[MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform

[Sébastien Proulx]

Hello Minc people,

My colleague gave me transformation files from a nonlinear registration 
to a template done with minctools. I'm trying to use those to bring some 
images (segmented in MNI space) back to their native space. Linear 
transforms are working fine, but I apply the inverse of the nonlinear part:

mincresample -inverse_transformation -transformation 
nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc 
templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc


doesn't work whatever I do (reloading files or try simple variants of 
the command):

Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc".
input_transform: error reading transform.
Error reading transformation file.


Here is the content of nonLinTransformFileName.xfm:
---------------------------------------------------------------------------------------------------
MNI Transform File
%Sun Aug  5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff 
-weight 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 
-step 4 4 4 -lattice_diam 12 12 12 -transformation 
/tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask 
/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc 
-model_mask 
/sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc 
/tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc 
/tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm
%(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain 
(x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010)

Transform_Type = Linear;
Linear_Transform =
  1 0 0 0
  0 1 0 0
  0 0 1 0;
Transform_Type = Grid_Transform;
Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc;
---------------------------------------------------------------------------------------------------


Is there something I'm missing, like non linear transformations use 
another command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc 
with register either, but I bet this is expected...

Thanks a lot for your help, I really have no idea what to do with 
that... apart from rerunning the segmentation in native space!

Sébastien Proulx, MSc
Research Assistant
McGill University
(514) 398-6644 #00445