[Freesurfer] Freeview 3D brush

Freesurfer devs, I attempted a modification of freeview to insert a 3D brush. I have got it working. If you want to review it to put it in the main version it is there a way to submit the diff with the changes? Cheers, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch

Re: [Freesurfer] mri_binarize --gm

Hello. I have installed the new version of mri_binarize. However, I got a new problem. -- GNU libc version: 2.19 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free).

[Freesurfer] mri_binarize --gm

Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown I found there was a previous post suggest to use the new mri_binarize from https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binar

[Freesurfer] Mindboggle official software release and publication!

Announcing the official release of Mindboggle (http://mindboggle.info), open source software and data for analyzing the shapes of brain structures from human MRI data (processed through FreeSurfer and optionally through ANTs). The relea

[Freesurfer] Make_average_subject

Dear Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial w

Re: [Freesurfer] hippocampal subfields - T1

Got it, thanks for the help! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Thursday, February 23, 2017 4:05 PM To: Freesurfer support list Subject:

Re: [Freesurfer] hippocampal subfields - T1

Hi Batool, It’s not ideal, but if FreeSurfer does a decent job with the recon, something decent should come out of the subfields. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl

[Freesurfer] hippocampal subfields - T1

Hi, I was wondering if the hippocampal subfields analysis can still run on a lower resolution T1 scan than 1mm? One of our datasets has T1 scans with these dimensions: .93 x .93 x 1.3 . Would it still run on this dataset, if it's not the standard 1mm to begin with? Thanks! Batool __

[Freesurfer] Fwd: a question about freeview

Hello! I have problems running freeview but it used to work for me. Apparently, I am not the only user troubled by this. Please see my message to Sam below for details. Was there anything changed in freeview or in the Freesufer package in the past 12 months or so that may have caused this prob

[Freesurfer] Segmentation question

Hello, I was wondering how does Freesurfer segment the white matter from the grey matter. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intend

[Freesurfer] How to output particular area from stats subdir

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina ___

[Freesurfer] deformation fields

Hi All, I am trying to use the subcortical segmentation of regions from the longitudinal template to propogate to each time point using deformation fields. Does anyone know how if this is possible and if so, how can I do it? Thanks in advance, Amanda ___

[Freesurfer] recon-all error (6.0)

Hi All I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it stops when trying to transform to the "conformed" space. I get the following error after about a minute. I have not seen this error before. mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mg

[Freesurfer] Virtualbox for FS v6.0 ?

In past releases of FreeSurfer, there had been a version of the software suite contained in a VirtualBox (alongside the MacOS and Linux versions). Currently, I only see Mac & Linux. Is there a plan to release a VirtualBox edition of 6.0 ? ___ Freesurfer

Re: [Freesurfer] FS 6.0 Freeview

I've had the same problem, the only solution I have is to only open Freeview from terminal Cheers, Kevo > On 23 Feb 2017, at 10:58 pm, peng wrote: > > Dear Ruopeng, > >I have the same problem even before the current version 6 release, and it > was "solved" by invoke freeview from the co

Re: [Freesurfer] FS 6.0 Freeview

Dear Ruopeng, I have the same problem even before the current version 6 release, and it was "solved" by invoke freeview from the command line (term). I guess, to start from the icon, it might use different setup files. best Peng On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang wrote: > Or woul