Working with structural data
This tutorial covers TractoR’s facilities for working with structural T1-weighted or T2-weighted MRI images. These are presently limited to importing files from DICOM and parcellating the brain into anatomical regions.
Structural images relevant to a particular session, say
/data/subject1, may be imported using a command like
tractor import /data/subject1 /data/dicom/subject1/T1W_sequence ImageWeighting:t1
ImageWeighting option tells TractoR that this is a T1-weighted volume. This option may also be set to
t2 for T2-weighted data,
pd for proton density weighted data, or
diffusion for diffusion-weighted data (although the
dpreproc script is usually preferable for the latter).
If multiple T1-weighted images are given then by default TractoR will coregister them and create a median image. This is then used as the standard registration target for structural imaging space for the session. An alternative is to let Freesurfer perform this coregistration operation later, in which case
Coregister:false can be given to the
Anatomical parcellation of a structural image is a prerequisite for some kinds of analysis, and must be performed before the parcellation can be propagated to any other space, such as diffusion. The key script for this is
parcellate. It is passed a parcellated image, of the same dimensions as the averaged reference T1-weighted image but with coherent regions labelled with an integer index. A lookup table is required to convert between numerical indices and region names, and some examples for typical atlases are included in
For example, to run FSL-FIRST on the reference T1 image for a session and import the parcellation created by it, you might run
cd /data/subject1 furrow run_first_all -i @refT1 -o first tractor parcellate . first_all_fast_firstseg Types:first
Note that TractoR does not provide a wrapper script for FIRST, but TractoR’s
furrow program can be used to create one. It replaces the session syntax
@refT1 with the full path to the relevant input file, and then calls the FIRST command line tool,
run_first_all. The TractoR
parcellate script then needs to be told that the parcellation was performed by FIRST, and since there is a standard parcellation lookup table for this type of parcellation, it will use it automatically.
Another alternative is to use Freesurfer, and in this case TractoR does provide a wrapper script, viz.
tractor freesurf /data/subject1 Parcellation:destrieux
parcellate script can also handle merging multiple parcellations together: for example, you can run
freesurf first to obtain a parcellation from Freesurfer, and then run FIRST and pass the result to
parcellate. In that case regions which appear in both parcellations will be overwritten by the FIRST parcellation. A merged parcellation image and lookup table gets written into the session directory.