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FSL  February 2008

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Subject:

Re: discrepancy with intensities using fslstats

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 1 Feb 2008 13:23:34 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (65 lines)

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
> ---------------------------------------------------------------------- 
> -----
>

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