I would like to use the MarsAtlas to parcellate an individual MRI. I ran the command recon-all in Freesurfer and I've encountered problems with the Freesurfer/Brainvisa interface and I hope that you can help me with it.
Some functions in the Freesurfer toolbox within BrainVisa are greyed out, and when I try to import the results from the Freesurfer pipeline, I get an error indicating that the Freesurfer was not found. So, this is the description of the problem:
- The Freesurfer environment is defined in the bashrc file.
- The userlevel in BrainVisa is set to Expert.
- Brainvisa and Freesurfer are both installed in the folder /usr/local/
- When I go to BrainVisa--> Preferences --> Freesurfer, every time I run BrainVisa, I have to define the HOME and SUBJECTS_DIR of Freesurfer.
- I do not receive any warning in the terminal when BrainVisa is open.
- A recommendation from a previous post in the forum (http://brainvisa.info/forum/viewtopic.php?t=1746) was to take out the libstdc* library, although, unlike said post, I don’t receive any warnings in the terminal when I run BrainVisa. I removed it but I have the same problem.
- When I go to Brainvisa--> Show Log--> BrainVisa session --> Read processes, for some functions of Freesurfer, it says:
Code: Select all
The process freesurfer/processes/Tools/freesurferPipeline.py is not available: FreeSurfer not available.
processes.py (4371) in readProcess:
raise ValidationError(HTMLMessage("The process <em>"+relative_path(processInfo.fileName, neuroConfig.toolboxesDir)+"</em> is not available: <b>"+unicode(e)+"</b>"))
The processes showing this error are: freesurferPipelineComplete.py , freesurferPipeline.py , freesurferMgzToNifti.py , freesurferNiftiToMgz.py , freesurferAverageSubjectLongitudinal.py , freesurferLongitudinalPipeline.py
I’m running BrainVISA 4.5.0 in Ubuntu 12.04, which is running in a virtual machine in a Windows laptop.
Please let me know if you have any ideas.