Based on work by Sherbondy, Dougherty, Wandell and others in the Stanford VISTA lab.
This library implements reading and writing of .pdb tractography files.
It also includes command-line interfaces to convert pdb files from/to trk files, which are used as follows:
pdb2trk pdb_file.pdb trk_file.trk
And:
trk2pdb trk_file.trk pdb_file.pdb
This software depends on numpy and on nibabel. To
install these dependencies, the easiest route is to install the Anaconda python distribution and then use pip to install nibabel:
pip install nibabel
To install the software itself, download the source code and run:
python setup.py install
To install the release version of pdb_files using pip, you can run:
pip install pdb_files
The following is the nominal specification of PDB files, version 3. Note that some of these things were not implemented in practice in many files, so the code implements a partial version of this spec.
The file-format is organized as a semi-hierarchical data-base, according to
the following specification:
[ header size] - int
-- HEADER FOLLOWS --
[4x4 xform matrix ] - 16 doubles
[ number of pathway statistics ] - int
for each statistic:
[ currently unused ] - bool
[ is stat stored per point, or aggregate per path? ] - bool
[ currently unused ] - bool
[ name of the statistic ] - char[255]
[ currently unused ] - char[255]
[ unique ID - unique identifier for this stat across files ] - int
** The algorithms bit is not really working as advertised: **
[ number of algorithms ] - int
for each algorithm:
[ algorithm name ] - char[255]
[ comments about the algorithm ] - char[255]
[ unique ID - unique identifier for this algorithm, across files ] - int
[ version number ] - int
-- HEADER ENDS --
[ number of pathways ] - int
[ pts per fiber ] - number of pathways integers
for each pathway:
[ header size ] - int
-- PATHWAY HEADER FOLLOWS --
** The following are not actually encoded in the fiber header and are
currently set in an arbitrary fashion: **
[ number of points ] - int
[ algorithm ID ] - int
[ seed point index ] - int
for each statistic:
[ precomputed statistical value ] - double
-- PATHWAY HEADER ENDS --
for each point:
[ position of the point ] - 3 doubles (ALREADY TRANSFORMED from
voxel space!)
for each statistic:
IF computed per point (see statistics header, second bool field):
for each point:
[ statistical value for this point ] - double
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