[MINC-users] mincresample changes voxel values

[Paul GRAVEL]

Thanks Jason!

The program reading these values is do_GTM_correction (program to correct
for partial volume effect).  The new label 37 was found in the output of
this program.  I then used Display, which confirmed that there was indeed
a new label 37; about half of the right hippocampus was changed to 37,
while the rest remained to 36.

I did try the mincmath command, and it seems to work, i.e. it changed the
whole (and not half of) right hippocampus to label 1.

But I am now using:
mincreshape -dimorder 'zspace yspace xspace' -dimsize 'zspace=91' -dimsize 'yspace=109' -dimsize 'xspace=91' -start '-1 -1 4' combined_labels_Display_format.mnc combined_labels_icbm_2mm.mnc

and it seems to do the trick.

Thanks again!

Paul

On Wed, 26 Jul 2006, Jason Lerch wrote:

> Quick word of caution: are you reading these values using Display or
> register? They do their own internal conversion - to make sure this
> problem is really a problem, try binarizing a label (use mincmath
> -const2 35.5 36.5 -seg labels.mnc one-label.mnc) and then loading it in
> some viewing program.
>
> Hope this helps - if not, see if the command resample_labels gives you
> more satisfaction.
>
> Jason
>
> Paul GRAVEL wrote:
>
> >Dear All,
> >
> >I am combining manually_modified_labels using Display:
> >
> >Display mri_stx_nuc.mnc -label label1.mnc -label label2.mnc ...
> >
> >(All the label files are in the icbm_template_2.00mm.mnc
> >format/dimensions/origin.)
> >
> >Then when I save the combined labels in Display, it does put the labels in
> >a different format than the icbm; which I guess is expected.
> >
> >But when I use mincresample on the combined labels to bring them back to
> >the icbm_template_2.00mm.mnc format, some of the original label numbers
> >are changed, e.g. Original right_hippocampus_voxels=36, but resampled
> >right_hippocampus will have some voxels=36 and some voxels=37.
> >My question is why is that, and/or is there a work-around ?
> >
> >I did use:
> >mincresample combined_labels_Display_format.mnc combined_labels_icbm_2mm.mnc -like /data/avgbrain/avgbrain1/brain/images/icbm_template_2.00mm.mnc
> >OR
> >mincresample -nearest_neighbour combined_labels_Display_format.mnc combined_labels_icbm_2mm.mnc -like /data/avgbrain/avgbrain1/brain/images/icbm_template_2.00mm.mnc
> >
> >But same outcome...
> >
> >Thanks in advance.
> >
> >Best Regards,
> >
> >Paul
> >
> >
> >
> >
> >
> >_______________________________________________
> >MINC-users at bic.mni.mcgill.ca
> >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
>
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