Try this
cd subject/mri
mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta
You can run with multiple threads by adding --threads N
where N is the number of threads
On 3/29/2021 5:18 PM, Edina Szabó wrote:
External Email - Use Caution
Dear All,
We are running recon-all on the latest version of FreeSurfer (v7.1.1).
We are using both T1 and FLAIR images to better define the pial
surfaces, but when we run the recommended command line (recon-all
-subject subjectname -i /path/to/input_volume -FLAIR
/path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very
underestimated (?.pial.FLAIR – and the aseg volume is based on these
surfaces), and we get better results without the FLAIR.
It seems that FreeSurfer mis-registers the FLAIR to the T1 during the
process. Is there a separate step we should do to register FLAIR to T1?
Thank you,
Edina
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