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Great – works now. Thanks!
From: on behalf of "Dicamillo, Robert"
Reply-To: Freesurfer support list
Date: Thursday, October 25, 2018 at 11:55 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer commands not found -
Hello Ashesh,
You need someone with admin or root privileges to install tcsh (and I would do
csh as well) shells on your machine so those scripts can run, i.e.
$ sudo apt-get install tcsh
$ sudo apt-get install csh
On Oct 25, 2018, at 13:35, Thaker, Ashesh A
mailto:ashesh.tha...@ucdenver.edu>>
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Dear Freesurfer team,
Surely there is a simple fix to my problem, but I've been unable to succesfully
run Freesurfer commands after many attempts (with my very basic bash knowledge)
and searching prior archives.
I'm running Freesurfer on a 64-bit
you can do something like
mri_cor2label --i aseg.mgz --id 17 --label left.hippo.label
This will output tkregisterRAS coordinates which you can convert to
voxel coords using
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems case #1
On 07/25/2017 02:02 AM, Aziz Nanthaamornphong wrote:
Hi Freesurfer Experts,
Currently, I am using these command excited in Matlab to extract the
coordinates of volume.
*mri = MRIread('aseg.mgz');pos = find(mri.vol == 17 | mri.vol == 53);*
*[i,j,k] = ind2sub(mri.volsize,pos);*
I would like to run these command in the Freesurfer itself rather than
Hi Markus,
Thank you for this, yes I am running Mac OS 10.9.2, and the freesurfer
command freeview loads the data fine when I start up matlab from the bash
terminal (even without using XQuartz, my equivalent of X11) and call this
command.
Thanks for the quick help!
Barbara
On Tue, Sep 9, 2014 a
Hi Barbara,
You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)
Best,
Markus
2014-09-09 13:45 GMT+02:00 Barbara
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they w
