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

[Vladimir S. FONOV]

Hello,


It looks like you received grid files in minc2 file format. And your 
computer (duncan) have minc1 installed.

On 13-06-20 04:03 PM, Sébastien Proulx wrote:
> 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;


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com