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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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drusso
May 16, 2021 06:04AM
Dear AFNI developers and users,

I am trying to run RetroTS.py on the BIDS-formatted phys files from this open dataset: [legacy.openfmri.org]

This is my input: 
(base) daniel@daniel-VivoBook-ASUSLaptop-X530FN-S530FN:~$ RetroTS.py -phys_file '/media/daniel/77669C5017CBE0AE/ds000030_R1.0.5/sub-10171/func/sub-10171_task-rest_physio.tsv.gz' \
-phys_json '/media/daniel/77669C5017CBE0AE/ds000030_R1.0.5/sub-10171/func/sub-10171_task-rest_physio.json' \
-prefix prova_regressione.1D -n 34 -v 2

This is the output on the terminal: 

[  7.403  14.519  17.486  68.533  69.501  71.471  72.508 105.442 115.262
 133.236 147.586 157.272 158.341 159.346 168.321 171.323 204.116 212.257
 224.815 235.713 254.724 273.607 294.784]
Traceback (most recent call last):
  File "/home/daniel/abin/RetroTS.py", line 700, in <module>
    phys_json=opt_dict["-phys_json"]
  File "/home/daniel/abin/RetroTS.py", line 294, in retro_ts
    main_info["resp_peak"] = respiration_peak
UnboundLocalError: local variable 'respiration_peak' referenced before assignment

The tsv file looks like this 

55.2458190918	98.1654427442	-8.59014299629	56.5339485236	-0.00387859479518
55.2471923828	98.1654427442	-8.59314602988	56.5339485236	-0.00387859479518
55.2430725098	98.0966750419	-8.59915209707	56.5148740835	-0.00387859479518
55.2252197266	98.1138669674	-8.59314602988	56.5339485236	-0.0014945254138
55.2307128906	98.1052710047	-8.59765058027	56.5148740835	-0.00387859479518
55.2348327637	98.1052710047	-8.60065361387	56.5339485236	-0.0014945254138
55.2334594727	98.1912306326	-8.59164451309	56.5339485236	-0.0014945254138
55.2389526367	98.1396548558	-8.59464754668	56.5148740835	-0.00626266417656
....

While the json looks like this 

{
    "Units": [
        "Volts", 
        "%O2 saturation", 
        "Pulse", 
        "BPM", 
        "Status"
    ], 
    "SamplingFrequency": 1000.0, 
    "Columns": [
        "respiration", 
        "O2_saturation", 
        "pulse", 
        "cardiac", 
        "O2_status"
    ], 
    "StartTime": 0.0
}

I updated AFNI two days ago, the OS is Linux Mint.

What could I do to solve the error and obtain the regression files?

Thank you,

Daniel
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RetroTS UnboundLocalError: local variable 'respiration_peak'

drusso May 16, 2021 06:04AM