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# Brain Imaging Data Structure (BIDS)
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PhysIO supports physiological logfiles prepared according to the [BIDS standard](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/06-physiological-and-other-continous-recordings.html)
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PhysIO supports physiological logfiles prepared according to the [BIDS standard](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/06-physiological-and-other-continuous-recordings.html)
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- In brief, BIDS files are (optionally compressed) tab-separated values (`\*.tsv\[.gz\]`) files that contain raw traces of peripheral recordings from cardiac and respiratory sources, as well as scan trigger events
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- The header of the columns of this `\*.tsv` file, as well as meta-information, such as sampling rate and relative onset of physiological logging to MRI scan onset is described in an accompanying `\*.json` file
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... | ... | @@ -113,11 +113,13 @@ If you have logfile data from any other vendor than the ones specified below, yo |
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# Siemens
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## Manual Recording
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## Manual Recording (`IdeaCmdTool`, `Siemens VB`)
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Physiological data collection on the Siemens scanners uses the physiological monitoring unit (PMU). The initial sampling is performed at 400 Hz, but through the PMU buffer the effective sampling intervals are ECG: 2.5 ms, RESP: 20 ms, PULS: 20 ms and EXT: 5 ms.
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There are several ways to control the physiological data collection. The 'manual' version is available on all platforms. It uses the telnet mpcu/ideacmdtool to manually start and stop the log file acquisition. The log files (`logFileName.ecg`, `logFileName.resp`, `logFileName.puls`, `logFileName.ext`) are stored in `\\MedCom\\log`. More details on how to record these data can be found [here](https://cfn.upenn.edu/aguirre/wiki/public:pulse-oximetry_during_fmri_scanning) or in the "Other Miscellaneous Topics" slides from the IDEA course.
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There are several ways to control the physiological data collection. The 'manual' version is available on all platforms. It uses the telnet `mpcu/ideacmdtool` to manually start and stop the log file acquisition. The log files (`logFileName.ecg`, `logFileName.resp`, `logFileName.puls`, `logFileName.ext`) are stored in `\\MedCom\\log`. More details on how to record these data can be found [here](https://cfn.upenn.edu/aguirre/wiki/doku.php?id=public:pulse-oximetry_during_fmri_scanning) or in the "Other Miscellaneous Topics" slides from the IDEA course.
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This is the classical method to do physiological recordings on a Siemens scanner. According to the [CMRR multi-band](https://www.cmrr.umn.edu/multiband/) sequence manual (see [this blogpost](https://david-e-warren.me/blog/physiological-data-from-mri/)), it used to be accurate in terms of timing until Siemens software release VB (hence the name in PhysIO), but has since been superseded by more integrated methods (like CMRR Tics logging or the AdvPhysio Work-in-progress (WIP) by Siemens, which can write the physiological traces as part of the DICOM image header files, see below).
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### General Properties
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... | ... | @@ -168,9 +170,9 @@ A logfile in version 3 therefore adheres to the following template (note the log |
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PhysIO automatically reads the Siemens logfiles correctly for all modalities and logfile versions 1,2 and 3.
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## CMRR Sequence / WIP Advanced Physio Logging
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## CMRR Sequence / WIP Advanced Physio Logging (`Siemens_VD`, `Siemens_Tics`)
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The CMRR sequence on VD/VE also allows the automatic recording of physiological log files (to be selected in the sequence special card). For more information have a look at the [manual](https://www.cmrr.umn.edu/multiband/). The physiological traces are stored in logFileName_PULS.log, logFileName_RESP, logFileName_ECG.log. Timing information is stored in logFileName_Info.log and external trigger events in logFileName_EXT.log.
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The CMRR sequence on VD/VE/XA also allows the automatic recording of physiological log files (to be selected in the sequence special card). For more information have a look at the [manual](https://www.cmrr.umn.edu/multiband/). The physiological traces are stored in logFileName_PULS.log, logFileName_RESP, logFileName_ECG.log or in the DICOM image file header (use [readCMRRPhysio](https://github.com/CMRR-C2P/MB/blob/master/readCMRRPhysio.m) to extract it into separate files for PhysIO). Timing information is stored in logFileName_Info.log and external trigger events in logFileName_EXT.log.
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An example of the current format (December 2017, Release 016a) for the logFileName_Info.log is given below:
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