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Hi Alan,

It looks like you have specified the ncpts variable but not the pathlist. If you do not specify pathlist, TRACULA will include all 42 tracts by default, so your pathlist and ncpts variables will have different lengths.

If you want to focus your analysis on a subset of tracts, specify those using pathlist (e.g., set pathlist = (rh.uf lh.uf)). If not, do not specify ncpts either (comment out or remove line 59 from your config file) and TRACULA will reconstruct all 42 tracts.

I also noticed you specified dob0 = 2 but did not set pedir. If you want to use topup to correct for b0 inhomogeneity distortions you need to provide the PE direction of your volumes.

Best,

Chiara


> On Jul 18, 2023, at 1:01 PM, Alan Francis <alandarkenergy@gmail.com> wrote:
>
>         External Email - Use Caution       
>
>
> Hi King-Wai:
>
> I have been running Tracula on 7T images and it keeps giving me an error. The error is as follows:
>
> copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
> Unmatched '"'.
>
> I have attached my config file. Can you please let me know what I am doing wrong?
>
> Thanks,
>
> Alan
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> Alan N. Francis PhD
> Assistant Professor of Neuroscience
> Institute of Neuroscience
> University of Texas, School of Medicine
> Rio Grande Valley
> Texas.
>                                                                                                           
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