Hi John
Is there a grad_dev.nii.gz file in the $HCPDIR/100307/T1w/Diffusion directory?
Can you try running without the “-g” option and see if this runs fine? I.e.
bedpostx $HCPDIR/100307/T1w/Diffusion -n 3 -model 2 --rician
Cheers
Stam
On 3 Aug 2015, at 23:22, John Plass <[log in to unmask]> wrote:
> Hello all,
> I was hoping I could get some help with an error I've been running into. In trying to run bedpostx, it seems that arguments that are meant to be passed along to xfibres are going unrecognized. If I run:
>
> bedpostx $HCPDIR/100307/T1w/Diffusion -n 3 -model 2 -g --rician --cnonlinear
>
> I get back:
>
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
>
> ----- Bedpostx Monitor -----
> Queuing post processing stage
> An error ocurred. Please check file [...censored...]/100307/T1w/Diffusion.bedpostX/logs/bedpostx.e96432.1
> Killed: 9
>
> In the log, it says "--rician: is an unrecognized token!". However, if I run the same command without the --rician or --cnonlinear, there is no error and I can see the xfibres process running. If I run xfibres with no arguments, I see both --rician and --cnonlinear noted as options in the help text. Any chance anyone could help me out with this?
>
> Other relevant information:
> -OSX Yosemite
> -Recently patched from FSL 5.0 to 5.0.8. As per the instructions, I just untarred the patch into the proper directory. Any chance there is something I am missing here?
>
> Any help would be greatly appreciated!
>
> Best regards,
> John Plass
>
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