macapype.pipelines.prepare.create_short_preparation_pipe

macapype.pipelines.prepare.create_short_preparation_pipe(params, name='short_preparation_pipe')

Description: short data preparation (average, reorient, crop/betcrop and denoise)

Processing steps;

• T1s and T2s are averaged (by modality).

• reorient (opt) makes the whole pipeline more neat)

• Cropped (bet_crop include alignement, and mask generation)

• denoising all images (no denoise_first)

Params:

• reorient (optional; new_dims as a string (e.g. “x z -y”))

• bet_crop (T1xT2BET ) or crop (see ExtractRoi for arguments). crop is also available as indiv_params

• denoise (see DenoiseImage for arguments))

Inputs:

inputnode:

list_T1:

T1 files (from BIDSDataGrabber)

list_T2:

T2 files

indiv_params (opt):

dict with individuals parameters for some nodes

arguments:

params:

dictionary of node sub-parameters (from a json file)

name:

pipeline name (default = “long_multi_preparation_pipe”)

Outputs:

outputnode:

preproc_T1:

preprocessed T1 file

preproc_T2:

preprocessed T2 file