[Freesurfer] can I run recon-all in parallel

2012-06-29 Thread Dian "Oscar" Jiao
Hi, I am new to freesurfer. It seems recon-all is the most time-consuming command. I tried to run it on a HPC cluster with MPI and got the error "ERROR: it appears that recon-all is already running and re-run" and the job stopped right away. Is the code even parallelized? I had no problem runnin

[Freesurfer] error running FS on mac

2012-06-27 Thread Dian "Oscar" Jiao
Hi, I just installed Freesurfer on my Mac Lion. When I ran recon-all, I got the following error. Can't locate MNI/Startup.pm in @INC (@INC contains:) at Applications/freesurfer/mni/bin/nu_coorect line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line