Frequently Asked Questions about MNI N3
Updated Aug. 11, 1999

How can I convert raw data to the format that N3 uses?

N3 uses data in the MINC file format. The minc package provides two programs rawtominc and minctoraw for converting raw data to and from minc format respectively. An example of using these programs is as follows. Suppose the data is unsigned short integers consisting of twenty-four 256 by 256 slices. If this data came from an MRI scanner producing 12 bit data with different endian than the machine running rawtominc then one might do the conversion as follows:

dd conv=swab if=mydata.raw | rawtominc -transverse -short -unsigned -xstep -1 -ystep -1 -zstep 5.5 -mri -origin 0 0 0 -range 0 4095 -real_range 0 4095 -clobber mydata.mnc 24 256 256

And the conversion back to raw as follows:

minctoraw -range 0 1800 -normalize somedata.mnc | dd conv=swab of=somedata.raw

N3 produces an error message when I specify a mask volume. What's wrong?

The masked region for N3 is defined as any voxel greater than zero. However, the program extracttag which resamples the mask into the working resolution has some peculiarities which can result in errors. The trouble is that extracttag is fussy about the real range of the data set. In the minc format the mapping between the raw binary data (so called voxel values) and their interpretation as real numbers (so called real values) is somewhat arbitrary.

By default rawtominc sets the mapping to map the entire range of voxel values to the range [0, 1]. This can be overridden by giving the -range and -real_range options. For example, for 12 bit MR data one might choose -range 0 4095 -real_range 0 4095. Anyway, I'm not exactly clear on what extracttag excepts and doesn't except. However, I have found the command

mincmath -gt -const 0 old_mask.mnc new_mask.mnc

fixes the problem.

As an aside about real and voxel ranges, keep in mind that N3 treats values less than one as part of the background. Hence, a data set created by rawtominc without a range specification will yeild a volume that is empty as far as N3 is concerned.

Can N3 be used on single slice data?

Yes, it works fine on single slice data. Note, however, that a bug in verison 1.02 may create erratic results for volumes with only a few slices. This is fixed in version 1.04.

Can I use N3 for surface coil data?

Yes, however the default settings are not optimal. Due to the extreme non-uniformity in surface coil data, N3 usually hits its iteration limit before the correction is complete. Try using nu_correct with the options -iterations 150. If that doesn't help, try reducing the stopping threshold as well by adding the option -stop 0.0001.

Why does nu_correct print ominous warnings while running?

Warning messages like

Not implemented yet in cache_volume_range_has_changed()

Not implemented yet in cache_volume_range_has_changed()

are harmless. They refer to a portion of the volume_io libary that N3 does not use.

Why do I get a different result when I run N3 a second time?

For volumes with particularly severe non-uniformity, N3 reachs its iteration limit before the algorithm has converged. In these instances running the algorithm a second time should improve upon the result. However, it is more straight forward to adjust the stopping criteria using the -iterations and -stop options to set the maximum number of iterations and minimum change in field estimate respectively. Try for example the option '-iteration 150'.