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

[Sébastien Proulx]

It seems like I don't have access to minccomplete, but see the following 
terminal output:
-------------------------------------------------------------------------------------
duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete 
TMS_CON_45_nlfit_It_grid_0.mnc
mincomplete: Command not found.
duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo 
TMS_CON_45_nlfit_It_grid_0.mnc
ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file 
format
miopen: MINC package entry point
-------------------------------------------------------------------------------------

Since I tried with two different subjects, I thought a corruption was 
unlikely, but I guess mincinfo should be able to read any intact minc 
file. Is it possible that minctracc (see content of .xfm) did correctly 
produce the nonlinearly registered images, but somehow screwed-up all 
the ..._nlfit_It_grid_0.mnc files?

Thanks a lot Alex!

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

Le 13-06-20 2:22 PM, Alex Zijdenbos a écrit :
> 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
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
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