macapype.pipelines.prepare.create_long_multi_preparation_pipe

macapype.pipelines.prepare.create_long_multi_preparation_pipe(params, name='long_multi_preparation_pipe')

Description: Long data preparation, each T1 and T2 is processed independantly (mapnode).

Processing steps:

• reorient (opt: reorient) 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))

• processed T1s and T2s are averaged (by modality)

• Finally, align average T2 to average T1

Params:

• mapnode_prep_T1 and mapnodes_prep_T2 (see _create_mapnode_prep_pipeline for arguments)

• 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