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
