Hi - Running topup is not a problem. Just make sure that there's as many entries in the gradient table and b-value table as there are frames in the DWI file. So if with topup you're combining 2 sets of DWIs (collected with opposite phase-encode directions), you also have to combine the corresponding gradient vectors and b-values.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Knut J Bjuland [knutjorgen@outlook.com] Sent: Thursday, February 09, 2017 4:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Topup before trac-all

Hi,

I would like to preprocess my dti data with topup (from FSL) before running trac-all. Is this a sensible approach? When I tried running trac-all -prep with the output file from topup (*_hifi_nodif.nii.gz) I got an error message:

mv -f /usit/abel/<....>/topuop/146/dmri/bvecs /usit/abel/<...>/topuop/146/dmri/bvecs.norot xfmrot /usit/abel/<...>/topuop/146/dmri/dwi.ecclog /usit/abel/<...>topuop/146/dmri/bvecs.norot /usit/abel/<...>/topuop/146/dmri/bvecs

R: Subscript out of range.

It seems that there's a problem with bvecs and bvals. Should I reorganise my bvec and bvals?

Thank you!

Knut J Bjuland