EPI factor `FSL` `topup` `datain` parameter values

Software Support
,
1

Hi,
I would like to apply FSL’s topup to a dMRI dataset that I have from a Siemens Prisma 3T scanner. In order to figure out waht my datain parameter values should be. Supposedly I was given an AP and PA acqusition, together with a pair of fieldmap volumes, which I believe are phase-encoding polarity volumes.

My DICOM metadata shows that the PhaseEncodingDirection are -j (AP) and j (P). Is there a way to know what these correspond to for the datain vector?

Additionally, I am unable to find the the EPI factor value in the metadata. Attached are the anonymized JSON sidecar data obtained when converting the DICOM data into BIDS format. Is there a particular name for the EPI factor that I ignore for this type of scanner?

Here, despite being a thread about Philips data,
https://neurostars.org/t/total-readout-time-for-fmriprep-with-topup-on-philips-scan-data-possible-dcm2niix-error/

they say "(…) “EchoTrainLength”, which I believe corresponds to (EPI factor + 1) after taking into account acceleration.”

In my dMRI data “MultibandAccelerationFactor” is 4, but I am not sure how that affects the EPI factor computation.

Finally, I am not very familiar with the possibilities of topup or susceptibility correction details, so I am not sure if there are ways in which the PE polarity volumes can be otherwise used together with the AP/PA dMRI data. Pointers are welcome.

Thanks

sub-0001_acq-dir99_dir-ap_dwi_anon.json.txt (17.4 KB)
sub-0001_acq-dir99_dir-ap_run-01_epi_anon.json.txt (6.6 KB)
sub-0001_acq-dir99_dir-pa_dwi_anon.json.txt (17.4 KB)
sub-0001_acq-dir99_dir-pa_run-02_epi_anon.json.txt (6.6 KB)

2

Hi @jhlegarreta,

Not a direct answer to your question, but QSIPrep can perform SDC as part of its processing pipeline. I encourage you to explore it.

Best,
Steven

3

Hi @jhlegarreta ,

If your AP and PA DWI acquisitions have b=0 volumes in each, then you should better use those b0 images for topup.

For your topup acquisition parameters file, the exact value of the 4th column is what is specified in "TotalReadoutTime".
For your dwi, the value to put in your 4th column is then: 0.0959097 (in s).

You should be able to follow the Topup user page for guidance: topup/TopupUsersGuide - FslWiki

Also fo FSL tools related qurestions, do not hesitate to look and ask for answers here, where the FSL developers are very friendly and responsive!

4

Thanks for your suggestions and explanations @Steven and @jsein.