Eugene,

Actually, I just noticed an error displayed in the terminal after running SIENA. I'm not sure how I missed this before. The error reads:

/pkg/software_depot/app/fsl/5.0.9/ubuntu_14.04/bin/viena_quant: 37: /pkg/software_depot/app/fsl/5.0.9/ubuntu_14.04/bin/viena_quant: Syntax error: "(" unexpected

Any idea what the issue might be?

Thanks,

James

On Tue, Dec 12, 2017 at 5:17 PM, James Gullickson <[log in to unmask]> wrote:

No problem. I had replied to a thread and thought my message would be tied to that. There aren't any viena files produced. Only a folder called "viena" with nothing inside. I am not using my own mask. I am using the SIENA option to tweak BET parameters, which seems to be producing a better brain extraction than I was getting without these options.

My command is:

siena timepoint1.nii.gz timepoint2.nii.gz -B "-f 0.3 -R" -V

Thanks,

James

On Tue, Dec 12, 2017 at 3:08 PM, Eugene Duff <[log in to unmask]> wrote:

Ah sure. Sorry, your email didn't contain the associated email.... 

Are there any viena files produced?  Are you trying to use your own  mask or are using any other siena options?  

Eugene

On 12 December 2017 at 20:28, James Gullickson <[log in to unmask]> wrote:

Hi Eugene,

I'm referring to VIENA, the ventricular analysis option within SIENA, It's supposed to be able to be invoked by adding the -V flag to the SIENA command. (i.e. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA/UserGuide )

I have been able to successfully run SIENA, but the VIENA option is not working. A folder called "viena" is being created by the SIENA command, but it is empty. I see no errors in the report.siena file. I'm using FSL version 5.0.9.

Thanks,

James

On Tue, Dec 12, 2017 at 2:22 PM, Eugene Duff <[log in to unmask]> wrote:

Hi James - 

It's not clear what you are referring to!  SIENA?

Eugene

On 12 December 2017 at 15:26, James Gullickson <[log in to unmask]> wrote:

All,

I recently tried to use VIENA and ran into this exact same issue. Does anyone know how to fix this?

Thanks,

James