Hi Veronica,
we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?
thanks
Bruce
On Mon, 15 Apr 2013, Popescu, Veronica wrote:
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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