Hi Gleb,

The path issues do sound a bit strange. Did you log out and back in again after installing FSL (Click FSL User (top left) -> Quit -> Log out)? And for the images themselves, I am assuming you do see them in the current directory when you type ls?

Regarding the slightly different results compared to the siena report in the tutorial data; such relatively subtle effects can occur between different versions of FSL, as many of the tools are continually being updated. This is the reason that it is generally recommended to perform a particular analysis step, such as running siena, with the same version for all subjects.

Hope that helps!

Cheers,
Eelke


> On 1 Sep 2015, at 20:23, Gleb Makshakov <[log in to unmask]> wrote:
> 
> Hi, Eelke!
> 
> Thank you for your response! I installed FSL on a Virtual Machine using instructions from FSL web page. It seems strange for me too but it works only when I type a full path to siena file (usr/local/fsl/bin/siena) and then also type a full path to both files. 
> 
> Yes, I do see a prompt $ before typing. When I type siena <input1> <input2> [options] after prompt $, the program shows me a description of siena and it's options but no calculations happen. As I've mentioned before, calculations begin only in case of typing the full path to the program and both files. I can't find the reason for that but nevertheless it works and I'm happy with that. Any ideas why could that be?
> 
> Btw, did you ever encounter the situation when siena counts different PBVC on two separate calculations of the same images? I've just run the images that are provided on FSL tutorial about siena (those pictures of a patient with AD) on my computer and siena counted slightly different results regarding that control sample (PBVC -3.7753800000 and -3.7129650000). Could that  potentially be? Or is there something working improperly? 
> 
> thank you in advance!
> 
> Regards,
> 
> Gleb