Hi,
I've just seen your data and the problem is that the data is in
neurological orientation
whereas the mask is in radiological orientation. That causes a
problem for the current
distribution of FSL, although a new version soon will fix this.
However, at the moment
we still recommend that everyone only use FSL with "radiologically
oriented" data.
See the FAQ for a definition of this and instructions on how to swap
the orientation
from neurological to radiological for your data.
All the best,
Mark
On 25 Dec 2007, at 12:44, Steve Smith wrote:
> Hi, thanks for sending the data. This all looks fine to me and
> fslstats gives sensible answers. There was briefly a bug in the -k
> option in fslstats in an older version of FSL, so make sure you
> have the very latest version (4.0.2) and maybe that will fix things
> for you.
>
> Cheers, Steve.
>
>
>
> On 18 Dec 2007, at 19:57, James Andrews wrote:
>
>> Hi,
>>
>> I am using fslstats to calculate summary statistics for DTI data.
>> I have
>> run TBSS, converted the significant voxels back into native space,
>> and now
>> would like to calculate statistics like mean FA for the masked
>> region.
>> However, the intensities that fslstats calculates when I run the
>> following
>> command line are not the same as when I click on the voxels in the
>> fslview GUI!?
>>
>> fslstats <my input in native space> -k <my mask in native space> -R
>>
>> Am I doing something wrong with fslstats?
>>
>> Many thanks,
>> James
>>
>
>
> ----------------------------------------------------------------------
> -----
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ----------------------------------------------------------------------
> -----
>
|