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.wat...@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-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.
