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How different does the extra b0 look from the rest of the data? The question will be whether it is best to chop it out at the end of preprocessing or if that will create problems for eddyıs model. Matt. On 8/27/18, 5:33 PM, "FSL - FMRIB's Software Library on behalf of Leonardo Tozzi" <[log in to unmask] on behalf of [log in to unmask]> wrote: >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 > >######################################################################## > >To unsubscribe from the FSL list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1