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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