fascicle

Fascicle is a tool to help manage multiple tractography files for ease of data management.

It's designed to ease the workflow with ANTs normalization tool for non-linear tractography deformations with large datasets.

Requirements

• numpy
• vtk
• sqlalchemy

Install

    python setup.py install

VTK file format

Fascicle import and export vtk files for tractography representation. It is capale of reading both .vtk ascii files and .vtp files.

Use .vtp for file import exports for scalar availability

Usage

Fascicle collections are sqlite databases, therefore they are compatible with any sqlite reader.

Create a new tractography collection

trkmanage.py init -d collection.tdb -i input.vtk

Add new tracts to existing collection

trkmanage.py init -d existing.tdb -i addthis.vtk

Export tracts as a merged file

trkmanage.py expvtk -d existing.tdb --merged -o mergedtracts.vtp

Export points as csv for ANTs

trkmanage.py expcsv -d collection.tdb -o points_before.csv

Then the csv file can be used with ANTs with

antsApplyTransformToPoints -d 3 -i points_before.csv -o pointss_after.csv -t [Affine.mat,1] -t WarpInverse.nii.gz

Note that Point transforms in ANTs is the inverse of the desired transform direction.

Import ANTs deformed points back into the collection

trkmanage.py tradd  -d collection.tdb -i points_after.csv -n mytransform -p "parameters I used"

Export tracts with the newly transformed coordinates Find out the avaiable tracts and transforms

trkmanage.py list -d collection.tdb

Export specifics

trkmanage.py expvtk -d collection.tdb -t tractname -m mytransform -o aftertrans.vtp