Veronica,
Hi, can you copy me on the subject data upload? You can upload data here: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote:
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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