You did not send your recon-all command but my guess is that it stopped without error because you did not include a directive (eg, -all). But in any event, you cannot run an MT image through recon-all

On 10/29/2021 3:35 AM, Marlene Tahedl wrote:

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Hi!

I have a couple of Magnetization Transfer MR images from a group of patients which I would like to analyze using the FreeSurfer pipeline. However, when applying "recon-all" to those images, the algorithm stops after just a few minutes. Although it says "finished without error", no images have been produced. Is there a way to apply recon-all to MT, maybe some conversion to make the MT images look more like a T1?

Thanks! Marlene.

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