Hi Amanda,
You should be fine with running TBSS directly after topup & eddy. Averaging and registration of the data to the subject T1 are not necessary.
I would recommend to extract the low b-value shell (b=1000) before performing dtifit. You can use the FSL tool "select_dwi_vols" for that. Note that this shell should include all b-values within a small range (i.e., 995 and 1005 should be included as well). "select_dwi_vols" will take care of that for you by including any b-value within 100 of the selected value.
Best wishes,
Michiel
> On 6 Apr 2022, at 21:54, Amanda Rodrigue <[log in to unmask]> wrote:
>
> Hello,
> I've inherited some partially processed HCP Diffusion data and I don't have the HCP pipelines set up on our servers to complete the missing processing.
>
> If one is only interested in running a standard TBSS pipeline, is it necessary to perform the averaging step and registration of the eddy corrected diffusion image to the T1?
>
> Like-wise, is it necessary to extract only the low bvalue volumes before performing dtifit? And if so, which of the following bvalues qualify from the following:
>
> 5 (used as the B0 value)
> 995
> 1000
> 1005
> 1810
> 1840
> 1850
> 1880
> 1920
> 1965
> 1995
> 2000
> 2005
>
> Thanks!
> Amanda
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1
This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
|