External Email - Use Caution
Hi Douglas,
Thank you for your response! I really appreciate it.
I ran the command – it works if I replace --i with --mov.
How can I use the new FLAIRraw.lta to create a new FLAIR-based pial
surface? For example, should I run recon-all -autorecon2 or some later step?
Also, we were assuming that registration of the FLAIR to the T1 was the
problem (underestimated pial surface), since the FLAIR.mgz produced by
Freesurfer was not well registered to the T1.mgz. So, if that's the case,
and I have another well-registered FLAIR (using FSL or SPM), is there a way
to skip the Freesurfer registration and use that FLAIR to create the FLAIR
pial surface?
Thank you for your help in advance!
All the best,
Edina Szabo
__
Edina Szabo, PhD
Research Fellow
Department of Anesthesiology, Critical Care and Pain Medicine
Boston Children's Hospital | Harvard Medical School
-----------------
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
_______________________________________________
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://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
