How to use .puls file in physIO

[SadiaJumana]

Hi!

I am facing some issues regarding how to use .puls file gotten from PPG while fMRI scan, in PhysIO. I used to use the .log files but after scanner update we have the physio files in .puls format.. I saw in the Tapas-master repo there’s an example using .puls in Siemens VB. That example uses a Dicom file. But I don’t have any dicom for physio. I only have .puls file. Can I use that to run PhysIO?

thanks in advance.

[mrikasper]

Dear Sadia @SadiaJumana ,

The latest versions of PhysIO (v9.0 or the master branch) should be able to use the .json sidecar file instead of the .dcm file. If you used dcm2niix or a similar tool, the .json file for the fMRI run data (.nii.gz) is automatically created and could be entered as a lo_files.scan_timing input. Alternatively, you may have a file called *_AcquisitionInfo or similar from the scanner that could be used.

One question about the .puls file: Does it look like having one long row of numbers (VB/ideaCmdTool format) or is it a text file with multiple columns (VD/AdvPhysio/CMRR format)?

If you don't mind, you could send me one of these files along to check.

Thank you and

All the best,
Lars

[SadiaJumana]

Hi Lars,
Thank you for responding. The .puls file is not supported here. Is there any other way that I can share that with you?

[mrikasper]

Dear Sadia,

you can just send me a message to the email address in the README file. Thank you!

All the best,
Lars

[SadiaJumana]

Thank you. I have found this email address( lars.kasper@alumni.ethz.ch) and send the files. I'd really appreciate if you can help me in this regard.

[SadiaJumana]

Hi Lars @mrikasper ,

Hope you're doing well. I was wondering if you got a chance to look at the materials that i sent you via email.

Looking forward to hearing from you.

Best regards
Sadia

[mrikasper]

Dear Sadia,

My apologies for the delay.

I looked at the .puls file you sent. It looks like the classical Siemens VB/ideaCmdTool format with one major difference: There are triggers recorded in the file itself and interleaved with the pulse trace by adding lines like this:

Trig: 1 103

This may trip PhysIO and I have to write a bugfix for that. Beforehand, I just wanted to make sure with you whether these triggers are cardiac triggers (my assumption) or scan triggers - how many volumes were acquired in your corresponding fMRI run for this .puls logfile?

Could you therefore provide the .json file for the corresponding fMRI run?
- It should be one of the mbep2d_bold .json files, maybe task1 or rest.
- I am not sure why you have multiple .json files per run, is this a multiecho sequence?

Once we have identified the right .json file, this is also the one you can use in log_files.scan_timing instead of a Dicom file.

I hope that helps!

All the best,
Lars