1. We don't have much experience with this. 3mm is pretty thick so it may not work, but the only way to find out is to try

2. I'll leave this for Eugenio.

3. Yes, I think it could help, although note that part of the point of using T1/T2 is that the bias field cancels

cheers Bruce

On Thu, 5 Nov 2015, Ajay Kurani wrote:

Hello Freesurfer experts,       I am working with a database of pre-collected scans.  Although the T1 images are collected at 1x1x1 mm^3 resolution, the T2 and proton density scans are .938x.938x3 mm^3.

1. I wanted to see if you think that using the T2 scans for recon-all would

hurt or help the pial reconstruction/cortical thickness measurements based on it being much thicker of a volume?

2. Would the scans help with hippocampal subfield analysis based on this

resolution?

3. I am interested in using T1/T2 scans for B1 bias field correction

(similar to the HCP minimum pipeline paper).  I think that using these scans would be ok since the bias field is supposed to be smooth, however I wanted to see your thoughts regarding using the T2 scans of this resolution for the B1 bias-field estimation.

Any guidance to any of these questions would be much appreciated!

Sincerely,

Ajay Kurani