[Freesurfer] Creating masks on a MNI averaged brain

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Dear Freesurfer experts,

My analysis is in FSL. But I wish to use the more detailed segmentaHA_T1.sh available in Freesurfer.

I wish to avoid the time & resource to ‘recon-all’ all my participants’ T1 images, and only to transfer a set of masks superimposed on an averaged (MNI 1x 1x1 mm) brain – from Freesurfer to fsl. All my T1 images are pre-processed and registered using the FSL pipeline.

So my first question is –

Would it be sensible to create anatomical masks in Freesurfer directly onto the MNI standard brain image, rather that each participants’ T1, one by one?

My second question is about running recon-all commands in parallel on a cluster –

I read online that there is a -parallel flag in recent version of FS, so no need of installing a parallel package. However I was not able to use this flag in my FS 7.2.0. Please could you let me know how parallelization work on a cluster?

Thank you very much! I look forward to hearing your advices!

Best wishes, Lin

-- Lin Qiu DPhil Student University of Oxford, Nuffield Department of Clinical Neurosciences John Radcliffe Hospital, Oxford OX3 9DU Email: lin.qiu@ndcn.ox.ac.ukmailto:lin.qiu@ndcn.ox.ac.uk