[MINC-users] minctracc and mincresample question

[Andrew Janke]

Hi Andrew,

> We've been using minctracc and mincresample to register skull-stripped
> images as part of our workflow, but we recently found out that registration
> might work better using the whole image before skullstripping. I was hoping
> to save some work by registering the images with the skull on using
> minctracc, and then take the xfm output file from that and apply it to the
> skull-stripped versions with mincresample. However, when I do that, I end up
> with blank registered images. Looking at the matrices in the xfm files of
> the registered with skull on and registered with skull off images, I noticed
> that the first three columns are fairly similar but the last column is very
> different. Does anyone have any ideas as to why it's not working? I can post
> the script I wrote to do this if it helps.

The last column of a xfm matrix can be thought of as linear shifts in
X, Y and Z. As such,
my guess is that if you are using BET (via a conversion to NIFTI) to
skull strip the images the co-ordinates of the stripped image is being
altered along the way. The last column of a xfm matrix is the
transformation parameters.

Perhaps can you post the results of mincinfo on both your original and
skull stripped images?  if they are different then you can do
something hackish like this:

   $ cp original.mnc final.mnc
   $ minccopy stripped.mnc final.mnc

To get your original co-ordinates back. This will just copy the data
from the stripped image into final.mnc leaving the co-ordinate
information intact.

Thanks


a