Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

Smooth surface overlay
by Jacobs, H (NP) 13 Aug '19

13 Aug '19

External Email - Use Caution Hi all, I created an overlay surface map of my analyses (with pvalues in log10) using R. Now I would like to smooth this map to extract clusters and I tried to use: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 3 --sval lh_analyses.mgh --tval lh_analyses_smoothed.mgh --cortex This seems to work, but is there a way to also map the original values in the output surface overlay? I now have clusters that are colored yellow with no statistical information anymore. I also tried to use: mri_surfcluster --in lh_analyses.mgh --thmin 1.3 --thmax 6 --no-adjust --subject fsaverage --fwhm 3 --sum lh_analyses_smoothed_summary --hemi lh --sign pos But whether or not I add in the smoothing, the output is the same. Any help would be greatly appreciated. Thanks! Heidi

2 2

reconstructing female vs male data
by Carissa Liana Grijalva 13 Aug '19

13 Aug '19

External Email - Use Caution Hello, I am a graduate student at the University of Arizona and we have been using the FreeSurfer Program to reconstruct MRI data from healthy patients and patients with a mild cognitive impairment. We are comparing the statistics for different brain regions, however, we would like to take age and gender into consideration. Does the main atlas used to map/segment regions in the brain have a default (male) brain or certain age? If so, is there a way to specify the data is from a female during the recon all code? Such as a tag at the end? Is it possible to include something like this for age as well? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

2 2

Which registration file to choose when to using tksurfer
by Hang Zeng 13 Aug '19

13 Aug '19

External Email - Use Caution Dear freesurfers, I ran the retinotopy pipline (like preproc-sess, mkanalysis-sess, Selxavg3-sess) and now I want to view the results with tksurfer. When I call tksurfer <subject> <hemisphere> inflated and try to overlay the reall.nii.gz and imag.nii.gz, I need to choose a registration file. I don't see any registration file in the eccen or polar folder, but in the '/Sess/bold' folder I see the ''init.register.dof6.dat', 'register.dof6.dat.mincost', 'register.dof6.dat.param', 'register.dof6.dat.sum', 'register.dof6.dat~' and some other files. I am not sure whether the ''init.register.dof6.dat' is the right one to choose. Or did I miss some steps? Also, I am wondering what do the angle.nii, angle.masked.nii and fieldsign.nii mean. Thank you so much! Zoe

2 1

hippocampal subfields {Disarmed}
by 郑凤莲 13 Aug '19

13 Aug '19

External Email - Use Caution Dear experts, I have segmented hippocampus into 13 subfields using FS6.0. Then, I want to study the function connectivity between sibfields. How can I utilize this template to do this research? Is it possible? Thanks for your reply in advance. Sincerely, Zhemg | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

1 0

Deconvolution with FSFAST
by Caspar M. Schwiedrzik 12 Aug '19

12 Aug '19

External Email - Use Caution Hi! I was wondering whether it is possible to do deconvolution of an fMRI time series with FSFAST? Specifically, I would like to get a deconvolved signal from a region of interest to prepare predictors for a PPI analysis. Additional considerations: data is from an event-related design, and was acquired with MION contrast agent. I found some older documentation on selxavg2, but I am not sure whether that still applies (I am using version 5.3). Also, I do not need an event-related average as output, but a continuous time series. Thanks for any advice! Caspar

2 2

overlay on subcortical surfaces
by cr439＠cam.ac.uk 12 Aug '19

12 Aug '19

External Email - Use Caution Dear Freesurfer Experts, As it happens for cortical surface mapping I would like to obtain the same for subcortical structures. I have generated the subcortical surfaces using fsaverage brain’s aseg.mgz with the tool given in: https://github.com/thomas-vincent/nipic/wiki/%5BFreesurfer%5D-Get-surfaces-… <https://github.com/thomas-vincent/nipic/wiki/[Freesurfer]-Get-surfaces-of-s…> With this I would like overlay data on them. I have used mrf_vol2surf command mri_vol2surf --src sub_me_c.nii --out lh.sub_me_c_surf.mgz --hemi lh --mni152reg as my overlays are in MNI space. However, I am not able to overlay these on the surface. I think this is because the data file that is generated (lh.sub_me_c_surf.mgz) hasn’t got the same number of vertices as the subcortical generated surface (163842 vertices of the overlay file to 37722 vertices of the surface file). Could you advice me on the best way to approach this? Many thanks. Best wishes, Catarina -------------------------------------------- Dr Catarina Rua Post-Doctoral Researcher University of Cambridge Telephone: 01223 746 458 Email: cr439(a)cam.ac.uk

2 1

Re: [Freesurfer] libs dependents for ''preproc-sess'' command {Disarmed}
by fsbuild 11 Aug '19

