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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