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
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