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:
External Email - Use CautionHi!
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer