I had a freesurfer-Rstudio issue today which I solved by just working on a Linux shell script. However, I wanted to know if it is possible to send freesurfer related commands from R studio out of curiosity.

My Problem:

• I was trying to use freesurfer commands like mri_convert by sending them through the "system()" function in R.   
• However, I got a "sh: mri_convert command not found" error. This indicates freesurfer is not sourced into the Linux terminal in the R Session.
  

My Question: Is it possible to run freesurfer related commands from the rstudio terminal?

What I did:

1. I looked up this problem online and found a similar example where the user needed the function bedtools. But updating the system path still threw the same error with .
2. In addition, I was able to send commands like "dcm2niix" from R using the system function mentioned above.  I am certain this is a sourcing issue. 
   

Shrikanth