[MINC-users] Problem with mritotal

[Andrew Janke]

On 8/17/07, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:

> > 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.

Ed, I what does xfm2param return for your final xfm? If it doesnt have
a scale of 0.8 or so in both X and Y I would suspect that you have an
error in your conversion to MINC or that you are scanning people with
small heads.

As Claude said, the MNI tools are (inadvertently) best at 1.5T data of
about "adult head" size. This is not to say that they will not work on
other sized data, just that this is how they have been most tested.

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

By all means I think that bestlinreg.pl is ready for prime time.  My
plan was to include it (and nlpfit) in the next release of mni-autoreg
if that is OK by you. For now you can always put it on packages for
others to have a go with it.  You can always use the scripts directory
for now.


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