... | ... | @@ -60,7 +60,7 @@ If you have logfile data from any other vendor than the ones specified below, yo |
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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/public:pulse-oximetry_during_fmri_scanning) or in the "Other Miscellaneous Topics" slides from the IDEA course.
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An example of a .puls logfile is given below. The data are stored in one long line. The text between 5002 and 6002 forms the header, and the text between 5003 and 6003 the footer. Important information in the footer is the LogStartMDHTime and the LogStopMDHTime (in ms since midnight), which can be used to synchronize the logfiles with the dicom images using the AcquisitionTime in the dicom header (in hhmmss.ms). The values 5000 and 6000 are inserted into the signal trace and indicate trigger events. Note that only the modality which is selected to be displayed during the acquisition will have triggers.
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... | ... | @@ -150,7 +150,7 @@ PhysIO uses the logFileName_Info.log to synchronize the physiological traces wit |
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Disclaimer: Most of the information below is a best guess from the developers, but without any guarantee of accuracy.
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The physiological log file (*paradigm*_Physio_log.txt) distributed with the Human Connectome Project data contains respiratory and puls-oximeter data in one file. The first column marks when data acquisition is performed, the second and third contain the respiratory and puls-oximeter traces, respectively. The files are written at a sampling rate of 400Hz and start and end with the scan. PhysIO does provide a reader, you just need to select the appropriate option in the file format tab. An example is provided below:
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The physiological log file (`*paradigm*_Physio_log.txt`) distributed with the Human Connectome Project data contains respiratory and puls-oximeter data in one file. The first column marks when data acquisition is performed, the second and third contain the respiratory and puls-oximeter traces, respectively. The files are written at a sampling rate of 400Hz and start and end with the scan. PhysIO does provide a reader, you just need to select the appropriate option in the file format tab. An example is provided below:
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```
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1 1904 1756
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