[Freesurfer] 'Best practice' for dealing with lesioned brains

Dear Freesurfer Team, I am attempting to complete a surface reconstruction on a dataset with traumatic lesions both to the grey and white matter. I am hoping to get some opinions on what would be considered as the 'Best practice' pipeline for dealing with such a dataset. We have access to T1 an

[Freesurfer] BBRegister + partial FoV fail

Dear List, I've been quite frustrated with the BBRegister results when trying to register a partial field of view EPI mean functional image to a T1 scan. I've tried different init arguments (fsl, spm, header) and none really work. I've found that the initial registration is causing the problem, si

Re: [Freesurfer] BBRegister + partial FoV fail

Hi Glad can you send us the full command line you are using and screen output? thanks Bruce On Tue, 11 Jul 2017, Paul Glad Mihai wrote: > Dear List, > > I've been quite frustrated with the BBRegister results when trying to > register a partial field of view EPI mean functional image to a T1 sc

Re: [Freesurfer] BBRegister + partial FoV fail

sure. I'll leave the rest to Doug except to say that a full head EPI is a pretty cheap and useful thing to get, and that it is not surprising the using the header (assuming they are same session) works better than anything else cheers Bruce On Tue, 11 Jul 2017, Paul Glad Mihai wrote: > Hi Bru

[Freesurfer] freeview command error

Hello, I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject. lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean:

Re: [Freesurfer] freeview command error

Hi Idil how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: Hello, I am inst

Re: [Freesurfer] freeview command error

Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I should set up freeview by sourcing those three files and use the *.csh extension? When opening the terminal again after recon-all to run this I did not do

Re: [Freesurfer] freeview command error

Hi Idil do you know what shell you are using in the terminal that you are trying to call freeview from? On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I s

Re: [Freesurfer] freeview command error

It is using bash. Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:30 PM To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] Simple math with freesurfer surface

? ? ? ? ? ? test.surf > > > ? ? ? ? ? ? This doesn't work as it wants me to > specify a type but I have no clue what > ? ? ? ? ? ? the type for the?surface is (or better, > it doesn't seem to be an option >

Re: [Freesurfer] GLM question

Thanks for your reply, I have a follow up on my first question - if however I was not looking for a main effect of gender, but for the main effect of something else (e.g. diagnosis), will it then be ok to include the unbalanced group (i.e. A-male), to control for gender? Thanks! Regards Yann On

Re: [Freesurfer] freeview command error

then you shouldn't be sourcing a script that uses setenv. Try sourcing $FREESURFER_HOME/FreeSurferEnv.sh cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: It is using bash. Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun.

[Freesurfer] mkbrainmask-sess: couldn't find register.dof6.lta

Dear freesurfer developers, I’d like to ask about an error I encountered in Freesurfer v6.0 with mkbrainmask-sess. I am using macOS Sierra. Here is the error: error:"ERROR: cannot find /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you might need to run register-ses

[Freesurfer] Please post to list: Subject: Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking to hire full time post-doctoral fellows in Computational Modeling of Brain Networks for their Cognitive & Systems Neuroscience Laboratory. This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertis

[Freesurfer] Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking to hire full time post-doctoral fellows in Computational Modeling of Brain Networks for their Cognitive & Systems Neuroscience Laboratory. This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertis

Re: [Freesurfer] viewing mri_glmfit FDR corrected results

Dear Doug, thank you so much for the feedback and all of your help! Best wishes Marco On Thu, Jul 6, 2017 at 1:45 AM, Douglas Greve wrote: > You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr > to the FDR you want. Set --subject fsaverage and set the ---hemi. Set > --a