Ah, that explains it.
The NIfTI standard is quite clear that scl_slope really must be used
to interpret the intensities correctly.  It is rather naughty of ImageJ
to display the unscaled intensities.  I definitely recommend sticking
with FSLView!  :)

All the best,
	Mark


On 21 Jun 2010, at 22:02, Anil Krishna Vasireddi wrote:

> Hm, I see what you mean. I have been looking at these images as raw  
> files through ImageJ since I'm reading them as raw files when  
> processing them. The large differences in intensity between the  
> input and output FLAIRs are evident in this case. When I look at  
> them in fslview, I see that the difference in intensities is not as  
> significant.
> -Anil
>
>
>
> ----- Original Message ----
> From: Mark Jenkinson <[log in to unmask]>
> To: [log in to unmask]
> Sent: Mon, June 21, 2010 3:10:20 PM
> Subject: Re: [FSL] Issues with intensity scaling when using FLIRT
>
> Dear Anil,
>
> I see no problem with any of these.
> Everything seems consistent - the values in the FSLView intensity
> window, the histogram generated by FSLView and the stats output
> by fslstats.  For example:
>
> ws183$ fslstats FLAIR_masked.nii -r -R
> 0.000000 6163.926270 0.000000 18566.042969 1009.216190 3510.841900
> ws183$ fslstats cFLAIR_masked.nii -r -R
> 0.000000 5669.895996 0.000000 17078.000000 857.194649 2773.019085
>
> These differences are certainly consistent with interpolation effects.
>
> What version of FSL and FSLView are you using?
> I am using FSL version 4.1.5 and FSLview version 3.1.5.
>
> I notice that the scl_slope in your nifti images is
> set to non-unity values (e.g. 15.069840 in FLAIR_masked
> and 3.338950 for PD_masked).  These values represent
> scalings of the intensities which FSL will apply to the
> values stored in the non-header part of the image, as
> dictated by the NIFTI format.  There may have been
> older versions of FSLView that did not display the
> scaled intensities, in which might explain why you
> quote a mean value in the original FLAIR around 130
> whereas I see values that are much bigger than this.
>
> If this is the problem then you can easily save
> a scaled version (where the scl_slope is reset to
> 1.0 and the stored values are scaled instead) by doing:
>  fslmaths FLAIR_masked ScaledFLAIR_masked
>
> I hope this helps solve the problem.
>
> All the best,
>    Mark
>
>
>
>
> On 21 Jun 2010, at 20:27, Anil Krishna Vasireddi wrote:
>
>> The reference number is 979615.
>> I have uploaded a set of three images from the same brain. The  
>> input FLAIR (FLAIR_masked.nii), the input PD (PD_masked.nii), and  
>> the output FLAIR (cFLAIR_masked.nii).
>>
>> Thanks again-Anil
>>
>>
>>
>> ----- Original Message ----
>> From: Mark Jenkinson <[log in to unmask]>
>> To: [log in to unmask]
>> Sent: Fri, June 18, 2010 10:42:43 AM
>> Subject: Re: [FSL] Issues with intensity scaling when using FLIRT
>>
>> Him
>>
>> This sounds very concerning and very unusual.
>> Can you please upload the relevant images to:
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>> and send us the reference number.
>>
>> Hopefully we will be able to identify the problem quickly.
>>
>> All the best,
>>   Mark
>>
>>
>>
>> On 18 Jun 2010, at 16:35, Anil Krishna Vasireddi wrote:
>>
>>> The resolution of the PD is higher than the resolution of the FLAIR.
>>>
>>> PD: 288x288x42
>>> FLAIR: 160x160x40
>>>
>>> To test the increase in intensity, I look at intensities in the  
>>> same regions of the brain within the two volumes. To quantify the  
>>> degree of scaling, I compare the mean intensity of the two  
>>> volumes. The mean intensity within the original FLAIR typically  
>>> rests around 130. The mean intensity in the registered FLAIR  
>>> varied for different volumes, ranging from 900 to 2500.
>>>
>>>
>>> -Anil
>>>
>>>
>>>
>>> ----- Original Message ----
>>> From: Mark Jenkinson <[log in to unmask]>
>>> To: [log in to unmask]
>>> Sent: Thu, June 17, 2010 4:59:57 PM
>>> Subject: Re: [FSL] Issues with intensity scaling when using FLIRT
>>>
>>> Hi,
>>>
>>> There is no scaling or modification of the intensities except for
>>> interpolation.  Is it possible that what you are seeing are just
>>> interpolation effects?  If the resolution of the PD is lower than
>>> the FLAIR then that will make the effects worse.
>>>
>>> If you still do not think it is just interpolation effects then can
>>> you describe how you are testing this and give us some
>>> numerical examples?
>>>
>>> All the best,
>>>  Mark
>>>
>>>
>>>
>>>
>>> On 17 Jun 2010, at 22:40, Anil Vasireddi wrote:
>>>
>>>> Hi,
>>>>
>>>> I have been using FLIRT to register FLAIR volumes of a given  
>>>> brain to the corresponding proton density (PD) volumes. I am  
>>>> using the following simple command for this purpose:
>>>>
>>>> flirt -in <FLAIR volume> -ref <PD volume> -out <registered FLAIR  
>>>> volume>
>>>>
>>>> The input and reference volumes were similar enough for the above  
>>>> command to be sufficient for a successful registration.
>>>>
>>>> However, the I have been noticing that the image intensities of  
>>>> voxels in the output FLAIR volumes are considerably larger than  
>>>> the intensities from the input FLAIR volumes. It doesn't seem as  
>>>> though the intensities were simply multiplied by a scalar factor  
>>>> either.
>>>>
>>>> Is it possible to use the flirt command without altering the  
>>>> image intensities from the input volumes during registration?
>>>>
>>>> Any help would be greatly appreciated.
>>>>
>>>> -Anil
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
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