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

[Alex Zijdenbos]

Hi Sébastien,

My guess would be that the deformation field (grid_0.mnc) file is
corrupt. What happens when you run this:

minccomplete TMS_CON_44_nlfit_It_grid_0.mnc

and/or mincfinfo?

-- A

On Thu, Jun 20, 2013 at 2:00 PM, Sébastien Proulx
<sebastien.proulx2 at mcgill.ca> wrote:
> 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
>
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