Dear FreeSurfers,
I am using "mri_vol2surf" to map my SPM processed t images onto 9 intermediate surfaces created by "mris_expand". When every step is done manually it works perfectly. However, for very large datasets I would need to run mri_vol2surf for multiple subjects, multiple conditions, multiple ROIs, and etc. Therefore, automising the command to be executed on multiple datasets at once is a requirement. Unfortunately there is no Matlab function for mri_vol2surf, this brings me to my question: how can I use mri_vol2surf in Matlab for multiple datasets, how the command must be written, how the variables and directories must be redefined so Matlab and FreeSurfer both have access to what they need. In other words, how mri_vol2surf should be used, either in Matlab or in shell, in order to be executed on multiple datasets at once? As a side note I am using Mac OS 10.9.5 with FreeSurfer v5.3.0. Thank you in advance for your guidance.
Kind Regards,
Fatemeh Molaei-Vaneghi
Max Planck Institute for Biological Cybernetics Tübingen Germany