3 d@'@sddlZddljZddlmZmZmZmZm Z ddlm Z GdddeZ Gdd d eZ Gd d d e Z Gd d d eZGdddeZGddde ZGdddeZGdddeZGddde ZdS)N)CommandLineInputSpectraits TraitedSpecFile isdefined) MRTrix3Basec @seZdZedddd+ddZeddd,ddZed ddd-dd d Zejd dddZ ej dddZ ej dddZ ej dddZej dddZejdddddddd dZedd!d"d#Zedd$d%d#Zej d&d'dZej d(d)dZd*S).BuildConnectomeInputSpecTz%szinput tractography)existsargstr mandatorypositiondescrzparcellation file)r r rrzconnectome.csvrzoutput file after processing)r rr usedefaultrz -nthreads %dzEnumber of threads. if zero, the number of available cpus will be used)r rnohashz-assignment_voxel_lookupz;use a simple voxel lookup value at each streamline endpoint)r rz-assignment_radial_search %fzperform a radial search from each streamline endpoint to locate the nearest node. Argument is the maximum radius in mm; if no node is found within this radius, the streamline endpoint is not assigned to any node.z-assignment_reverse_search %fztraverse from each streamline endpoint inwards along the streamline, in search of the last node traversed by the streamline. Argument is the maximum traversal length in mm (set to 0 to allow search to continue to the streamline midpoint).z-assignment_forward_search %fzproject the streamline forwards from the endpoint in search of aparcellation node voxel. Argument is the maximum traversal length in mm.countZ meanlengthZ invlengthZ invnodevolumeZ mean_scalarZinvlength_invnodevolumez -metric %szspecify the edge weight metricz -image %sz7provide the associated image for the mean_scalar metric)r r rz-tck_weights_in %sz>> import nipype.interfaces.mrtrix3 as mrt >>> mat = mrt.BuildConnectome() >>> mat.inputs.in_file = 'tracks.tck' >>> mat.inputs.in_parc = 'aparc+aseg.nii' >>> mat.cmdline # doctest: +ELLIPSIS 'tck2connectome tracks.tck aparc+aseg.nii connectome.csv' >>> mat.run() # doctest: +SKIP Ztck2connectomecCs"|jj}tj|jj|d<|S)Nr) output_specgetopabspathinputsr)selfoutputsrrr _list_outputsxs zBuildConnectome._list_outputsN) rrr__doc___cmdr input_specr!r#r*rrrr r"cs r"c@seZdZeddddddZedddddZed ddddd d Zed ddZedddZedddZ edddZ edddZ e j ddddZdS)LabelConfigInputSpecTz%sr zinput anatomical image)r r rrrrzconnectome configuration file)r r rrzparcellation.mifrzoutput file after processing)r rrrrz -lut_basic %szJget information from a basic lookup table consisting of index / name pairs)r rz-lut_freesurfer %szRget information from a FreeSurfer lookup table(typically "FreeSurferColorLUT.txt")z -lut_aal %szFget information from the AAL lookup table (typically "ROI_MNI_V4.txt")z-lut_itksnap %sz^get information from an ITK - SNAP lookup table(this includes the IIT atlas file "LUT_GM.txt")z -spine %szprovide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that this can become a node in the connection matrix.z -nthreads %dzEnumber of threads. if zero, the number of available cpus will be used)r rrNrrr)rrrrr in_configrZ lut_basicZlut_fsZlut_aalZ lut_itksnapspinerrrrrrr r.~sDr.c@seZdZedddZdS)LabelConfigOutputSpecTzthe output response file)r rN)rrrrrrrrr r1sr1cs6eZdZdZdZeZeZdfdd Z ddZ Z S) LabelConfiga Re-configure parcellation to be incrementally defined. Example ------- >>> import nipype.interfaces.mrtrix3 as mrt >>> labels = mrt.LabelConfig() >>> labels.inputs.in_file = 'aparc+aseg.nii' >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt' >>> labels.cmdline # doctest: +ELLIPSIS 'labelconfig aparc+aseg.nii mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run() # doctest: +SKIP Z labelconfigNcsv|dkr g}t|jjsdddlm}||j}|dkrDtjtd}nt j t j |}t j |d|j_t t |j|dS)Nr)find_executablez /opt/mrtrix3z@src/dwi/tractography/connectomics/example_configs/fs_default.txt)skip)rr'r/distutils.spawnr3r,osgetenv MRTRIX3_HOMEr%dirnamejoinsuperr2 _parse_inputs)r(r4r3path) __class__rr r<s    zLabelConfig._parse_inputscCs"|jj}tj|jj|d<|S)Nr)r#r$r%r&r'r)r(r)rrr r*s zLabelConfig._list_outputs)N) rrrr+r,r.r-r1r#r<r* __classcell__rr)r>r r2s r2c@speZdZeddddddZeddddddZedddd d Zed ddddd dZedddZe j ddddZ dS)LabelConvertInputSpecTz%szinput anatomical image)r r rrrr zJget information from a basic lookup table consisting of index / name pairsrzconnectome configuration file)r r rrzparcellation.mifrzoutput file after processing)r rrrrz -spine %szprovide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that this can become a node in the connection matrix.)r rz -nthreads %dzEnumber of threads. if zero, the number of available cpus will be used)r rrNrrr) rrrrrZin_lutr/rr0rrZ num_threadsrrrr r@s8r@c@seZdZedddZdS)LabelConvertOutputSpecTzthe output response file)r rN)rrrrrrrrr rCsrCcs6eZdZdZdZeZeZdfdd Z ddZ Z S) LabelConverta Re-configure parcellation to be incrementally defined. Example ------- >>> import nipype.interfaces.mrtrix3 as mrt >>> labels = mrt.LabelConvert() >>> labels.inputs.in_file = 'aparc+aseg.nii' >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt' >>> labels.inputs.in_lut = 'FreeSurferColorLUT.txt' >>> labels.cmdline 'labelconvert aparc+aseg.nii FreeSurferColorLUT.txt mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run() # doctest: +SKIP Z labelconvertNcsv|dkr g}t|jjsdddlm}||j}|dkrDtjtd}nt j t j |}t j |d|j_t t |j|dS)Nr)whichz /opt/mrtrix3z@src/dwi/tractography/connectomics/example_configs/fs_default.txt)r4)rr'r/Znipype.utils.filemaniprEr,r6r7r8r%r9r:r;rDr<)r(r4rEr=)r>rr r<*s    zLabelConvert._parse_inputscCs"|jj}tj|jj|d<|S)Nr)r#r$r%r&r'r)r(r)rrr r*>s zLabelConvert._list_outputs)N) rrrr+r,r@r-rCr#r<r*r?rr)r>r rDs rD)r6os.pathr=r%baserrrrrr r r!r"r.r1r2r@rCrDrrrr s  S8.)