From thomas.funck at mail.mcgill.ca Fri Feb 22 09:31:35 2019 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Fri, 22 Feb 2019 14:31:35 +0000 Subject: [MINC-users] Converting ANTs transform to MINC Message-ID: 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 From vladimir.fonov at gmail.com Fri Feb 22 09:37:04 2019 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 22 Feb 2019 09:37:04 -0500 Subject: [MINC-users] Converting ANTs transform to MINC In-Reply-To: References: Message-ID: just run antsRegistration with ?minc option > On Feb 22, 2019, at 09:31, Thomas Funck 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 > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info From thomas.funck at mail.mcgill.ca Sat Feb 23 14:12:25 2019 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Sat, 23 Feb 2019 19:12:25 +0000 Subject: [MINC-users] Converting ANTs transform to MINC In-Reply-To: References: Message-ID: 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. ________________________________ From: minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca Sent: Friday, February 22, 2019 12:00 PM To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 156, Issue 1 Send MINC-users mailing list submissions to minc-users at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-users-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." 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 To: "minc-users at bic.mni.mcgill.ca" Subject: [MINC-users] Converting ANTs transform to MINC Message-ID: 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" To: MINC list Subject: Re: [MINC-users] Converting ANTs transform to MINC Message-ID: Content-Type: text/plain; charset=utf-8 just run antsRegistration with ?minc option > On Feb 22, 2019, at 09:31, Thomas Funck 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 > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info ------------------------------ _______________________________________________ MINC-users mailing list MINC-users at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest, Vol 156, Issue 1 ****************************************** From gabriel.devenyi at mcgill.ca Mon Feb 25 12:24:54 2019 From: gabriel.devenyi at mcgill.ca (Gabriel Allan Devenyi, Dr) Date: Mon, 25 Feb 2019 17:24:54 +0000 Subject: [MINC-users] Converting ANTs transform to MINC In-Reply-To: <4b775e43c3114afe8d3e5f8ba8ac69c2@YTBPR01MB3070.CANPRD01.PROD.OUTLOOK.COM> References: <4b775e43c3114afe8d3e5f8ba8ac69c2@YTBPR01MB3070.CANPRD01.PROD.OUTLOOK.COM> Message-ID: 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 On Sat, 23 Feb 2019 at 14:12, Thomas Funck > 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. ________________________________ From: minc-users-bounces at bic.mni.mcgill.ca

> on behalf of minc-users-request at bic.mni.mcgill.ca

> Sent: Friday, February 22, 2019 12:00 PM To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 156, Issue 1 Send MINC-users mailing list submissions to minc-users at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-users-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." 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 > To: "minc-users at bic.mni.mcgill.ca" > Subject: [MINC-users] Converting ANTs transform to MINC Message-ID: > 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" > To: MINC list > Subject: Re: [MINC-users] Converting ANTs transform to MINC Message-ID: > Content-Type: text/plain; charset=utf-8 just run antsRegistration with ?minc option > On Feb 22, 2019, at 09:31, Thomas Funck > 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 > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info ------------------------------ _______________________________________________ MINC-users mailing list MINC-users at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest, Vol 156, Issue 1 ****************************************** _______________________________________________ MINC-users at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users From pvcorrection at yahoo.com Mon Feb 25 15:57:14 2019 From: pvcorrection at yahoo.com (Olivier Rousset) Date: Mon, 25 Feb 2019 20:57:14 +0000 (UTC) Subject: [MINC-users] dcm2mnc of dynamic PET files References: <735144119.5400502.1551128234469.ref@mail.yahoo.com> Message-ID: <735144119.5400502.1551128234469@mail.yahoo.com> Dear fellow MINC users, I am having some issues with dcm2mnc on dynamic PET data (1155 DICOM files = 35 slices x 33 time-points): ?mincinfo 041_003_20131122_080151_0_pet.mnc? file: 041_003_20131122_080151_0_pet.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace ? ? dimension name ? ? ? ? length ? ? ? ? step? ? ? ? start ? ? -------------- ? ? ? ? ------ ? ? ? ? ----? ? ? ? ----- ? ? zspace ? ? ? ? ? ? ? ? ? 1155 ? ? ? ? 4.25? ? ? ? ? ? 0 ? ? yspace? ? ? ? ? ? ? ? ? ? 128 ? ? ? ? ? -2? ? ? ? ? 128 ? ? xspace? ? ? ? ? ? ? ? ? ? 128 ? ? ? ? ? -2? ? ? ? ? 128 So it looks like the program mixes up time-frames for slices, for lack of better words.I have tried all options with dcm2mnc to no avail. ?I am using the latest version of MINC tools for Mac OS High-Sierra dcm2mnc -version program: 2.3.01 built Aug 28 2018 22:43:28 libminc: 2.4.03 netcdf : 4.5.0 of Aug 28 2018 22:34:44 $ HDF5 ? : 1.8.20 Thank you for your insight and best wishes, - Olivier Olivier G. Rousset, Ph.D. Johns Hopkins Medical Institutions Radiology Department JHOC 3243 601 N. Caroline Str. Baltimore, MD 21287 U.S.A. tel. +1-410-955-2900 fax +1-410-955-0696 e-mail: pvcorrection at yahoo.com From bert at phalarope.com Tue Feb 26 13:28:23 2019 From: bert at phalarope.com (Robert D. Vincent) Date: Tue, 26 Feb 2019 13:28:23 -0500 Subject: [MINC-users] dcm2mnc of dynamic PET files In-Reply-To: <735144119.5400502.1551128234469@mail.yahoo.com> References: <735144119.5400502.1551128234469.ref@mail.yahoo.com> <735144119.5400502.1551128234469@mail.yahoo.com> Message-ID: Hi Olivier, It's common for the DICOM to contain useless, hidden, or missing information for the time dimension, and dcm2mnc won't fix all such issues. If you can share the sequence, or at least some data from it, I might be able to make a diagnosis. -bert On Mon, Feb 25, 2019 at 3:58 PM Olivier Rousset wrote: > Dear fellow MINC users, > I am having some issues with dcm2mnc on dynamic PET data (1155 DICOM files > = 35 slices x 33 time-points): > > mincinfo 041_003_20131122_080151_0_pet.mnc > > file: 041_003_20131122_080151_0_pet.mnc > > image: signed__ short -32768 to 32767 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 1155 4.25 0 > > yspace 128 -2 128 > > xspace 128 -2 128 > > So it looks like the program mixes up time-frames for slices, for lack of > better words.I have tried all options with dcm2mnc to no avail. > I am using the latest version of MINC tools for Mac OS High-Sierra > > dcm2mnc -version > > program: 2.3.01 built Aug 28 2018 22:43:28 > > libminc: 2.4.03 > > netcdf : 4.5.0 of Aug 28 2018 22:34:44 $ > > HDF5 : 1.8.20 > > Thank you for your insight and best wishes, > - Olivier > Olivier G. Rousset, Ph.D. Johns Hopkins Medical Institutions Radiology > Department JHOC 3243 601 N. Caroline Str. Baltimore, MD 21287 U.S.A. tel. > +1-410-955-2900 fax +1-410-955-0696 e-mail: pvcorrection at yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From pvcorrection at yahoo.com Wed Feb 27 09:01:22 2019 From: pvcorrection at yahoo.com (Olivier Rousset) Date: Wed, 27 Feb 2019 14:01:22 +0000 (UTC) Subject: [MINC-users] dcm2mnc of dynamic PET files In-Reply-To: References: <735144119.5400502.1551128234469.ref@mail.yahoo.com> <735144119.5400502.1551128234469@mail.yahoo.com> Message-ID: <250697024.6377098.1551276082825@mail.yahoo.com> Dear Bert, Thanks for the mail; I am attaching some sample data from that study, hoping you can figure out what is going on with the DICOM files.Thanks a lot and talk later, - Olivier Olivier G. Rousset, Ph.D. Johns Hopkins Medical Institutions Radiology Department JHOC 3243 601 N. Caroline Str. Baltimore, MD 21287 U.S.A. tel. +1-410-955-2900 fax +1-410-955-0696 e-mail: pvcorrection at yahoo.com On Tuesday, February 26, 2019, 1:29:37 PM EST, Robert D. Vincent wrote: Hi Olivier, It's common for the DICOM to contain useless, hidden, or missing information for the time dimension, and dcm2mnc won't fix all such issues. If you can share the sequence, or at least some data from it, I might be able to make a diagnosis. ? ? -bert On Mon, Feb 25, 2019 at 3:58 PM Olivier Rousset wrote: > Dear fellow MINC users, > I am having some issues with dcm2mnc on dynamic PET data (1155 DICOM files > = 35 slices x 33 time-points): > >? mincinfo 041_003_20131122_080151_0_pet.mnc > > file: 041_003_20131122_080151_0_pet.mnc > > image: signed__ short -32768 to 32767 > > image dimensions: zspace yspace xspace > >? ? dimension name? ? ? ? length? ? ? ? step? ? ? ? start > >? ? --------------? ? ? ? ------? ? ? ? ----? ? ? ? ----- > >? ? zspace? ? ? ? ? ? ? ? ? 1155? ? ? ? 4.25? ? ? ? ? ? 0 > >? ? yspace? ? ? ? ? ? ? ? ? ? 128? ? ? ? ? -2? ? ? ? ? 128 > >? ? xspace? ? ? ? ? ? ? ? ? ? 128? ? ? ? ? -2? ? ? ? ? 128 > > So it looks like the program mixes up time-frames for slices, for lack of > better words.I have tried all options with dcm2mnc to no avail. >? I am using the latest version of MINC tools for Mac OS High-Sierra > > dcm2mnc -version > > program: 2.3.01 built Aug 28 2018 22:43:28 > > libminc: 2.4.03 > > netcdf : 4.5.0 of Aug 28 2018 22:34:44 $ > > HDF5? : 1.8.20 > > Thank you for your insight and best wishes, > - Olivier > Olivier G. Rousset, Ph.D. Johns Hopkins Medical Institutions Radiology > Department JHOC 3243 601 N. Caroline Str. Baltimore, MD 21287 U.S.A. tel. > +1-410-955-2900 fax +1-410-955-0696 e-mail: pvcorrection at yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users