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In order to use FreeSurfer-generated surfaces as masks in probtrackx, you need to add the following command line options (which can also be set in the GUI):
--meshspace=freesurfer --seedref=orig.nii.gz
Where the orig.nii.gz file can be generated by converting the orig.mgz file (found in the FreeSurfer output directories) using FreeSurfer's mri_convert.
Additionally, using FreeSurfer with probtrackx requires a few specific steps that we describe below.
FreeSurfer Registration
FreeSurfer operates in a conformed space, which is different from the original structural image space that it has received as an input. When tracking from FreeSurfer surfaces, it is necessary to provide a transformation between conformed space and diffusion space. Below are a few steps that show how to achieve this.
We assume that you have ran dtifit on your diffusion data with an FA map called dti_FA.nii.gz (we recommend using an FA map to register to T1 structural images), and also that you have a file called struct.nii.gz that you have used as an input to FreeSurfer recon_all program.
We will carry on a few steps that aim at calculating the following transformations: fa<->struct<->freesurfer. Then we will concatenate these transformations to get fa<->freesurfer.
Let us start with struct<->freesufer (assuming john is the subject's name):
GIFTI-format surface-based connectivity with probtrackx2.0 GPU
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#PROBTRACKX_-_probabilistic_tracking_with_crossing_fibres
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