Hi,
I'm afraid that we don't have sufficient time and resources to debug third party scripts.
It is difficult to know what is going wrong with the run_first_all.
Have you checked if the registration has worked?
Have you checked if it works with a single structure?
All the best,
Mark
On 15 Sep 2014, at 18:50, Ishani Sahama <[log in to unmask]> wrote:
> Dear FSL Experts,
>
> I'm having issues running FSL First with T1 data that have motion artefact. Due to the specific condition of my subjects, this artefact is characteristic of their scans.
>
> I'm running a script called act_anat_prepare_fsl supplied by mrtrix3 developers, that uses FSL First. I received the attached error log for both FSL First by itself and for the act_anat_prepare_fsl script (attachment-1).
>
> In both error logs, First fails silently and notifies that a particular vtk file is not created, thereby ending the First process.
>
> I tried to manually run the act_anat_prepare_fsl script using separate commands as per the script, to get a better idea of the exact error. The commands and the error messages are attached (attachment-2 and attachment-3 respectively) for your persual.
>
> Any assistance to overcome this issue is much appreciated!
>
> Kind regards,
> Ishani
>
>
> <Error_log_FIRST.docx><Commands.docx><FIRST_Error_Messages.docx>
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