macapype.pipelines.prepare.create_long_single_preparation_pipe

macapype.pipelines.prepare.create_long_single_preparation_pipe(params, name='long_single_preparation_pipe')[source]

Description: Long data preparation, T1s and T2s are averaged (by modality) and then average imgs are processed.

Processing Steps:

  • average imgs (by modality).

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

  • start by denoising all input images (opt: denoise_first in json)

  • crop T1 and T2 based on individual parameters

  • running N4biascorrection on cropped T1 and T to help T2 and T1 alignment

  • finish by denoising all input images (opt: denoise in json))

  • Finally, align T2 to T1

Params:

  • prep_T1 and prep_T2 (see _create_prep_pipeline)

  • align_T2_on_T1 (see FLIRT for more 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