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FSL  August 2018

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Subject:

No b0 at the beginning of DWI sequence

From:

Leonardo Tozzi <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 27 Aug 2018 23:33:58 +0100

Content-Type:

text/plain

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text/plain (15 lines)

To Whom it may concern, 

We are acquiring multiband diffusion data on a GE scanner, which has a set b0s interspersed throughout the acquisition. At first, we thought we had also a b0 volume at the start of the scan, but it turned out that this volume was a b0 calibration scan with different TR compared to the rest of the volumes. Since we did not want to introduce a volume with different properties in the analysis, we cut it and tried to first process our data without it. However, when we tried to do so using the diffusion processing pipeline from the Human Connectome Project, the processing failed, since it assumes the data to start with a b0 volume. 
My questions are: how is eddy in particular affected by not having a b0 at the start of the file? Is it still able to use the b0s interspersed in the acquisition to correct for motion/eddy currents or is the procedure invalid? In the HCP pipelines in particular (I was advised to post here from the HCP mailing list for my diffusion questions), does the motion correction step consider the closest b0 to each volume and if yes, could it be edited to run without a b0 as first scan? 
We can also consider not removing the calibration volume or adding an additional b0 at the start of our scan for all future participants, but we were wondering what the consequences are for the data collected so far. 
Thank you very much for your help, 

Yours sincerely, 

Leonardo Tozzi

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