From minc-development@bic.mni.mcgill.ca Mon Feb 7 23:18:02 2005 From: minc-development@bic.mni.mcgill.ca (Joongnam Yang) Date: Mon, 07 Feb 2005 18:18:02 -0500 Subject: [MINC-development] rawtominc to convert a functional *.img file Message-ID: Hi, I used rawtominc to convert a functional *.img into *.mnc format, but when I checked the *.mnc file, the fourth "time" dimension had information missing. as shown below. How can I do it with rawtominc to fix it? (I've tried with "time_frames" and "frame_widths" options, but it keeps giving me error message. I don't know how to use the options.) FYI, I have 240 frames, each frame collected during 2.5 seconds. I would appreciate any comment. Nam. image: unsigned byte 0 to 255 image dimensions: time zspace yspace xspace dimension name length step start -------------- ------ ---- ----- time 240 unknown unknown zspace 23 5 -57.5 yspace 64 3.8 -121.6 xspace 64 3.75 -150 [ From minc-development@bic.mni.mcgill.ca Tue Feb 8 21:03:44 2005 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Wed, 9 Feb 2005 07:03:44 +1000 (EST) Subject: [MINC-development] rawtominc to convert a functional *.img file In-Reply-To: References: Message-ID: On Mon, 7 Feb 2005, Joongnam Yang wrote: > I used rawtominc to convert a functional *.img into *.mnc format, but when I > checked the *.mnc file, the fourth "time" dimension had information > missing. > as shown below. > How can I do it with rawtominc to fix it? > (I've tried with "time_frames" and "frame_widths" options, but it keeps > giving me error message. I don't know how to use the options.) > FYI, I have 240 frames, each frame collected during 2.5 seconds. -frame_widths and -frame_times are only used to specify time slices that vary in width and starting point. If you really wish to add the start and step information for the time dimension use minc_modify_header after the conversion is done. minc_modify_header -dinsert time:start 0 foo.mnc minc_modify_header -dinsert time:step 1 foo.mnc For an acquisition with a step of 1 second each. -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From nikelski@bic.mni.mcgill.ca Tue Feb 8 22:36:54 2005 From: nikelski@bic.mni.mcgill.ca (EJ Nikelski) Date: Tue, 08 Feb 2005 17:36:54 -0500 Subject: [MINC-development] DICOM to minc build errors In-Reply-To: References: Message-ID: <42093F06.2010409@bic.mni.mcgill.ca> Hi, I initially sent this message to minc-users (perhaps the wrong mailing list?) and received no response. I really need a response to this ... since, transitioning to a minc volume format requires a reliable conversion program and community support. I'm trying to get an imaging center to start using minc, but I need to demonstrate that they won't be left high and dry. Any advice on the below problem would be appreciated. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am trying to help some people set up a processing pipeline to convert their DICOM files (from a GE 3T magnet) to minc. A build of Peter Neelin's DICOM_to_Minc package fails, as it is looking for "Make_machine_specific" and "Make_configuration" in the minc build directory ... and these elements do not exist in minc-1.3. Am I trying to build an old (deprecated) tool? What is currently my best bet for converting DICOM to Minc? I have tried the PERL implementation of dicom3_to_minc, but it's a bit slow. Ideas? I am building on Linux (Debian). BTW, I have noticed that netcdf-3.6 is out. The build process seems to be a bit more robust and up-to-date than under 3.5. Initial build on Debian was magic. If nobody knows of any incompatibility problems with minc-1.3, I shall build it on Mac OS X as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, Jim From minc-development@bic.mni.mcgill.ca Thu Feb 10 00:49:31 2005 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Thu, 10 Feb 2005 10:49:31 +1000 Subject: [MINC-development] DICOM to minc build errors In-Reply-To: <42093F06.2010409@bic.mni.mcgill.ca> References: <42093F06.2010409@bic.mni.mcgill.ca> Message-ID: On Tue, 8 Feb 2005, EJ Nikelski wrote: > I initially sent this message to minc-users (perhaps the wrong > mailing list?) and received no response. I really need a response to > this ... since, transitioning to a minc volume format requires a > reliable conversion program and community support. I'm trying to get an > imaging center to start using minc, but I need to demonstrate that they > won't be left high and dry. Any advice on the below problem would be > appreciated. > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am trying to help some people set up a processing pipeline to > convert their DICOM files (from a GE 3T magnet) to minc. A build of > Peter Neelin's DICOM_to_Minc package fails, as it is looking for > "Make_machine_specific" and "Make_configuration" in the minc build > directory ... and these elements do not exist in minc-1.3. Am I trying > to build an old (deprecated) tool? What is currently my best bet for > converting DICOM to Minc? I have tried the PERL implementation of > dicom3_to_minc, but it's a bit slow. Ideas? I am building on Linux (Debian). > > BTW, I have noticed that netcdf-3.6 is out. The build process seems > to be a bit more robust and up-to-date than under 3.5. Initial build on > Debian was magic. If nobody knows of any incompatibility problems with > minc-1.3, I shall build it on Mac OS X as well. > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I missed your message Jim, dicom3_to_minc is the most supported DICOM conversion tool that i know of at the moment. Bert Vincent is working on ressurecting Peter Neelins older version The Make_configuration type files it is looking for during the build used to be part of the minc build process. My approach at the moment is to use dicom3_to_minc untill Bert is finished his new version. -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3390 6332 || M: +61 4 2138 8581