mrikasper
commented
2 hours ago Dear Yana,
Thank you very much for your detailed description and taking the time to read the PhysIO documentation.
- It looks indeed as if your logfile does not have any gradient time stamps and you have to resort to nominal/manual timing synchronization. I am not sure that the clock of the system that logs the SCANPHYSLOG time is the same as the one that writes the DICOM headers, but if so, what you did with setting the
relative_start_acquisitionseems reasonable (maybe double-check the sign) - Regarding the low heart rates, can you horizontally zoom into the Diagnostic Raw Data Figure to a window of about 20 or 30 seconds, so that we can look at the peak detection a bit better?
All the best, Lars
Dear Lars,
Thank you very much for wonderful PhysIO!
I'm trying this toolbox for the first time and have carefully read the documentation. Processing of my data seems to go well, however, the estimated heart rate looks suspicious (it is in the range of 30-40 bpm). At the same time, the heart rate estimated online during scanning (displayed via Philips system) was normal. Could you please clarify why this might happen?
I'm working with PPU Wi-Fi data (Philips 3T Ingenia, a sampling rate of 496 Hz). TR = 2 s, 34 slices, 225 volumes, and 0 dummies.
A Philips logfile: ScanPsaLog20241014143359.log
Parameters from the SPM batch: matlabbatch{1}.spm.tools.physio.save_dir = {'G:\example\physio_out'}; matlabbatch{1}.spm.tools.physio.log_files.vendor = 'Philips'; matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'G:\example\scanphyslog\ScanPsaLog20241014143359.log'}; matlabbatch{1}.spm.tools.physio.log_files.respiration = {'G:\example\scanphyslog\ScanPsaLog20241014143359.log'}; matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''}; matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = 0.00201612903225806; matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition = 0; matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last'; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 34; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = []; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 2; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 225; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 17; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = []; matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = []; matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal = struct([]); matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'PPU_Wifi'; matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no = struct([]); matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.min = 0.4; matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat'; matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.max_heart_rate_bpm = 90; matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]); matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband = [0.01 2]; matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false; matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors = 'multiple_regressors.txt'; matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat'; matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none'; matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals = false; matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3; matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4; matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1; matlabbatch{1}.spm.tools.physio.model.rvt.yes.method = 'hilbert'; matlabbatch{1}.spm.tools.physio.model.rvt.yes.delays = 0; matlabbatch{1}.spm.tools.physio.model.hrv.yes.delays = 0; matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]); matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]); matlabbatch{1}.spm.tools.physio.model.other.no = struct([]); matlabbatch{1}.spm.tools.physio.verbose.level = 2; matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = 'figure_output.jpg'; matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;
PhysIO output figures:
P.S. I have noticed that the x-axis in nearly all figures above includes 1000 s, but I don't understand why (2s TR x 225 volumes = 450 s). Is it normal?
Also, I have found a thread https://github.com/translationalneuromodeling/tapas/issues/207 where Marni has ScanPsa (not SCANPHYSLOG) files and no gradient data -- the same as in my case. Is my case therefore a problem of synchronization?
Additionally, I have tried to adjust log_files.relative_start_acquisition = 26 (this is the difference between time stamps in ScanPsaLog and DICOM) but this did not change anything.
I would be very grateful for your help and apologize if there are some obvious mistakes.
Yana