Dear Todd,

The inconsistencies are eliminated by having a common standard
that is properly defined and that everyone has agreed upon how
to interpret.  The scaling information is now contained in fields
called scl_slope and scl_inter rather than in the funused* fields.
In the Analyze format some packages decided to use the funused
fields to store information about scaling, but the standard said
nothing about this, as these fields were designated as *unused*.
Hence some packages do use this info and some don't.  In Nifti
it is defined at the outset and so packages need to be able to
deal with it in order to be properly nifti-compliant.

When converting to and from SPM outputs, these scalings in Analyze
can be a problem, but in the nifti format they will be read in correctly
and dealt with by FSL.  Note that images that we output always have
scaling set to unity, however, in order to simplify our internal code  
base.

Hope this answers your questions.
I expect that the use of Analyze format will diminish rapidly over the
next couple of years, so I strongly encourage everyone to use the
nifti format if they can.

All the best,
	Mark


On 6 Mar 2006, at 17:38, Todd Penney wrote:

>  Hi Mark,
>
>  I just had a question about his response you sent.  How does NIFTI  
> file format get rid of these inconsistencies in format?  What does  
> NIFTI file format do to avoid the issues with intensity scaling the  
> images?  Are the funused1, funused2 and funused3 fields in Analyze  
> files the variables that control the image intensity?  What are  
> these variables normally set to?  Are there any issues you are  
> aware of with scaling (or anything else) when using avwmerge/ 
> avwsplit with NIFTI files?
>
> Thanks
>
> Todd Penney
>
>
> Quoting Mark Jenkinson <[log in to unmask]>:
>
>> Dear Ged,
>>
>> Nifti was introduced precisely in order to get rid of these   
>> inconsistencies
>> in format, like the scaling in the Analyze format.  As all the major
>> software packages, including FSL and SPM, are moving away from
>> Analyze support, this is no longer going to be an issue in the  
>> future.
>>
>> I would strongly encourage you to avoid Analyze format if possible.
>> It is likely to support for the Analyze format will be dropped in the
>> future.
>>
>> |f you really need to extract this information from the SPM Analyze
>> files you can script it yourself by looking at the funused1 and  
>> funused2
>> fields in the avwhd output.  By using these with avwmaths it is easy
>> enough to rescale appropriately.
>>
>> All the best,
>> 	Mark
>>
>>
>>
>>
>>
>> On 28 Feb 2006, at 16:52, Ged Ridgway wrote:
>>
>>> Andreas Bartsch wrote:
>>>> Hi,
>>>>  it is a non-standard analyze extension.
>>>
>>> But if converting from such an image to NiFTI -- where it is  
>>> standard:
>>>
>>> http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/  
>>> nifti1fields_pages/scl_slopeinter.html
>>>
>>> couldn't this be preserved? It seems to be used in the exact way   
>>> suggested in the NiFTI standard, and it does seem to be a useful   
>>> extension (e.g. for having probability images stored as integers).
>>>
>>> Best,
>>> Ged.
>>
>>