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FAQ · Changes

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BIDS mentioned in FAQ authored Mar 18, 2019 by Lars Kasper's avatar Lars Kasper
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FAQ.md
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......@@ -102,17 +102,24 @@ No, the basic functionality of PhysIO, i.e. creating nuisance regressors for you
Currently, PhysIO natively supports the following physiological logfile types:
- Brain Imaging Data Structure (BIDS)
- [Standard for peripheral recordings]
(https://bids-specification.readthedocs.io/en/latest/04-modality-specific-files/04-physiological-and-other-continous-recordings.html)
- both raw physiological traces and pre-computed pulse events are
supported
- BioPac formats
- Biopac `.mat`-export
- assuming the following variables (as columns): `data`, `isi`, `isi_units`, `labels`, `start_sample`, `units`
- See `tapas_physio_read_physlogfiles_biopac_mat.m` for details
- Biopac `.txt`-export
- assuming the following 4 columns, with one sample per row: respiratory, skin conductance (GSR), cardiac (PPG), and trigger signal (on/off)
- General Electric
- Philips SCANPHYSLOG files (`SCANPHYSLOG<DateTime>.log`; all versions from release 2.6 to 5.3)
- Siemens VB (files `.ecg`, `.resp`, `.puls`)
- Siemens VD/VE (files `*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
- including CMRR-derived multiband-files
- Siemens Human Connectome Project log files (preprocessed 3 column files `*_Physio_log.txt`)
- Biopac `.mat`-export
- assuming the following variables (as columns): `data`, `isi`, `isi_units`, `labels`, `start_sample`, `units`
- See `tapas_physio_read_physlogfiles_biopac_mat.m` for details
- Biopac `.txt`-export
- assuming the following 4 columns, with one sample per row: respiratory, skin conductance (GSR), cardiac (PPG), and trigger signal (on/off)
- Siemens formats
- Siemens VB (files `.ecg`, `.resp`, `.puls`)
- Siemens VD/VE (files `*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
- including CMRR-derived multiband-files
- Siemens Human Connectome Project log files (preprocessed 3 column files `*_Physio_log.txt`)
See [Read-In of Logfiles](MANUAL_PART_READIN) for a detailed description of the expected file formats.
......@@ -204,7 +211,8 @@ Have a look at the following figure:
This figure can be found as [figure S1](https://www.sciencedirect.com/science/article/pii/S016502701630259X#sec0125) in the supplementary material of our [paper](https://doi.org/10.1016/j.jneumeth.2016.10.019).
The following heuristics might help with the `sync` settings:
The following heuristics might help with the threshold settings in the `sync`
structure:
1. Note that these thresholds have to be set correctly only once for each
functional sequence, i.e., usually once per study. Even small changes to scan
......
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