Hi Cristian and Anna

just do it outside of FS. Convert the volume to minc with mri_convert and run the MNI nu_correct on it directly

cheers Bruce

On Thu, 11 Jul 2013, Cristian Paz wrote:

Hi Anna and all Freesurfers,

I have sort of the same problem.  I know there is a flag called --noconform - but it doesnt seem to work on my data with mri_nu_correct.mni . (does not recognize the flag )  I also tried the flag --cm which is supposed to only minimally conform - but here I also got an error message. "ERROR: dimension mismatch between input volume and seg"

Does any of you FS-experts or someone on the list know how to get around this problem? in other words: how to do N3 Intensity normalization WITHOUT changing the output voxel size?

Thanks a lot in advance! best, Cris

2013/7/10 Anna Josefson anna.b.josefson@gmail.com Hi list,

I have been trying to test out bias correction on  hi-res post mortem animal MRI data. (which is not going through regular FS analysis pipeline)

Is there any option for not changing the resolution ?

from mri_nu_correct.mni.log:

Original Data has (0.234375, 0.234375, 0.400003) mm size and (384, 384, 137) voxels. Data is conformed to 1 mm size and 256 voxels for all directions.

Thanks a lot! Anna

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