Processed data outputs

The application outputs will generally mirror the structure of the inputs. The overall output folder structure can be seen below:

<output_dir>/sub-<label>/ses-<label>/motion/

Within this folder, the following can be found:

a] PARAMETERS.json
b] sub-<label>_ses-<label>_leg-left_desc-calibrated_recording-20_motion.tsv
c] sub-<label>_ses-<label>_leg-right_desc-calibrated_recording-20_motion.tsv
d] Kinematics/sub-<label>_ses-<label>_desc-kinematics_recording-20_motion.json
e] Kinematics/sub-<label>_ses-<label>_desc-kinematics_recording-25_motion.json
f] PA/sub-<label>_ses-<label>_leg-<label>_desc-<label>PA_LOG.txt
g] PA/sub-<label>_ses-<label>_leg-<label>_desc-<label>PA_BOUTS.tsv
h] PA/sub-<label>_ses-<label>_leg-<label>_desc-<label>PA_RAW.tsv
i] PA/sub-<label>_ses-<label>_leg-<label>_desc-<label>PA_SUMMARY.json
j] LOG.txt

Intermediate data files: a] ~ c]

a] lists the parameters provided when using the docker container.

  • bids_dir

  • output_dir

  • analysis_level

  • participant_label

  • session_id

  • interval

  • pa_measure

  • pa_side

  • entropy_type

  • entropy_measure

Please refer to Command-Line Arguments in the usage documentation to see possible choices for each parameter.

b] and c] are 72-hour left and right leg movement data. They are first calibrated using (found in /bids_dir/sub-<label>/ses-<label>/motion/):

  • sub-<label>_ses-<label>_task-LeftLegMovement_tracksys-imu_acq-calibration_motion.tsv

  • sub-<label>_ses-<label>_task-RightLegMovement_tracksys-imu_acq-calibration_motion.tsv

and then resampled at 20 Hz. These files are required to estimate physical activity levels (f] - i]).

Processed data outputs: d] ~ i]

d] and e] contain summary kinematic measures based on the 72-hour leg movement data.
d] is based on the resampled data, a] and b], and e] is based on the non-resampled data (No intermediate data files exist).
Please refer to the table below to understand what each measure is about:

measure

description

Participant_id

<label> of sub-<label>

Session_id

<label> of ses-<label>

Left_positive_threshold

a positive acceleration magnitude threshold to identify left leg movements

Right_positive_threshold

a positive acceleration magnitude threshold to identify right leg movements

Left_negative_threshold

a negative acceleration magnitude threshold to identify left leg movements

Left_positive_threshold

a negative acceleration magnitude threshold to identify right leg movements

Left_total_count

the total left leg movement count

Right_total_count

the total right leg movement count

Left_movement_rate

left leg movement rate per hour awake

Right_movement_rate

right leg movement rate per hour awake

Left_sleep_time

time estimated to be asleep from the left leg movement data

Right_sleep_time

time estimated to be asleep from the right leg movement data

Left_average_acc_median

median of the average accelerations of left leg movements

Left average_acc_iqr

inter-quartile-range of the average accelerations of left leg movements

Left_peak_acc_median

median of the peak accelerations of left leg movements

Left_peak_acc_iqr

inter-quartile-range of the peak accelerations of left leg movements

Left_movement_duration_median

median of the durations of left leg movements

Left_movement_duration_iqr

inter-quartile-range of the durations of the left leg movements

Right_average_acc_median

median of the average accelerations of right leg movements

Right average_acc_iqr

inter-quartile-range of the average accelerations of right leg movements

Right_peak_acc_median

median of the peak accelerations of right leg movements

Right_peak_acc_iqr

inter-quartile-range of the peak accelerations of right leg movements

Right_movement_duration_median

median of the durations of right leg movements

Right_movement_duration_iqr

inter-quartile-range of the durations of the right leg movements

entropies

sample entropy (SampEn) and/or fuzzy entropy (FuzzEn) of a time series (average_acc or peak_acc)
f] lists the parameters provided to process data and generate *PA_RAW.json, *PA_SUMMARY.json, and *PA_BOUTS.tsv (*denotes wildcard).
In addition, the content of *PA_SUMMARY.json is available in this file.

g] saves bouts of activity as they occur over time. There are 4 columns of data.

start time of a bout

end time of a bout

duration of a bout

classification of a bout

…

…

…

…
The unit for time is seconds. The first line contains the headings, and the rest contain the data.
Classification of bouts is:

value

classification

0

sedentary

3

light activity

6

moderate-to-vigorous (MV) activity

999

undefined (could not be computed)
h] lists instantaneous levels of activity as they occur over time.
There are 2 columns of data, separated by commas: Unix epoch time (in seconds) at each instance, and classification at each instance. Classification of instance is described in g].

i] provides the overall summary of physical activity in terms of 3 different measures:

  • counts (instances) recorded

  • percentage time spent

  • actual time spent in minutes.

For each measure, values will be listed for the total, sedentary, light, and moderate-to-vigorous (MV) activity. The fifth label, “undefined”, can be ignored.

Error log: j]

j] will be created only if data are not processed by the pipeline.

Downloading from LASSO

You can directly download the processed data outputs from LASSO.

_images/lasso_derivative.png

Labels are straightforward. motion (tsv) corresponds to b] and c]. motion (json) at the bottom refers to d] and e].