosseins-MacBook-Pro:~ dhs$ > export FREESURFER_HOME=/Applications/freesurfer Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory Hosseins-MacBook-Pro:~ dhs$ I have checked the mail archives but there no answer to my problem. Please help me solve the issue and setup freesurfer successfully. Bests regard Hossein [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/01/20, 11:04:28 AM

1 0

kill recon-all programatically/remotely
by Octavian Lie 31 Mar '20

31 Mar '20

External Email - Use Caution Dear All, Is there a way to kill a recon-all run on linux via ssh/putty. Ctrl+C is not working, obviously, and it is not easy to figure out which process encodes the recon-all runs with commands such as ps aux, top etc. One gross way may be removing the subject directory all together midway, but not sure how this affects FS, subsequent runs Thank you, Octavian

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 April 2020