Hi Nicole – You can skip the eddy current correction, check the TRACULA tutorial for how to do so. BET thresholds don’t matter here, because TRACULA will make a brain mask out of the freesurfer segmentation and use it to mask your DWIs.

Best,

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nicole Mckay <nmck031@aucklanduni.ac.nzmailto:nmck031@aucklanduni.ac.nz> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, January 25, 2018 at 5:36 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula

Hi all,

I have previously run full diffusion preprocessing using FSL and would like to now use tracula to construct the paths.

Is it possible to input my already processed data into the tracula pipeline for just the path reconstruction and stats steps? I have already run recon-all too. Or perhaps is there a way I can insert my own corrected images into the prep step if it is running extra steps.

My main reason for not wanting to start again from scratch is timing (I have 100 participants), but also that my preprocessing steps are slightly different. I use Eddy instead of Eddy_correct, and some of my participants needed individualised values for BET to work correctly.

Any advice would be great, Nicole