Source code for fsl.wrappers.tbss

#!/usr/bin/env python3
#
# tbss.py - Wrappers for FSL command-line tools for tract based spatial
# statistics (TBSS).
#
# Author: Evan Edmond <eedmond@gmail.com>
#

"""This module contains wrapper functions for various `TBSS
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/>`_ command-line tools.
"""


import fsl.utils.assertions as asrt
from . import wrapperutils  as wutils


[docs]@wutils.fslwrapper def preproc(*images): """Wrapper for the ``tbss_1_preproc`` command. Usage: ``tbss_1_preproc(<image1>, <image2>, ...)`` """ for img in images: asrt.assertIsNifti(img) return ["tbss_1_preproc"] + list(images)
[docs]@wutils.fslwrapper def reg(**kwargs): """Wrapper for the ``tbss_2_reg`` command. Refer to the ``tbss_2_reg`` command-line help for details on all arguments. """ valmap = { 'T' : wutils.SHOW_IF_TRUE, 'n' : wutils.SHOW_IF_TRUE, } cmd = ["tbss_2_reg"] cmd += wutils.applyArgStyle("-", valmap=valmap, valsep=" ", **kwargs) return cmd
[docs]@wutils.fslwrapper def postreg(**kwargs): """Wrapper for the ``tbss_3_postreg`` command. Refer to the ``tbss_3_postreg`` command-line help for details on all arguments. """ valmap = { 'T' : wutils.SHOW_IF_TRUE, 'S' : wutils.SHOW_IF_TRUE, } cmd = ["tbss_3_postreg"] cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs) return cmd
[docs]@wutils.fslwrapper def prestats(threshold): """Wrapper for the ``tbss_4_prestats`` command. The normal recommendation for <threshold> is 0.2 """ return ["tbss_4_prestats", f'{threshold}']
[docs]@wutils.fslwrapper def non_FA(alt_img_root): """Wrapper for the ``tbss_non_FA`` command. e.g.: ``tbss_non_FA("L2")`` """ return ["tbss_non_FA", alt_img_root]
[docs]@wutils.fileOrImage("stats_image", "mean_FA", "output") @wutils.fslwrapper def fill(stats_image, threshold, mean_FA, output, **kwargs): """Wrapper for the ``tbss_fill`` command. Refer to the ``tbss_fill`` command-line help for details on all arguments. """ valmap = { 'n' : wutils.SHOW_IF_TRUE, } cmd = ["tbss_fill", stats_image, f'{threshold}', mean_FA, output] cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs) return cmd