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