ok, then I don't see what's going wrong. Nick: any thoughts? On Tue, 16 Apr 2013, Popescu, Veronica wrote:
> > 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:fis...@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.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 >>> >>> >> >> >> > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
