m2m_import_tract

Download all streamlines for each Allen mouse brain connectivity atlas experiments and combine into a single tractogram.

Please note that Allen tractogram may have overlapping points, you can use scil_remove_invalid_streamlines to remove them : https://github.com/scilus/scilpy

Important: The script should be called in a specific order Warning: Choose the same resolution as your transformation matrix !

Using a csv file from : https://connectivity.brain-map.org/

>>> allen_import_tract path/to/output.trk path/to/matrix.mat
    path/to/reference.nii.gz resolution
    --ids_csv path/to/ids.csv

Setting ids manually:

>>> allen_import_tract path/to/output.trk path/to/matrix.mat
    path/to/reference.nii.gz resolution
    --ids id1 id2 id3 . . .

usage: m2m_import_tract.py [-h] (--ids_csv IDS_CSV | --ids IDS [IDS ...]) [-f]
                           [-c]
                           out_tract file_mat reference {25,50,100}

Positional Arguments

out_tract

Path to output tractogram (trk)

file_mat

Path to transform matrix (.mat)

reference

Path to reference volume (.nii.gz)

res

Possible choices: 25, 50, 100

Resolution of the Allen files Please use the same resolution as the transformation matrix.

Named Arguments

--ids_csv

Path to a csv file containing ids

--ids

List of experiment ids.

-f

Force overwriting of the output files.

Default: False

-c, --nocache

Update the Allen Mouse Brain Connectivity Cache

Default: False

Author : Mahdi