Dear Paul,


I mean the intensity values are different between the different viewers (when read from the cursor tool or fslviewer or the interface of other viewers), given the same voxel coordinates.


It is very strange: I am not sure why this is the case.


Thank you,


Kind regards,

Bianca

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: 18 October 2016 22:17:26
To: [log in to unmask]
Subject: Re: [FSL] Incorrect display of PET images
 
Hi Bianca,

Do you just mean that the colours don't match exactly? The different viewers may be using different colour maps - not all greyscale colour maps are identical. 

To check the actual intensity value at a given voxel in FSLView, look in the "Cursor" tool at the bottom left (http://fsl.fmrib.ox.ac.uk/fsl/fslview/views.html). The other viewers you are using should have a similar intensity readout somewhere in their interface.
fsl.fmrib.ox.ac.uk
The image views. Images can be displayed using several kinds of 2 & 3-D views, selectable via the Tools menu: Orthographic - the default view showing one slice each ...


Cheers,

Paul

On 18 October 2016 at 16:50, De Blasi, Bianca <[log in to unmask]> wrote:

Dear Paul,


thanks, it worked when I adjusted the displaying range to be the same used in the other viewers. On the other hand, the intensity value displayed is not the same between fslviewer and other viewers. Do you know why is this the case?


Sorry for these basic questions but I am quite new fsl user,


Thank you,


Kind regards,


Bianca 

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: 18 October 2016 15:46:34
To: [log in to unmask]
Subject: Re: [FSL] Incorrect display of PET images
 
Hi Bianca,

Have you tried adjusting the brightness/contrast settings in the toolbar at the top of the FSLView window?

Cheers,

Paul

On 18 October 2016 at 14:51, Bianca De Blasi <[log in to unmask]> wrote:
Dear all,

I am experiencing an issue when displaying some PET images in fsl. Using fslview the brain appear completely bright (with no contrast between the structures) while with any other viewers (ITK snap, SPM) the brain structures are distinguishable and the image appears fine. This happens in fsl, no matter if the file is zipped (.nii.gz) or unzipped (.nii).

Any idea on where the problem could be?

Thank you very much in advance,
Bianca De Blasi