3 d7/@sbddljZddlmZmZmZddlmZmZGdddeZ Gdd d eZ Gd d d eZ dS) N)traits TraitedSpecFile)MRTrix3BaseInputSpec MRTrix3Basec @seZdZejejejejejddZeddddgddZeddddhdd d Z ej d d ddddddddd Z ej eddedddZ ej eddedddZej eddedddZejdddZejd d!dZejd"d#d$d%Zejd&d'd$d(Zejd)d*dZejd+d,dZejd-d.dZejd/d0dZejd1d2dZejd3d4dZejd5d6dZejejejejd7d8dZejd9d:dZejd;dd?dZ ejd@dAdZ!ejdBdCdZ"ejdDdEdZ#eddFdGdHZ$ejdIdJdZ%ejdKdLdZ&ejejejejejdMdNdZ'eddOdPdHZ(ejeddejdQdRdSgdTdUZ)ejeddejdVdRdWgdXdUZ*eddYdZdHZ+edd[d\gd]d^Z,edd_d`dHZ-ejdadbdZ.edcddddedZ/dfS)iTractographyInputSpecz %f,%f,%f,%f)argstrTz%srzinput file to be processed)existsr mandatorypositiondescz tracked.tckrzoutput file containing tracks)r r r usedefaultrZiFOD2ZFACTZiFOD1ZNulldistZ SD_StreamZ Tensor_DetZ Tensor_Probz -algorithm %szxTractography algorithm to be used -- References:[FACT]_, [iFOD1]_, [iFOD2]_, [Nulldist]_, [Tensor_Det]_, [Tensor_Prob]_.)rr r)r z -include %szgspecify an inclusion region of interest, streamlines must traverse ALL inclusion regions to be accepted)r rz -exclude %szdspecify an exclusion region of interest, streamlines that enter ANY exclude region will be discardedz-mask %sz_specify a masking region of interest. If defined,streamlines exiting the mask will be truncatedz-step %fzaset the step size of the algorithm in mm (default is 0.1 x voxelsize; for iFOD2: 0.5 x voxelsize)z -angle %fzXset the maximum angle between successive steps (default is 90deg x stepsize / voxelsize)z -number %dz0.4zset the desired number of tracks. The program will continue to generate tracks until this number of tracks have been selected and written to the output file)r Zmax_verrz -select %d3)r Zmin_verrz -maxnum %dzset the maximum number of tracks to generate. The program will not generate more tracks than this number, even if the desired number of tracks hasn't yet been reached (default is 100 x number)z -maxlength %fzFset the maximum length of any track in mm (default is 100 x voxelsize)z -minlength %fzDset the minimum length of any track in mm (default is 5 x voxelsize)z -cutoff %fzJset the FA or FOD amplitude cutoff for terminating tracks (default is 0.1)z-initcutoff %fzdset the minimum FA or FOD amplitude for initiating tracks (default is the same as the normal cutoff)z -trials %dz^set the maximum number of sampling trials at each point (only used for probabilistic tracking)z-unidirectionalzXtrack from the seed point in one direction only (default is to track in both directions)z-initdirection %f,%f,%fznspecify an initial direction for the tracking (this should be supplied as a vector of 3 comma-separated valuesz-noprecomputedzxdo NOT pre-compute legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4z -power %dz>> import nipype.interfaces.mrtrix3 as mrt >>> tk = mrt.Tractography() >>> tk.inputs.in_file = 'fods.mif' >>> tk.inputs.roi_mask = 'mask.nii.gz' >>> tk.inputs.seed_sphere = (80, 100, 70, 10) >>> tk.cmdline # doctest: +ELLIPSIS 'tckgen -algorithm iFOD2 -samples 4 -output_seeds out_seeds.nii.gz -mask mask.nii.gz -seed_sphere 80.000000,100.000000,70.000000,10.000000 fods.mif tracked.tck' >>> tk.run() # doctest: +SKIP ZtckgencsDd|kr0t|tr0dd|D}|jdj|Stt|j|||S)NZroi_cSsg|] }d|qS)z%fr().0vr(r(r) osz,Tractography._format_arg..,) isinstancetupler joinsuperr+ _format_arg)selfnameZ trait_specvalue) __class__r(r)r4mszTractography._format_argcCs"|jj}tj|jj|d<|S)Nr) output_specgetopabspathinputsr)r5outputsr(r(r) _list_outputsts zTractography._list_outputs) rrr__doc__Z_cmdr Z input_specr*r9r4r? __classcell__r(r()r8r)r+9s . r+) os.pathpathr;baserrrrrr r*r+r(r(r(r)s )