Dear Bruce, I ran the follwing: autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all. And my file was indeed a 3D T1 scan. Thank you very much! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, 16 April, 2013 15:02 To: Popescu, Veronica Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] pial surface with FLAIR
Hi Veronica
what recon-all command lines did you run? You did run it with a T1 first, right?
Bruce On Tue, 16 Apr 2013, Popescu, Veronica wrote:
Hi, Christopher! Best of luck to you all in these difficult times! Thank you very much for your advice. I'll try this as well. Best wishes, Veronica
-----Original Message----- From: Watson, Christopher [mailto:Christopher.Watson@childrens.harvard.edu] Sent: Tuesday, 16 April, 2013 07:15 To: Bruce Fischl; Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: 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
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