PUMI.pipelines.multimodal package

PUMI.pipelines.multimodal.image_manipulation module

PUMI.pipelines.multimodal.image_manipulation.get_info(in_file, volume='first')[source]

Adapted from C-PAC (https://github.com/FCP-INDI/C-PAC) Function to get the right index, from which the slicing requested by the user, starts.

  • In case no value was given, the first volume will be returned.

  • In case of a non-valid value, a ValueException will be thrown.

  • Beaware : This function will be called only if the volume != ‘mean’

Parameters:

  • in_file (str) – Path to input functional run.

  • volume (str) – The volume specified by the user. Possible Values: (first | middle | last | mean | arbitrary number)

Returns:

The index in the 4d-sequence, from which we start slicing.

Return type:

start_idx (integer)

PUMI.pipelines.multimodal.image_manipulation.pick_volume(wf, volume='middle', **kwargs)[source]

Sub-Workflow that deals with extracting a 3D-volume choosen by the user from a functional 4D-Sequence

Parameters:

  • wf (str) – Name of the workflow.

  • volume (str) – The volume specified by the user. - Possible Values : (first | middle | last | mean | arbitrary number). - In case no value was given, the first volume will be returned. - In case of a non-valid value, a ValueException will be thrown.

Returns:

The sub-workflow itself.

Return type:

wf(Workflow)

PUMI.pipelines.multimodal.image_manipulation.timecourse2png(wf, plot_type='all', sink=True, **kwargs)[source]
plot_type: ‘all’: nothing to specify, will input everything greater than zero

‘vox’: use ‘x’, ‘y’, ‘z’ fields for voxel then ‘roi’: use ‘mask’ for roi

PUMI.pipelines.multimodal.image_manipulation.vol2png(wf, overlay=True, **kwargs)[source]

# Todo Docs