[MINC-users] installation problem with N3 on Linux (red hat 9)

[John G. Sled]

I have a couple of comments to add.  N3 comes with a test suite that
can be run with the 'make test' command.  This should verify that the
volumes are being corrected.  Also, for any given correction, one can
generate the field estimate as follows

nu_correct input.mnc output.mnc
imp2field -like output.mnc output.imp output_field.mnc

This is easier than dividing the output by the input and contending with
division by zero issues.

John


On Fri, Dec 12, 2003 at 09:47:16AM -0500, Andrew Janke wrote:
> On Fri, 12 Dec 2003, siamak ardekani wrote:
> 
> > Thanks again for the comment. Finally, I was able install N3 and make it
> > run. To test the performance I tried to run nu_correct on one of the data
> > files located in the N3/testing folder named block.mnc. However, I didn't
> > see any difference before and after correction. I also ran the program on a
> > real MRI brain data without any success (using different combinations
> > of -stop, -distance, -iteration and -fwhm). Is there any appropriate way to
> > check the algorithm and make sure that installation has been done ok.
> 
> John Sled (the Author of N3) is really the one who should comment here but...
> 
> The variations in intensity that N3 removes are often very subtle, and often
> subtle enough that the eye cannot pick them out without a bit of "help".
> 
> To see if there really is any difference between the images do this:
> 
>    $ mincdiff input.mnc output.mnc
> 
> If there are differences (apart from the header) reported continue to something
> like this:
> 
>    $ mincmath -sub input.mnc output.mnc diff.mnc
>    $ register input.mnc diff.mnc
> 
> --
> Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
> Australia->University of Queensland->Centre for Magnetic Resonance
> W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581
> 
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