... | ... | @@ -6,7 +6,7 @@ Physiological data collection on the Siemens scanners uses the physiological mon |
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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 contained 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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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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```
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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 ...
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... | ... | @@ -30,7 +30,9 @@ LogStopMPCUTime: 47652240 |
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## CMRR Sequence
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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/). There were a few iterations, an example of the current format (December 2017, Release 016a) is given below. The physiological traces are stored in logFileName_PULS.log, logFileName_RESP, logFileName_ECG.log. Timing information is stored in logFileName_Info.log an external trigger events in logFileName_EXT.log.
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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 an 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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```
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UUID = 7a16ea95-ac36-4ee3-9b76-bbb686ac07ca
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... | ... | @@ -61,4 +63,29 @@ VOLUME SLICE ACQ_START_TICS ACQ_FINISH_TICS ECHO |
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0 41 21754787 21754795 0
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0 5 21754795 21754803 1
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0 17 21754795 21754803 1
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``` |
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\ No newline at end of file |
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```
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The accompanying logFileName_PULS.log looks like this:
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```
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UUID = 7a16ea95-ac36-4ee3-9b76-bbb686ac07ca
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ScanDate = 20171206_150609
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LogVersion = EJA_1
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LogDataType = PULS
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SampleTime = 2
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ACQ_TIME_TICS CHANNEL VALUE SIGNAL
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21747857 PULS 2086
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21747859 PULS 2076
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21747861 PULS 2071
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21747863 PULS 2057
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21747867 PULS 2038
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21747869 PULS 2024
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21747871 PULS 2010
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21747873 PULS 1991
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21747875 PULS 1976
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21747877 PULS 1962
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```
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PhysIO uses the logFileName_Info.log to synchronize the physiological traces with the data acquisition. Note that the reference slice does not yet take into account the multiband slice ordering, but just assumes an even distribution. Older version of the CMRR sequence produced slightly different output files, which might work. Please log an issue if you have a very different format that is not supported. |
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\ No newline at end of file |