Current version: Release 2022a, v8.1.0
+Current version: Release 2022b, v8.2.0
-Copyright (C) 2012-2022
+
Lars Kasper
kasper@biomed.ee.ethz.chCopyright (C) 2012-2022
Lars Kasper
kasper@biomed.ee.ethz.chTranslational Neuromodeling Unit (TNU)
Institute for Biomedical Engineering
University of Zurich and ETH Zurich
StartTime
refers to when the physiological recording started relative to the first scan volume of the fMRI run, which means that typically this value is negative, because one starts the recording before the onset of scan volumes.tapas_physio_read_physlogfiles_bids.m
for more details and technical
documentation.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.
-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 or in the "Other Miscellaneous Topics" slides from the IDEA course.
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.
+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 or in the "Other Miscellaneous Topics" slides from the IDEA course.
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.
We use the time stamp of the clock of the Measurement Data Header (MDH), i.e., computer that controls the scanner, to synchronize with the DICOMs, because this computer also controls the creation of the scan data, i.e., reconstructed DICOM images. This is in accordance to other packages reading Siemens physiological logfile data, e.g., Chris Rorden's PART, with a detailed explanation on the DICOM timestamp in AcquisitionTime
found here.
1 2 40 280 5002 Logging PULSE signal: reduction factor = 1, PULS_SAMPLES_PER_SECOND = 50; PULS_SAMPLE_INTERVAL = 20000 6002 1653 1593 1545 1510 1484 ...
ACQ FINISHED
6002 3093 3096 3064 5000 3016 2926 5003
@@ -1826,8 +1828,22 @@ Human Connectome Project
1 1904 1780
Current version: PhysIO Toolbox Release R2022a, v8.1.0
-April 5th, 2022
+Current version: PhysIO Toolbox Release R2022b, v8.2.0
+September 5th, 2022
+tapas_physio_test
to TAPAS-generic tapas_test
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