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Doughboys
May 11, 2021 05:08PM
Hello AFNI team,

I have a problem concerning the use of RetroTS.py:
I managed to convert SCANPHYSLOG data (from Phillips) in BIDS using:
[github.com]
If anyone knows a better way?

I tried to run the command: 

/abin/RetroTS.py -phys_file SCANPHYSLOG20210420091530.tsv.gz \
-v 1 -n 600 -prefix physio_regressors.1D -phys_json SCANPHYSLOG20210420091530.json


my .json looks like: 

{
    "SamplingFrequency": 496,
    "StartTime": -78.74798387096774,
    "Columns": [
        "cardiac",
        "respiratory",
        "trigger"
    ]
}


SCANPHYSLOG20210420091530.tsv.gz looks like: 

1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1921	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1864	0
1	-1921	0
1	-1921	0
1	-1921	0

....


cardiac is not varying since I do not have the data (so it stayed 1)
respiratory is varying
I have got 600 triggers (1) that do correspond to the 600 volumes (or slices)
When running the command I have got: 

pause
[]
Traceback (most recent call last):
  File "/home/cgarin/abin/RetroTS.py", line 647, in <module>
    phys_json=opt_dict["-phys_json"]
  File "/home/cgarin/abin/RetroTS.py", line 245, in retro_ts
    cardiac_peak, error = peak_finder(cardiac_info, v=phys_dat[k])
  File "/home/cgarin/abin/lib_RetroTS/PeakFinder.py", line 521, in peak_finder
    bounds_error=False,
  File "/home/cgarin/anaconda3/lib/python3.7/site-packages/scipy/interpolate/interpolate.py", line 468, in __init__
    self._y = self._reshape_yi(self.y)
  File "/home/cgarin/anaconda3/lib/python3.7/site-packages/scipy/interpolate/polyint.py", line 111, in _reshape_yi
    return yi.reshape((yi.shape[0], -1))
ValueError: cannot reshape array of size 0 into shape (0,newaxis)


Any idea of what is going on?

Thank you very much for your help!!
Clem
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Subject Author Posted

RetroTS.py problem using Phillips SCANPHYSLOG

Doughboys May 11, 2021 05:08PM

Re: RetroTS.py problem using Phillips SCANPHYSLOG

Peter Molfese May 12, 2021 12:32PM

Re: RetroTS.py problem using Phillips SCANPHYSLOG

Doughboys May 12, 2021 01:27PM

Re: RetroTS.py problem using Phillips SCANPHYSLOG

Doughboys May 19, 2021 11:58AM

Re: RetroTS.py problem using Phillips SCANPHYSLOG

Peter Molfese May 19, 2021 03:31PM

Re: RetroTS.py problem using Phillips SCANPHYSLOG

rick reynolds May 29, 2021 10:44PM