External Email - Use Caution Hi all,
Thanks for the reply. Can you clarify how the EPI factor is being used by Freesurfer's trac-all -prep workflow? I believe that the trac-all -prep workflow is using the EPI factor and echo spacing to compute the readout time for the acqp.txt file that is input to eddy. Is this correct? Is EPI factor used in any other way by the trac-all -prep workflow? Thanks, Jenna On Sun, Jun 25, 2023 at 9:29 AM Blujus, Jenna <jenna_blu...@brown.edu> wrote: > 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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