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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@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
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
