Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

re-running recon-all after aseg.presurf.mgz edits
by Alexopoulos, Dimitrios 17 Jul '23

17 Jul '23

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these changes? I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 3

Can I use Freeview (tksurferfv) Tools on surface?
by Andy Kim 17 Jul '23

17 Jul '23

External Email - Use Caution Dear FreeSurfer Developers, Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D…) On the other hand, unfortunately, it seems that it only works in 3d volume space. So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag. Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form? Thank you in advance. Kind Regards, Andy (Junghyun) Kim

3 2

some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
by zlseu2109 17 Jul '23

17 Jul '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: zlseu2109(a)163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers, I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal) | | zlseu2109 | | zlseu2109(a)163.com |

3 4

can't generate 3D rendering
by Magang Visa 16 Jul '23

16 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, i'm attempting to open a 3D freeview but i don't see the 3D rendering i'm using this code to open the file freeview T1.mgz norm.mgz brain.mgz aseg.mgz 1) FreeSurfer version:Version 7 Release is 7.4.1 2) Platform: CentOS thanks [image: image.png]

1 0

Re: [Freesurfer] pop up does not get focus
by fsbuild 16 Jul '23

16 Jul '23

External Email - Use Caution What you report looks like an issue with WSL and not the X-Ming X-server or the fressurfer distribution.  You could try following the advice in the postings below. This posting mentions focus and user input may be getting lost if the window has gone into “select” mode,  stackoverflow.com/questions/53939435/wsl-terminal-forgets-to-update-and-los… This posting recommends disabling Linux GUI support by setting guiapplications=false in your %USERPROFILE%\.wslconfig file.  I’m not sure about this, because I’ve never seen this previously reported or had to try that edit. github.com/microsoft/wslg/issues/443 - R. On Jul 16, 2023, at 15:36, Tsahi Asher <tsahi.asher(a)mail.huji.ac.il> wrote:        External Email - Use Caution        Hello,I have a problem when i use freeview.Setup:Windows 11wsl ubuntu 22.04windows xserver - xming (vcxsrv) 1.20.14.0 with the following parameters<XLaunch WindowMode="MultiWindow" ClientMode="NoClient" LocalClient="False" Display="-1" LocalProgram="xcalc" RemoteProgram="xterm" RemotePassword="" PrivateKey="" RemoteHost="" RemoteUser="" XDMCPHost="" XDMCPBroadcast="False" XDMCPIndirect="False" Clipboard="True" ClipboardPrimary="True" ExtraParams="" Wgl="False" DisableAC="False" XDMCPTerminate="False"/>freesurfer for ubuntu 7.4.1problem:When i use the app some popup windows do not get focused, I have no way to make any button of the popup work, not with the mouse and not with the keyboard, not any button in the popup, but also not main windows buttons (close maximize etc), i also can not drag and move the windows. Attached are two examples from the freeview app. The "load surface overlay" is a pop up that is responding, the "configure overlay" pop up is the one that i can not get to work.Thank you,Tsahi<load.jpg><configure.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Freesurfer installation issue
by fsbuild 16 Jul '23

16 Jul '23

External Email - Use Caution  Try using apt to do the install, and you could also preface the package name with its absolute path, /path/to/package $ sudo apt install /path/to/package/freesurfer_7.2.0_amd64.deb - R. On Jul 15, 2023, at 05:02, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debian format archivedpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install): dpkg-deb --control subprocess returned error exit status 2Errors were encountered while processing: freesurfer_7.2.0_amd64.debKindly request you to provide a solution to solve this issue.Thanks in advanceRamesh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

pop up does not get focus
by Tsahi Asher 16 Jul '23

16 Jul '23

1 0

Ask for help
by 楚佳悦 16 Jul '23

16 Jul '23

External Email - Use Caution Dear freesurfer: I don't want to receive external emails from freesurfer. Please help me cancel it! Thank you very much! Best wishes, Jiayue

2 1

Re: [Freesurfer] Password 7zip Ubuntu VM
by m tl 16 Jul '23

16 Jul '23

External Email - Use Caution Hello I hope this email finds you well. I am reaching out to inquire about obtaining the password for the 7zip file associated with the FreeSurfer VirtualBox VM Image. I recently downloaded the image from your website and encountered difficulty accessing its contents due to the password protection. I would be grateful if you could provide me with the necessary password or any instructions on how to obtain it. If there are any additional requirements or steps involved in the process, please let me know, and I will gladly comply with them. Thank you very much for your time and consideration. I look forward to your prompt response and to continuing my research using FreeSurfer. Best regards, Martin

1 0

Freesurfer virtual machine zip password
by José 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Freesurfer mailing list, I just downloaded the ubuntu virtual machine from the freesurfer wiki site, to run freesurfer in windows. However, when unzipping the file I'm asked for a password. Could you please provide me with the password so I can set up the VM and get started with freesurfer? Thanks in advance. Best regards, José Silva

1 0

← Newer
1
...
6
7
8
9
10
11
12
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2023