Hello there,
I am a begginer in brainstorm and have no computer backgraound. I have installed Freesurfer version 7.2.0 and also brainstorm. When I open the MRI segmentation in brainstorm, there is no Freesurfer option in it. Moreover when I try to run freesurfer manally in bash environment in Linux VM in my windows system the last command
source $FREESURFER_HOME/FreeSurferEnv.sh
does not work and it says that there is no file or directory.
I have delete the brainstorm3 file and downloaded it again but it does not get updated.
I have got stuck in this step for days.
Would you please help me with this problem?
When I open the MRI segmentation in brainstorm, there is no Freesurfer option in it.
If you have Matlab installed on a Windows system, this does not allow running FreeSurfer, which is available only on Linux and MacOS. If you have a Linux VM with FreeSurfer installed, then your Matlab+Brainstorm should be installed on that VM too. But I don't recommend this, as it would be complicated to set up and would slow down a lot the Brainstorm.
Moreover when I try to run freesurfer manally in bash environment in Linux VM in my windows system the last command
source $FREESURFER_HOME/FreeSurferEnv.sh
does not work and it says that there is no file or directory.
If you are not familiar with Linux systems at all and don't have time to learn this now, I don't recommend you try to use FreeSurfer at all... You can try to run CAT from Brainstorm instead:
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12
1 Like
Thank you so much for response.
Just another question about MacOS and Freesurfer:
I tried to run FreeSurfer manually on MacOS system and in terminal window when I tried to operate
source $FREESURFER_HOME/FreeSurferEnv.sh
it says that there is not such a file.
Whay does this errror occur?
Your $FREESURFER_HOME environment variable is not set, and/or FreeSurfer is not installed in the folder pointed by it.
Google will help you find better places than this forum to get help with setting environment variables, installing programs in Linux, or configuring FreeSurfer.
OK, for sure.
Thank you so much again.