Hi Cristian

it's not so much the difference in voxel size as it is the thickness and anisotropy of your FLAIR voxels. You would be much better off getting 1mm iso which would have comparable SNR to what you have now. You can try it, but the 3.5mm slice thickness will probably mess stuff up

sorry Bruce

On Thu, 18 Jul 2019, Leyton Moscoso, Cristian Eduardo wrote:

Dear Freesurfer experts,

I want to improve pial reconstruction by using FLAIR images in the pial reconstruction  (freesurfer v6.0).

Ø  recon-all -subject subjectname -FLAIR /path/to/FLAIR_volume -FLAIRpial -autorecon3

T1 was acquired in a 3T Phillips scanner with a isometric voxel size of 1 mm3, whereas FLAIR images have a voxel size of 0.5 x 0.5 x 3.5 mm.

Is there any issue in using different voxel sizes?

Thank you

Dr Cristian Leyton M

Research Fellow in Neurology Department of Neurology

Massachusetts General Hospital Harvard Medical School

149  13th Street

Charlestown, MA 02129