Surface-based connectivity

[pcamach2]

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

Using FreeSurfer surfaces

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):

tkregister2 --mov $SUBJECTS_DIR/john/mri/orig.mgz --targ $SUBJECTS_DIR/john/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat

Now transforming FA to struct:

flirt -in dti_FA -ref struct_brain -omat fa2struct.mat
convert_xfm -omat struct2fa.mat -inverse fa2struct.mat

The final stage is to concatenate these transformations:

convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat
convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat