Thanks for the quick response. I am aware of the many benefits of the 
nifti format, but unfortunately because I am doing high resolution 
imaging and several of my analyses rely on tools that are not yet 
compatible with nifti, I'm stuck with analyze for now...

But, just to clarify, it seemed to me that avwchpixdim was able to 
change negative values to positive values for my analyze files.  Is 
this something that I could batch and would be reliable? (I know that I 
originally asked to go from positive to negative, I am just trying to 
explore other options).

Thanks again,
Beth

On Feb 19, 2007, at 2:40 PM, Mark Jenkinson wrote:

> Hi,
>
> You can't easily change pixdim signs for Analyze with FSL.
> See the FAQ for why this is as it is - basically it is so that it is
> consistent with the avg152 images (which have negative pixdim).
>
> The solution is to use the nifti format which is what we strongly
> recommend.  Analyze is just incapable of correctly dealing with
> left-right issues (equivalently, radiological/neurological storage
> orderings).
>
> All the best,
> 	Mark
>
>
>
> On 19 Feb 2007, at 22:29, Beth Nichols wrote:
>
>> Hello-
>>
>> Does anyone know how I can change positive pixdim values into negative
>> pixdim values for analyze files (or if this is possible)? The command
>> avwchpixdim lets me change negative to positive values but not 
>> positive to
>> negative.  Alternatively, does anyone know how to run the avwswapdim 
>> command
>> in such a way that the pixdim value is NOT changed (i.e., by adding a 
>> flag
>> or some type)?
>>
>> Here is some background on how I analyze my data and why I want a 
>> negative
>> pixdim value:
>> I use SPM2 to analyze my data. Before I do slice timing, I flip my 
>> data
>> along the x and y axis using the fsl 3.3 command avwswapdim. When I 
>> do this,
>> fsl changes my data from radiological to neurological format (the 
>> desired
>> effect) and also changes the pixdim variable for the X axis to a 
>> positive
>> number (an undesired effect). However, fsl 3.2 only changed the 
>> format but
>> did not change the pixdim variable.  Because of this change from fsl 
>> 3.2 to
>> 3.3 in the pixdim value, SPM2 displays my images and results in 
>> radiological
>> format (even though they are stored in neurological format) and an 
>> in-house
>> program that fixes bad slices of data does not work properly.
>>
>> It is important to note that I do not actually want to change the
>> orientation of my data- I only want to change the value pixdim from a
>> positive to a negative value. I have explored the programs avwhd and
>> avwedithd, but these don't appear to have the pixdim value stored. I 
>> have
>> also tried to change the pixdim value in mricro and SPM2/matlab but 
>> have not
>> been able to find a way to do so.
>>
>> Any help would be greatly appreciated!
>>
>> Thanks,
>> Beth
>>


-- 
Elizabeth Nichols
Department of Psychology
Jordan Hall, bldg 420, room 478
Stanford, CA 94305
phone: (650) 725-8374
fax: (650) 725-5699
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