you shouldn't be running the initial recon with a flair volume though,
are you? That would utterly fail I would think
Bruce
On Tue, 16 Apr 2013, Watson,
Christopher wrote:
> 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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