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

Thu Jun 20 16:03:04 EDT 2013

It's not me who did the registration, I'm only trying to undo it :-P 
(apply the inverse transform). My colleague gave me one subject, didn't 
work. He sent it again along with another subject, didn't work either 
for both. He could send me more, but I guess it would be the same.

Same thing with min_cc_omplete. Trying stuff around, I copypasted the 
wrong lines.

As for the version:
duncan:~/transformTest_bis/Transforms_45/nonlinear> mincresample -version
program: 1.5.1
libminc: 1.5.1
netcdf : "3.6.3" of May 20 2011 16:00:48 $

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

Le 13-06-20 3:44 PM, Alex Zijdenbos a écrit :
> 'minccomplete' has two 'c's :)
>
> you get the same error for all grid_0.mnc files, or just one?
>
> my other guess would be you are looking at a MINC1/MINC2 issue, and/or
> that you might have an ancient MINC install. What does 'mincresample
> -version' tell you?
>
> On Thu, Jun 20, 2013 at 3:31 PM, Sébastien Proulx
> <sebastien.proulx2 at mcgill.ca> wrote:
>> 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
>>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>>
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