11 Aug '19

External Email - Use Caution Hello Zoe, You should use the package install tools on Debian to install libpng (or any other missing libraries) for your distribution. On CentOS 7 you would do something like, $ sudo yum install libpng12.x86_64 libpng12-devel.x86_64 But like Ubuntu linux, I’m not sure that libpng12 is directly available in recent releases of Debian linux.  I found this link for getting and installing libpng12 for Debian,https://packages.ubuntu.com/xenial/amd64/libpng12-0/download Although we do not officially support building freesurfer on Debian Linux, it would be good to know what version of Debian linux you are running. - R. On Aug 11, 2019, at 05:38, Hang Zeng <zenghang14(a)gmail.com> wrote:        External Email - Use Caution        Dear Sir or Madam,I am running preproc-sess command on Linux Debian. The thing is it shows error msg like '3dvolreg.afni error while loading shares library :libXp.so.6. No such file or directory. After I installed the libXp.so.6, other lib like libpng is required. I am wondering what might be the causes, and how to fix it. If it is indeed the problem of libs, can I have a list of the dependent libraries for that command? Best regards,Zoe_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] I got a problem with open Freeview via X
by fsbuild 11 Aug '19

11 Aug '19

External Email - Use Caution Did you use the Ubuntu package manager tools to install X and also a driver for the graphics card?   It may not work to download a driver from the NVIDIA web site depending upon what is on your machine - or if it is not supported. For X install you could do, $ sudo apt-get install xorg xorg-dev libx11-dev This post might help for installing the NVIDIA drivers, https://linuxconfig.org/how-to-install-the-nvidia-drivers-on-ubuntu-18-04-b… - R On Aug 11, 2019, at 11:53, 송민석학부생 <21700371(a)handong.edu> wrote:        External Email - Use Caution        When I try to execute commands "glxgears" or "glxinfo", I got similar error message.Both of error message says same messages.X Error of failed request:  BadValue (integer parameter out of range for operation)  Major opcode of failed request:  149 (GLX)  Minor opcode of failed request:  24 (X_GLXCreateNewContext)  Value in failed request:  0x0  Serial number of failed request:  19  Current serial number in output stream:  20I thought my graphic card is ok because the Firefox run on X11 after I install graphic card driver, but... umm.. it is sure that error on graphic card settings. I try to found the error about GLX. Thanks for your help.2019년 8월 11일 (일) 오후 5:59, Tim Schäfer <ts+ml(a)rcmd.xn--org>-4f21ay07k 작성:        External Email - Use Caution        I'm quite sure that this is a general problem with your graphics setup that is unrelated to FreeSurfer. Can you run other software that uses your graphics card (e.g., does running glxgears produce load on your nvidia GPU), and could you post the output of `glxinfo`?Tim> On August 11, 2019 at 8:44 AM 송민석학부생 <21700371(a)handong.edu> wrote:> > >         External Email - Use Caution        > > I installed ubuntu 18.04.3 in my new server and also installed Freesurfer..> In this server, I have two graphic cards which are RTX 2080 ti.> > First, I tried to open Freeview without graphic driver, it is failed.> So I install the graphic driver.>   NVIDIA 418.56 / CUDA 10.1> > After I run the Freeview, I got this error message.> > X Error: BadValue (integer parameter out of range for operation) 2> >   Extension:    149 (Uknown extension)> >   Minor opcode: 3 (Unknown request)> >   Resource id:  0x0> > Abort (core dumped)> > > I can't find any log files, and can't get help on google search.> How can I solve this?> If you need any information about my server, please let me know.> > Thank you.> Harine.> _______________________________________________> Freesurfer mailing list> Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________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

1 0

TRACULA - OrientLAS issue for a subject
by Daniel Callow 11 Aug '19

11 Aug '19

External Email - Use Caution Hello, An additional one of my subjects (2/66) is having the exact same issue. I can send his dcminfo.dat information and .log info if that might help with troubleshooting the issue? I have still had no luck determining why OrientLAS in TRACULA doesn't seem to be working for these two subjects. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 0

I got a problem with open Freeview via X
by 송민석학부생 11 Aug '19

11 Aug '19

External Email - Use Caution I installed ubuntu 18.04.3 in my new server and also installed Freesurfer. In this server, I have two graphic cards which are RTX 2080 ti. First, I tried to open Freeview without graphic driver, it is failed. So I install the graphic driver. NVIDIA 418.56 / CUDA 10.1 After I run the Freeview, I got this error message. X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) I can't find any log files, and can't get help on google search. How can I solve this? If you need any information about my server, please let me know. Thank you. Harine.

2 2

← Newer
1
...
7
8
9
10
11
12
13
14
15
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 August 2019