Currently this assumes that you have recorded your physiological responses through Cigal.

There's a python program, than can take your run's bxh header along with your cigal pdigm file to create various types of corrected text files to be used for physio corrections in a number of different packages.

This tools uses various fields from the bxh and pdigm file to output “corrected” data. “Corrected” here means accounting for potential time locking issues, different TR in the cigal recording verses the actual data acquisition, ddqs, etc.

The python tool will call cigal functions directly, then output new text data in the format requested.

physio_create.py --help

physio_create.py --bxh /path/to/run4.bxh --pdigm /path/to/pdigm5_12345_4_2 -f fsl --outpath /here/

Program to produce formatted physiological data:
    Data will be corrected and recreated from the pdigm file based on information from run data
    BXH and PDIGM required
    OUTPATH defaults to PWD
    FORMAT: defaults to fsl
        - fsl = cardio,resp,TR pulse ( 3 column file ) 
        - npm = time,cardio,resp ( 3 column file )
        - afni = cardiac.txt, respiration.txt


Options:
  -h, --help            show this help message and exit
  -b FILE, --bxh=FILE   bxh file for run
  -p FILE, --pdigm=FILE
                        pdigm file for run
  -f string, --format=string
                        output format ( fsl,npm,afni )
  -o PATH, --outpath=PATH
                        location to store output files

Create the AFNI formated physiological text data.

physio_create.py -b Data/Func/20111025_12345/run004.bxh -p Data/Behav/12345/pdigm5_12345_4_2 -f afni

This would create my “cardiac.txt” and “respiration.txt”.

Now set-up build the regressors that will be used in afni with their matlab tool.

addpath /usr/local/packages/MATLAB/afni/
Opt.Respfile = '/tmp/there/respiration.txt'
Opt.Cardfile = '/tmp/there/cardiac.txt'
Opt.VolTR = 1.5
Opt.Nslices = 34
Opt.PhysFS = 100
 
RetroTS(Opt)