general_plot_bold_timeseries_list

qx_mri.general.general_plot_bold_timeseries_list(flist, elements, filename, skip, fformat, verbose)

general_plot_bold_timeseries_list(flist, elements, filename, skip, fformat, verbose)

Creates and saves a plot of BOLD timeseries for a list of sessions.

Parameters

--flist (str):

List of files in the standard format.

--elements (struct | str, default 'type=stats|stats>type=dvarsme,img=1>type=fd,img=1;type=image|name=V|mask=1;type=image|name=WM|mask=1;type=image|name=GM|mask=1;type=image|name=V|mask=1|img=2|use=1|scale=2;type=image|name=GM|mask=1|img=2|use=1|scale=4'):

Plot element specification.

--filename (str, default ''):

Prefix of root filename to save the plot to.

--skip (int, default 0):

How many frames to skip at the stat of the bold run.

--fformat (str, default 'pdf'):

Plot output format.

--verbose (bool, default false):

Whether to be talkative.

Notes

This function runs general_plot_bold_timeseries function on a list of sessions making it simpler to generate BOLD timeseries plots for a set of sessions. For more information on generation of plots, please see documentation for general_plot_bold_timeseries.

Parameter details:

flist

A path to the standard list file. The list has to provide for each sessions as many 'file:' entries as there are images refered to by the element specification, and one 'roi:' entry to be used as a mask. For typical use the first file would be a raw bold image, the second file a preprocessed bold image, and roi file an aparc or aparc+aseg segmentation in the same resolution as the bold files. Do note that these should be NIfTI files as most often signal from ventricles and white matter is plotted and this information is not present in cifti files. If these signals are not required, the function can work with cifti files as well.

elements

Either a structure or a well formed string that can be processed using the general_parse_options function that specifies wha should be plotted. Please see documentation for general_plot_bold_timeseries for detailed information on how to specify plot elements. The default string is:

'type=stats|stats>type=dvarsme,img=1>type=fd,img=1;
type=image|name=V|mask=1;
type=image|name=WM|mask=1;
type=image|name=GM|mask=1;
type=image|name=V|mask=1|img=2|use=1|scale=2;
type=image|name=GM|mask=1|img=2|use=1|scale=4'

This creates a document with a single stats plot that includes frame displacement and dvarsme statistics for the first image, ventricle, white matter, and gray matter plots for the first image, each scaled individually, and ventricle and gray matter plots for the second image, with bad frames masked and scaled to the same scale as the first image.

filename

The root filename for the generated plot. The plots are saved in the sessions's images/functional/movement folder and named using the following formula:

<filename parameter><the filename of the first specified file>_tsplot.<fformat>

An example with bold1.nii.gz as the first file, QA_ as value of the filename parameter, and pdf as the value of fformat parameter would be:

QA_bold1_tsplot.pdf

fformat

File format in which the plot is to be saved. 'pdf' by default.

skip

If no initial dummy scans were used during image acquisition, the number of frames to skip from the start of the bold image. 0 by default.

verbose

Whether to provide a report of what is being done while the function is running. False by default.

Examples

qunex general_plot_bold_timeseries_list \
    --flist='bolds.list' \
    --elements='[]' \
    --filename='QA_' \
    --skip=5 \
    --fformat=png \
    --verbose=true