[Insight-users] Recommend imageediting tool

[Daniel Mace]

Arne,

ImageJ is a pretty good program for pre-processing images: 
http://rsb.info.nih.gov/ij/ .  I tend to use it for pre-processing 
confocal images before passing them into ITK.  Not sure how well it 
handles the header information, but would be worth a shot.

Cheers,
Dan

Arne Hansen wrote:
> Hello. I have some MR-volumes stored in ANALYZE format which i need 
> to modify.
> I just need to be able to invert contrast, flip dimensions and cut 
> noisy slices away.
>  
> In matlab i read these using SPM2-toolbox, and in c++ i use ITK to 
> read and VTK to visualize. But these are all for developing algorithms 
> to analyze the images, and a visual tool would be better to do these 
> rough preprocessing i think.
>  
> Before I use these tools i would really like to preprocess the images 
> very roughly, meaning making sure they are all turning the same way 
> and all have removed noise slices and so.
>  
> I have tried this tool called MIPAV which is written in java. This is 
> a good tool, but unfortunately it seems that MIPAV does not change the 
> header information when i for example flip dimension 1 and 2, or when 
> slices are cut away etc.
> This means that the changes i perform in mipav does not take effect 
> when i load the images in matlab using SPM2,(and I am not sure about 
> ITK, but i think its the same there).
>  
> So is there a good tool for performing these small preprocessing 
> steps, which also stores the changes in the header file?
>  
> And how do you guys perform this simple tasks, Do you use ITK for it 
> or what?
>  
> I hope somebody has a good recommendation :)
>  
> Thank you very much.
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