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

[Michael Ferreira]

Hi Sebas,

Since I see from your BIC home directory that you are a bash shell user, 
type this:

export PATH='/usr/local/bic/bin:'$PATH

Then retry your mincresample command, it should work now.  Your output 
will be in MINC2 format though, so it may be wise to always use MINC2.

To do this, add the above PATH definition to your ~/.bashrc file.  This 
way, every time you login to the BIC you will be using the MINC2 tools.

Regards,

mike


On 20/06/13 04:35 PM, Vladimir S. FONOV wrote:
> 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;
>
>