[MINC-users] Problem with mritotal

[Claude LEPAGE]

Hello Ed,

> Currently we are acquiring MRI volumes on a 3T machine. After
> conversion to minc format I used the command 'insect' to preprocess
> the scans. I noticed that for some scans this resulted in too small
> brains which, in addition, were also not correctly orientated in
> stereotaxic orientation. Most probably 'mritotal' is not able to
> derive a correct (linear) transformation. To check this I artificially
> multiplied the pixel size in X and Z by a factor 1.2 in the conversion
> to minc format (so without changing the voxel data). This resulted in
> a correctly sized and orientated volume.
> 
> Is there some limitation in mritotal or a bug?

I will attempt to answer your questions. Hopefully, perhaps Andrew
can fill-in some more details.

The MNI tools were developed and tuned for a 1.5T scanner. We are
starting to process scans from 3T scanners, with limitations. The
non-uniformities are much stronger on a 3T scanner and I found
that a -distance 25 to 50 must be given to nu_correct for better
results. This is not optimal, but it is better than the default
distance of 200 (or is it still 60 in some older versions?). It's
worth trying.

At the Brain-Imaging Centre (BIC) of the MNI, I came up with a
replacement script for mritotal. Based on experience, linear
registration is more reliable and robust when the source and
the target are masked (keep only brain tissues). This will avoid
neck cropping issues (autocrop option) for scans with the full
neck. Non-uniformities must also be corrected in native space 
prior to registration (in particular for 3T). 

These new tools are used internally at the BIC and haven't been
officially packaged. Andrew, what do you think? 

Yours,

Claude Lepage