you are trying to run a DWI image through recon-all? Sorry, it can only take T1w right now

On 3/12/2020 3:28 PM, Yixin Ma wrote:

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Hi Freesurfer experts,

I'm writing to ask if it's possible to run FreeSurfer Cortical Parcellation by just using the isoDWI image. If it's possible, it will reduce the scan time and avoid misregistration between T1 and DWI.

I started from just input the masked isoDWI (mask generated from MRtrix3) for -reconall command, and attached is a screenshot of the image of NU.mgz, which shows a clear delineation of WM/GM matter. So I think it's promising, although the recon-all stopped because of the wrong contrast. My ideas on tackling this problem are:

1. generate a corresponding "fake" T1-weighted image by

either adjusting the value directly or using a brain Atlas and deformable registration to create one. 2) Tweak some parameters in FreeSurfer.

Any suggestions or comments on my ideas are appreciated.

Thank you very much and all the best,

Yixin Ma

Screen Shot 2020-03-12 at 3.06.22 PM.png

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