Sure - you can script this easily enough, as long as you want to do
the same procedure on all input images.
Steve.
On 19 Feb 2007, at 22:52, Beth Nichols wrote:
> 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
> [log in to unmask]
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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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