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That EPI factor is wrong (if it is a single shot EPI sequence the EPI factor should equal the number of phase encoding steps). That said, it should not matter for eddy/topup unless you want correctly scaled field coefficients (these algorithms internally don’t care about this scaling and estimate the distortions directly from the data). Note that if you do not distortion correct your images, they will not accurately align with your structural data.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Blujus, Jenna" jenna_blujus@brown.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, June 25, 2023 at 8:29 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] EPI Factor generated by dmri_bids_config

External Email - Use Caution Hi all,

I am using TRACULA (v7.3.2) to examine longitudinal changes in WM integrity by diagnostic groups.

For preprocessing, I did not use topup because my data have a single acquisition (i.e., I do not have two acquisitions with opposing polarities of the phase-encode blips). But I did utilize the Eddy command for eddy current and motion correction. To do so TRACULA requires information regarding the epi factor, echo spacing, and phase encoding direction. My data are in BIDS format and so I used the dmri_bids_config script to extract these factors. While the echo spacing and PE direction match the information in my json files, I am finding that I am getting a large EPI factor (e.g., 115001.0273).

I looked at the acqp.txt file generated for use with Eddy and the correct values are stored in the file for each subject (PE direction [0 1 0] and total readout time) so I believe the command was executed properly despite the large magnitude EPI factor.

My questions are: 1. How is the EPI factor used in preprocessing by TRACULA? 2. Will the magnitude difference in the EPI factor affect the preprocessing of the DWI data if topup is turned off and only eddy is used?

Thanks, Jenna

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