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:

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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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