A script to generate a session summary from a fmriprep (or fmriprep-babies) analysis
Documentation for nibabies output can be found here
Each functional run generates a file called: sub-XXXX_ses-Y_task-{rest, other_task_name}_run-ZZ_desc-confounds_timeseries.tsv
(or specifically, for example: sub-BB06601_ses-1_task-rest_run-02_desc-confounds_timeseries.tsv)
While this confound file contains a large number of metrics, we have specific interest in summarising the following metrics:
-
Estimated head-motion parameters - the 6 rigid-body motion parameters (3 translations and 3 rotation), estimated relative to a reference image:
- trans_x
- trans_y
- trans_z
- rot_x
- rot_y
- rot_z
-
bulk-head motion calculated using formula proposed by [Power2012]
- framewise_displacement (FD)
-
Global signals:
-
csf - the average signal within anatomically-derived eroded CSF mask;
-
white_matter - the average signal within the anatomically-derived eroded WM masks;
-
global_signal - the average signal within the brain mask.
-
-
Count of motion outliers - Scans occurring at times of particularly high motion are flagged by the motion_outlierXX column. For summary, we want the count of 'motion_outliers' (or equally, the largest XX).
Given a pointer to a nibabies result directory, find each functional run, and create a table that aggregates the following content:
| Subj | Session | Task | Run | FD_AVG | FD_STD | trans_x_AVG | trans_x_STD | trans_y_AVG | trans_y_STD | trans_z_AVG | trans_z_STD | rot_x_AVG | rot_x_STD | rot_y_AVG | rot_y_STD | rot_z_AVG | rot_z_STD | CSF | WM | Global | Outliers |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BB06601 | 1 | rest | 02 | ||||||||||||||||||
| BB06601 | 1 | rest | 03 |
Note: We can debate if the STD values are useful or not...
Example Script call (on DNK's system locally):
> ./SumarizeNibabies.sh ~/Data/Sohye/Infants/CHBabies/BB066_01/nibabies/ ExampleOutput/OutputFile.csv
./summarize_confounds -h
usage: summarize_confounds [-h] source_directory output_file
Summarize nibabies-reported confounds.
positional arguments: source_directory output_file
options: -h, --help show this help message and exit
Version 0.1
See the example real output here.