Hi Saad,
Thanks for the reply. This is indeed in relation to simple mode.
It was through looking at the source that I figured out what was
happening, so I could make the change, but the script that is confused
by this is in use on several computers, so I'll have to figure out
whether it's quicker to change the script or to recompile FSL... :)
Cheers,
Jon
On 9 November 2010 11:33, Saad Jbabdi <[log in to unmask]> wrote:
> Hi Jon,
>
> I assume you are talking about using probtrackx in simple mode?
>
> I don't think there is an easy way of changing the output file names to use the input coordinates.
> However, it is very easy to change the code (ptx_simple.cc) to do what you want.
> So I can either email you a slightly different version of that file, or build probtrackx for you using that version?
>
> Cheers,
> Saad.
>
>
> On 9 Nov 2010, at 11:18, Jon Clayden wrote:
>
>> Dear all,
>>
>> It seems that probtrackx will internally change the seed coordinates
>> given to it if the data is stored using the neurological convention,
>> to whatever they would have been under the radiological convention. Of
>> course, what coordinate system is used internally doesn't necessarily
>> matter to users, but it seems that output images and "particle" files
>> all use the switched coordinates as well, making it unpredictable what
>> file names will be produced by the program, and therefore creating
>> difficulties in scripts that call probtrackx.
>>
>> I'm not sure how long this has been part of the code, since I
>> generally use the radiological convention, but I would be interested
>> to know whether there's a simple way to handle this so that the
>> output, at least, uses the same convention as the input. I realise
>> that switching all data to use radiological convention would have this
>> effect, but that is not really an ideal solution. Is there any
>> alternative?
>>
>> Many thanks,
>> Jon
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
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