From minc-users@bic.mni.mcgill.ca Tue Oct 1 19:38:32 2002 From: minc-users@bic.mni.mcgill.ca (Morgan Hough) Date: Tue, 1 Oct 2002 11:38:32 -0700 (PDT) Subject: [MINC-users] NETCDF_PREFIX question Message-ID: I am making a fink package (Mac OS X package management system) of MINC and ./configure is not seeing that netcdf is installed. This might be a Mac OS X problem or maybe a fink problem (I am doing this on Mac OS X 10.2 as well) but if you had netcdf.h installed somewhere non-standard how would you tell ./configure? Do you set it as a envvar or do you pass it to configure as an option? Thanks in advance. Take care. -Morgan From minc-users@bic.mni.mcgill.ca Wed Oct 2 03:26:38 2002 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Tue, 1 Oct 2002 22:26:38 -0400 Subject: [MINC-users] NETCDF_PREFIX question In-Reply-To: Message-ID: On Tue, 1 Oct 2002, Morgan Hough wrote: > I am making a fink package (Mac OS X package management system) of MINC > and ./configure is not seeing that netcdf is installed. This might be a > Mac OS X problem or maybe a fink problem (I am doing this on Mac OS X 10.2 > as well) but if you had netcdf.h installed somewhere non-standard how > would you tell ./configure? Do you set it as a envvar or do you pass it to > configure as an option? Thanks in advance. Set the environment variable NETCDF_PREFIX (see the README). The configure script only looks in .. and /usr/local. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Thu Oct 24 03:32:45 2002 From: minc-users@bic.mni.mcgill.ca (Julie Pelletier) Date: Wed, 23 Oct 2002 19:32:45 -0700 Subject: [MINC-users] dicom to minc Message-ID: <000801c27b05$a32d40a0$102bc918@julie> This is a multi-part message in MIME format. --Boundary_(ID_btgVmqHPfAU1xsGXcpiOmw) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT I have Ct-Scan and MRI images in Dicom format and I want to transform them in MINC. How can I do it? Julie Pelletier PhD Students Brain Imaging Center pelletj@bic.mni.mcgill.ca --Boundary_(ID_btgVmqHPfAU1xsGXcpiOmw) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT

I have Ct-Scan and MRI images in Dicom format and I want to transform them in MINC. How can I do it?

Julie Pelletier

PhD Students

Brain Imaging Center

pelletj@bic.mni.mcgill.ca

--Boundary_(ID_btgVmqHPfAU1xsGXcpiOmw)-- From minc-users@bic.mni.mcgill.ca Thu Oct 24 00:49:49 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Thu, 24 Oct 2002 09:49:49 +1000 Subject: [MINC-users] dicom to minc In-Reply-To: <000801c27b05$a32d40a0$102bc918@julie> Message-ID: On Wed, 23 Oct 2002, Julie Pelletier wrote: > I have Ct-Scan and MRI images in Dicom format and I want to transform them in > MINC. How can I do it? dicom_to_minc is what you are after. assuming your images are in a folder called "dicom_images" and you want to put the mnc images in "minc_images", something akin to this should work. $ dicom_to_minc minc_images dicom_images/*.DCM -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance Work: +61 7 3365 4100 || Home: +61 7 3800 4042 From minc-users@bic.mni.mcgill.ca Thu Oct 24 01:06:04 2002 From: minc-users@bic.mni.mcgill.ca (Jon Erick Ween) Date: Wed, 23 Oct 2002 17:06:04 -0700 Subject: [MINC-users] dicom to minc Message-ID: <7755A88025C.AAA408E@som.llu.edu> Make sure your DICOM implementation does not insert illegal headers, or dicom-to-minc and other converters might choke. AGFA/PACS likes to insert (0003,0300) subject header lines which are non-standard. The best is to get files off the scanner itself, but most radiology departments don't like this. Jon Julie Pelletier wrote: >I have Ct-Scan and MRI images in Dicom format and I want to transform them in MINC. How can I do it? > >Julie Pelletier >PhD Students >Brain Imaging Center >pelletj@bic.mni.mcgill.ca > From minc-users@bic.mni.mcgill.ca Thu Oct 31 06:46:51 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Thu, 31 Oct 2002 16:46:51 +1000 Subject: [MINC-users] Siemens DICOM MOSAIC converter. Message-ID: (predominately for the fMRI types amongst us). A few of you out there may be interested in an initial stab at a dicom mosaic converter that I've been working on in the last few weeks. I can't as of yet guarantee it'll extract the correct world co-ordinate start position, (but direction cosines, steps and lengths should be correct) Get it from here: http://www.cmr.uq.edu.au/~rotor/software/progs/siemens_conversion/siemens_mosaic2mnc $ siemens_mosaic2mnc -help for more info Let us know if it works for you! :) It was written from data from a Siemens Sonata scanner so your mileage may well vary for other scanners/platforms as it relies pretty heavily upon the ### ASCCONV ### section that IDEA currently outputs with all DICOM files. -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance Work: +61 7 3365 4100 || Home: +61 7 3800 4042 From minc-users@bic.mni.mcgill.ca Thu Oct 31 10:56:50 2002 From: minc-users@bic.mni.mcgill.ca (Mauricio Anes) Date: Thu, 31 Oct 2002 08:56:50 -0200 Subject: [MINC-users] Siemens DICOM MOSAIC converter. References: Message-ID: <000b01c280cc$3768e460$d03384c8@PUCRS.BR> Andrew, Do you believe this could work with a Siemens Vision Mosaic? Mauricio ----- Original Message ----- From: Andrew Janke To: The MINC mailing list Sent: Thursday, October 31, 2002 4:46 AM Subject: [MINC-users] Siemens DICOM MOSAIC converter. > > (predominately for the fMRI types amongst us). > > A few of you out there may be interested in an initial stab at a dicom mosaic > converter that I've been working on in the last few weeks. > > I can't as of yet guarantee it'll extract the correct world co-ordinate > start position, (but direction cosines, steps and lengths should be correct) > > Get it from here: > http://www.cmr.uq.edu.au/~rotor/software/progs/siemens_conversion/siemens_mo saic2mnc > > $ siemens_mosaic2mnc -help for more info > > Let us know if it works for you! :) It was written from data from a Siemens > Sonata scanner so your mileage may well vary for other scanners/platforms as it > relies pretty heavily upon the ### ASCCONV ### section that IDEA currently > outputs with all DICOM files. > > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > Work: +61 7 3365 4100 || Home: +61 7 3800 4042 > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Thu Oct 31 23:03:29 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 1 Nov 2002 09:03:29 +1000 Subject: [MINC-users] Siemens DICOM MOSAIC converter. In-Reply-To: <000b01c280cc$3768e460$d03384c8@PUCRS.BR> Message-ID: On Thu, 31 Oct 2002, Mauricio Anes wrote: > Do you believe this could work with a Siemens Vision Mosaic? Can't say really, however if: $ strings BIG_MOSAIC_FILE.IMA | grep ASCCONV returns something like this: ### ASCCONV BEGIN ### ### ASCCONV END ### Chances are it might. If not, I doubt it. Either way let us know how you get on. -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance Work: +61 7 3365 4100 || Home: +61 7 3800 4042