After bedpostx has been applied it is possible to run tractography analyses using probtrackx.
To call the FDT GUI, either run Fdt, or run fsl and press the FDT button. Use the top left drop down menu to select PROBTRACKX.
PROBTRACKX GUI has two main sections:
Also, probtrackx requires the specification of a bedpostX directory. This directory must contain the following images:merged_thsamples
, etc.)As explained below, results from probtrackx can be binned in any available space -e.g.,
diffusion space, structural space or standard space. Note, however,
that tractography itself ALWAYS takes place in diffusion space - it is
simply the results of probtrackx that are stored in the
required space. If probtrackx results are to be stored in a space
other than diffusion space then you will need transformations from
this space back into the space of the diffusion data.
You can use the FDT registration tab to create the required transformations, which will all be stored in the xfms
subdirectory of the bedpostX directory.
Probtrackx can take either linear (FLIRT) or nonlinear (FNIRT) transformations. In the latter case, both forward (diffusion to seed space) and backward (seed space to diffusion) transformations are needed. Eg:
For running analyses in structural space:
For running analyses in standard space:
GUI Options:
Seed reference image Use the browse button to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz if seed space is structral space or subject1.bedpostX/standard.nii.gz if seed space is standard space).
Seeds: Enter the x,y,z co-ordinates of a single seed voxel. Use the buttons to the right to specify whether the co-ordinates are given in voxels or millimetres. Note if the "seed space is not diffusion" is set, and the seed space reference image is the MNI152 average brain, then mm coordinates will have their origin at the AC.
The output will be a single image in the space of the specified seed. All brain voxels will have a value (though many of these will be zero) representing the connectivity value between that voxel and the seed voxel (i.e., the number of samples that pass through that voxel). The example on the right shows the connectivity distribution from a single seed in the internal capsule overlaid on an FA image. Note that when the seed space is a single voxel, the classification targets in the Optional Targets tab is turned off.
GUI Options:
Seed image: Use the browse button to locate the seed image. Probabilistic tractography will be run from every voxel with a value different than 0 in this mask.
The output directory will contain:
probtrackx.log - a text record of the command that was run.
fdt.log - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type Fdt fdt.log
fdt_paths - a 3D image file containing the output connectivity distribution to the seed mask.
waytotal - a text file containing a single number corresponding to the total number of generated tracts that have not been rejected by inclusion/exclusion mask criteria.
The output connectivity distribution file will be a single image in the space of the specified seed mask. All brain voxels will have a value (though many of these may be zero) representing the number of samples that pass through that voxel from the seed mask. Connectivity distributions from multiple seed voxels are summed to produce this output. Therefore the connectivity values will depend on the number of voxels in the seed mask.
GUI Options:
Masks list: Use the add button to locate each seed mask. Seed masks should all be in the same space (e.g., diffusion, structural or standard space). When all masks are loaded you can press the save list button to save the list of masks as a text file. If you already have a text file list of required seed masks (including their path) then you can load it with the load list button.
The output directory will contain:
probtrackx.log - a text record of the command that was run.
fdt.log - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type Fdt fdt.log
fdt_paths - a 3D image file containing the output connectivity distribution.
waytotal - a text file containing one number per seed mask (in the order that has been specified when listing them). These numbers correspond to the total number of generated tracts from each seed mask that have reached at least one of the other masks and have not been rejected by inclusion/exclusion mask criteria.
The output file will be a single image in the space of the specified masks. All brain voxels will have a value (though many of these may be zero) representing the number of samples that pass through that voxel from either of the seed masks and which also pass through at least one of the other seedmasks. Connectivity distributions from multiple seed voxels are summed to produce this output. Therefore the connectivity values will depend on the number of voxels in the seed masks.
fslmaths mywaypoint1 -add mywaypoint2 -add ... myORwaypoint
There are command line utilities that can be run on these outputs:
Number of samples (default 5000): This determines the number of individual pathways (or samples) that are drawn through the probability distributions on principle fibre direction (see appendix for more details on the modelling and tractography methods). By default this is set to 5000 as we are confident that convergence is reached with this number of samples. However, reducing this number will speed up processing and can be useful for preliminary or exploratory analyses.
Curvature Threshold (default 0.2): We limit how sharply pathways can turn in order to exclude implausible pathways. This number is the cosine of the minimum allowable angle between two steps. By default this is set to 0.2 (corresponding to a minimum angle of approximately ±80 degrees). Adjusting this number can enable pathways with sharper angles to be detected.
Verbose: If this option is selected then FDT prints additional logging information to screen while it is running.
Loopcheck: By default, we terminate pathways that loop back on themselves -i.e paths that travel to a point where they have already been.
Use modified Euler streamlining: Use modified Euler integration as opposed to simple Euler for computing probabilistic streamlines. More accurate but slower.
Maximum number of steps (default 2000): By default, samples are terminated when they have travelled 2000 steps. Using a step length of 0.5mm this corresponds to a distance of 1m. These values can be adjusted if required.
Step length (default 0.5mm): This determines the length of each step. This setting may be adjusted from default e.g., depending on the voxel size being used, or if tracking is being performed on different sized brains (e.g., infants or animals).
Use anisotropy to constrain tracking: Use this option if you want the fractional anisotropic volumes (stored in merged_f<i>samples) to influence the tractography. The tracts stop if the anisotropy is lower than a random variable between 0 (low anisotropy) and 1 (high anisotropy).
Use distance correction: This option corrects for the fact that connectivity distribution drops with distance from the seed mask. If this option is checked, the connectivity distribution is the expected length of the pathways that cross each voxel times the number of samples that cross it.