Veronica, Can you send me the recon-all.log? The one where it is getting hung when you run this:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial this should work, by importing the flair and then re-running the surface creation code, but perhaps there is a dependency bug that was missed. Nick On Tue, 2013-04-16 at 09:27 -0400, Bruce Fischl wrote: > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer