[MINC-users] Converting ANTs transform to MINC

Mon Feb 25 12:24:54 EST 2019

Looks like you're using a version of ANTs that doesn't have the MINC support compiled in.

Either use the ANTs built into minc-toolkit-v2, or turn on MINC support in the ANTs build.

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca<mailto:gabriel.devenyi at mcgill.ca>

On Sat, 23 Feb 2019 at 14:12, Thomas Funck <thomas.funck at mail.mcgill.ca<mailto:thomas.funck at mail.mcgill.ca>> wrote:
Hi Vlad,

Thanks for the info!  I tried the following command, but it ran into a problem when writing the .xfm. The output MINC files seem to be created with no problem. Am I missing something? Do I have to enable something when compiling ANTs?

antsRegistration --minc --write-composite-transform 1 --verbose 1 -d 3 -a -o [test,test_warp.mnc,test_warp_inv.mnc] -c [1x1x1x1,1e-06,10] -f 8x4x2x1 -s 3x2x1x0  -m Mattes[${f},${m}] -t Rigid[0.1]

Can't write transform file test.xfm
Exception Object caught:

itk::ExceptionObject (0x41d5b60)
Location: "unknown"
File: /opt/ANTs/build/ITKv5/Modules/IO/TransformBase/include/itkTransformFileWriter.hxx
Line: 167
Description: itk::ERROR: TransformFileWriterTemplate(0x41c24e0): Could not create Transform IO object for writing file test.xfm
  Tried to create one of the following:
    HDF5TransformIOTemplate
    HDF5TransformIOTemplate
    MatlabTransformIOTemplate
    MatlabTransformIOTemplate
    TxtTransformIOTemplate
    TxtTransformIOTemplate
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Can't write transform file test_inverse.xfm
Exception Object caught:

itk::ExceptionObject (0x41d7a10)
Location: "unknown"
File: /opt/ANTs/build/ITKv5/Modules/IO/TransformBase/include/itkTransformFileWriter.hxx
Line: 167
Description: itk::ERROR: TransformFileWriterTemplate(0x41c24e0): Could not create Transform IO object for writing file test_inverse.xfm
  Tried to create one of the following:
    HDF5TransformIOTemplate
    HDF5TransformIOTemplate
    MatlabTransformIOTemplate
    MatlabTransformIOTemplate
    TxtTransformIOTemplate
    TxtTransformIOTemplate
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

________________________________
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Today's Topics:

   1. Converting ANTs transform to MINC (Thomas Funck)
   2. Re: Converting ANTs transform to MINC (Vladimir S. FONOV)

----------------------------------------------------------------------

Message: 1
Date: Fri, 22 Feb 2019 14:31:35 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca<mailto:thomas.funck at mail.mcgill.ca>>
To: "minc-users at bic.mni.mcgill.ca<mailto:minc-users at bic.mni.mcgill.ca>" <minc-users at bic.mni.mcgill.ca<mailto:minc-users at bic.mni.mcgill.ca>>
Subject: [MINC-users] Converting ANTs transform to MINC
Message-ID:
        <YT1PR01MB33219D1A6A0454FCB894D6EBA67F0 at YT1PR01MB3321.CANPRD01.PROD.OUTLOOK.COM<mailto:YT1PR01MB33219D1A6A0454FCB894D6EBA67F0 at YT1PR01MB3321.CANPRD01.PROD.OUTLOOK.COM>>

Content-Type: text/plain; charset="iso-8859-1"

Hi,

Does anyone have experience transforming the output of a NL transformation (ie. deformation volume + affine) from ANTs into a minc friendly format? Is there an easy way to do this?

Best,

Thomas

------------------------------

Message: 2
Date: Fri, 22 Feb 2019 09:37:04 -0500
From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com<mailto:vladimir.fonov at gmail.com>>
To: MINC list <minc-users at bic.mni.mcgill.ca<mailto:minc-users at bic.mni.mcgill.ca>>
Subject: Re: [MINC-users] Converting ANTs transform to MINC
Message-ID: <A0BB4313-7BDE-4576-AEAD-4ED06872F777 at gmail.com<mailto:A0BB4313-7BDE-4576-AEAD-4ED06872F777 at gmail.com>>
Content-Type: text/plain;       charset=utf-8

just run antsRegistration with ?minc option

> On Feb 22, 2019, at 09:31, Thomas Funck <thomas.funck at mail.mcgill.ca<mailto:thomas.funck at mail.mcgill.ca>> wrote:
>
> Hi,
>
>
> Does anyone have experience transforming the output of a NL transformation (ie. deformation volume + affine) from ANTs into a minc friendly format? Is there an easy way to do this?
>
>
> Best,
>
>
> Thomas
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca<mailto:MINC-users at bic.mni.mcgill.ca>
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users

Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info<http://ilmarin.info>

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