> On 30 Aug 2017, at 03:59, Chelsea <[log in to unmask]> wrote:
> Hi there,
> I am trying to do tractography from a standard space mask (to another standard space termination mask). In the FSL tutorial (fdt2) it says to use standard as a reference image. Where in the Fdt gui do we input the reference image? Additionally, if running probtrackx2 from the command line, how do we specific standard as the reference image?
For the command line, you can find a standard space image in $FSLDIR/data/standard. In the GUI, the seed mask is taken to be the reference volume, unless you are using surfaces in which case a box will appear for you to input a reference volume.
> Finally, when clicking nonlinear it asks to Select Seed to diff transform and Select diff to Seed transorm. Would those be standard2diff_warp and diff2standard_warp respectively?
> Thank you for your help,