Dear all,

I have already run the FreeSurfer 5.2 -all, and I would like to improve the pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following syntax:

recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

It starts running but then it hangs, I never get an output. The FLAIR file is in nifti format.

I am not sure what I am doing wrong: it is the syntax? Should I first convert the FLAIR file to .mgz?

Thank you in advance for the help!

Veronica Popescu, MD, MSc

Department of Radiology & Nuclear Medicine

VU University Medical Center

Amsterdam, The Netherlands