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Hello,

I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker which is a tool that emulates a docker environment but does not require root user privileges in order to do so.

Anyway long story short when I attempt to run the udocker container of freesurfer 5.3.0-HCP with the default backend (PRoot) I receive a mmap error with mri_convert which reads: PROT_EXEC | PROT_WRITE. I am able to work around this error in certain instances, but that is not important here. What is important is that when I run a udocker container with freesurfer 6 mri_convert runs without issue.

My two questions are:

1) What differences exist between mri_convert between freesurfer 6 and 5.3.0 - HCP 2) Is there any way that I can download/install the newer version of mri_convert used for freesurfer 6 within 5.3.0 - HCP?

-Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay)