RetroTS.py¶
Contents
This function creates slice-based regressors for regressing out components of
heart rate, respiration and respiration volume per time.
Windows Example:
C:\afni\python RetroTS.py -r resp_file.dat -c card_file.dat -p 50 -n 20 -v 2
Mac/Linux Example:
/usr/afni/python RetroTS.py -r resp_file.dat -c card_file.dat -p 50 -n 20 -v 2
Input
================================================================================
Following are the mandatory and optional parameters that can be entered
after RetroTS.py, each separated by a space.
Mandatory:
----------
:param -r: (respiration_file) Respiration data file
:param -c: (cardiac_file) Cardiac data file
:param -p: (phys_fs) Physiological signal sampling frequency in Hz.
:param -n: (number_of_slices) Number of slices
:param -v: (volume_tr) Volume TR in seconds
Note: These parameters are the only single-letter parameters, as they are
mandatory and frequently typed. The following optional parameters
must be fully spelled out.
Optional:
---------
:param -prefix: Prefix of output file
============================================================================
:param -rvt_shifts: Vector of shifts in seconds of RVT signal.
(default is [0:5:20])
:param -rvt_out: Flag for writing RVT regressors
(default is 1)
============================================================================
:param -respiration_cutoff_frequency: Cut off frequency in Hz for
respiratory lowpass filter
(default 3 Hz)
:param -cardiac_cutoff_frequency: Cut off frequency in Hz for
cardiac lowpass filter
(default 3 Hz)
:param -cardiac_out: Flag for writing Cardiac regressors
(default is 1)
:param -respiration_out: Flag for writing Respiratory regressors
(default is 1)
============================================================================
:param -interpolation_style: Resampling kernel.
(default is 'linear', see help interp1 for more options)
:param -fir_order: Order of FIR filter.
(default is 40)
============================================================================
:param -quiet: Show talkative progress as the program runs
(default is 1)
:param -demo: Run demonstration of RetroTS
(default is 0)
:param -show_graphs:
============================================================================
:param -slice_offset: Vector of slice acquisition time offsets in seconds.
(default is equivalent of alt+z)
:param -slice_major: ? (default is 1)
:param -slice_order: Slice timing information in seconds. The default is
alt+z. See 3dTshift help for more info.
alt+z = alternating in the plus direction
alt-z = alternating in the minus direction
seq+z = sequential in the plus direction
seq-z = sequential in the minus direction
custom = allows the program to use the values stored in the
-slice_offset list
filename = read temporal offsets from 'filename', including file
extension; e.g. slice_file.dat
(expecting a 1D / text file containing the times for
each slice in seconds)
============================================================================
:param -zero_phase_offset:
============================================================================
:param legacy_transform: Important-this will specify whether you use the
original Matlab code's version (1) or the potentially bug-corrected
version (0) for the final phase correction in
lib_RetroTS/RVT_from_PeakFinder.py
(default is 0)
Output:
================================================================================
Files saved to same folder based on selection for "-respiration_out" and
"-cardiac_out". If these options are enabled, than the data will be written
to a single output file based on the filename assigned to the
option "-prefix".
Example:
C:\afni\python RetroTS.py -r resp_file.dat -c card_file.dat -p 50 -n 20
-v 2 -prefix subject12_regressors -respiration_out 1 -cardiac_out 1
Output:
The file "subject12_regressors.slibase.1D" will be saved to current
directory, including respiratory regressors and cardiac regressors.
