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
> >>>
> >>>
> >>
> >>
> >>
> >
> >
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> >
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