Re: [Freesurfer] pial surface with FLAIR

Hi Veronica, Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"? And then, when you do the remaining recon-all steps:

recon-all -autorecon3 -s $SUBJECT -FLAIRpial

It has worked for me. (And worked very well! No edits necessary for the pial surface!) ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, April 15, 2013 12:31 PM To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] pial surface with FLAIR

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