Hello!
In our multi-modal MRI session, we’re running a dual-echo pCASL sequence. This dual-echo sequence allows to acquire BOLD and perfusion data simultaneously (at rest in my case). The issue I’m having is that the BIDS standards puts BOLD fmri data in the /func modality and the ASL data in the /perf modality. I am not sure what’s the correct way to deal with my dual-echo sequence. Where to put this data so it complies with BIDS standards? This case doesn’t seem to be covered in the recent BIDS-ASL extenstion (https://psyarxiv.com/e87y3/).
Any insights from the ASL and/or BIDS experts out there?
Many thanks!
Gabriel
Hello,
I will soon start to also acquire simultaneous BOLD and perfusion data; so I was wondering if you found any answer to your question ?
Edouard
Hi there,
It’s been a while and I have now changed positions, before the dataset was fully and successfully converted to BIDS. I did make a little progress before I left, so here is where I got so far/what I remember:
First, my /perf vs. /func question was solved like so:
The dual-echo sequence captures BOLD-optimized and pCASL-optimized data in the same TR, but separately (one with the first Echo value, the other with the second Echo value). What you can then do is simply grab the DICOMs and convert to 2 different .nii image files. Taking all the DICOMS with the Echo-1 value and converting them into an nii that goes into /perf, and taking all the DICOMS with the Echo-2 value and converting them into a nii that goes into /func. I do not have the code that I used to do this at hand, but I can dig it up for you if needed.
Secondly, after having solved this problem, I still had several issues regarding the required values in the metadata sidecar json files for the /perf. Data were acquired with a Siemens scanner. I am in no way an pCASL expert and had a hard time understanding what some of required values were, and how to get them/ calculate them from the DICOM header values, and whether I needed to get something more that was not in the DICOM headers. The person that replaced me was supposed to talk to pCASL-experienced people that helped us set-up the sequence (but that were not BIDS savvy) to sort this out. Not sure were they are at with this.
P.S. While I am not working that same lab anymore, I am working in the same institution and I am in touch with them. I still have a strong interest in BIDS and would be grateful if you could keep me updated on whether this solution makes sense to you, and what you end up doing so I can help them out.