From minc-users@bic.mni.mcgill.ca Wed Aug 7 07:37:33 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Wed, 7 Aug 2002 16:37:33 +1000 Subject: [MINC-users] Siemens conversion. Message-ID: Morning all. A few of you out there might also have a Siemens Sonata (or any siemens scanner that uses IDEA and MOSAIC as output, as such I'm offering a few perl scripts (and wrappers to dicom_to_minc) available for others. http://www.cmr.uq.edu.au/~rotor/software/progs/siemens_conversion/ There should be 3 files: siemens_dcmdir_rename - pads IMA file numbers with 0's to ensure the shell sorts them correctly siemens_dcmdir2mnc - convert a series of IMA files to minc. this script is capable of separating patient series into separate files. siemens_raw2mnc - An initial stab at converting siemens RHP (Raw Handling Package) .raw files to MINC. use -help for more info. I did mail these out a while back to a few here, but I've made a few changes since then. Let us know if you have any problems. Andrew Janke e-mail: rotor@cmr.uq.edu.au PhD Candidate http://www.cmr.uq.edu.au/~rotor/ Centre for Magnetic Resonance Phone: +61 7 3365 4100 Uni of Qld. (Australia) Home: +61 7 3297 6167 From minc-users@bic.mni.mcgill.ca Wed Aug 7 08:08:15 2002 From: minc-users@bic.mni.mcgill.ca (Jon Harald Kaspersen) Date: Wed, 7 Aug 2002 09:08:15 +0200 Subject: [MINC-users] Siemens conversion. In-Reply-To: Message-ID: <71B62796-A9D4-11D6-8763-00039364CC7A@sintef.no> --Apple-Mail-2-1004772112 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Andrew, this is great ! Do, you by any chance know the output format from GE Advantage Workstation (Adv 3D XR), a multi angle angio (and thereby 3D) ? It is supposed to be some sort of Dicom format, but I have not been able to read it (or understand it). Regards Jon On Wednesday, August 7, 2002, at 08:37 AM, Andrew Janke wrote: > > Morning all. > > A few of you out there might also have a Siemens Sonata (or any > siemens scanner > that uses IDEA and MOSAIC as output, as such I'm offering a few perl > scripts > (and wrappers to dicom_to_minc) available for others. > > http://www.cmr.uq.edu.au/~rotor/software/progs/siemens_conversion/ > > There should be 3 files: > > siemens_dcmdir_rename - pads IMA file numbers with 0's to > ensure the shell sorts them correctly > siemens_dcmdir2mnc - convert a series of IMA files to minc. > this script is capable of separating > patient series into separate files. > > siemens_raw2mnc - An initial stab at converting siemens > RHP (Raw Handling Package) .raw files > to MINC. use -help for more info. > > I did mail these out a while back to a few here, but I've made a few > changes > since then. > > Let us know if you have any problems. > > > > Andrew Janke e-mail: rotor@cmr.uq.edu.au > PhD Candidate http://www.cmr.uq.edu.au/~rotor/ > Centre for Magnetic Resonance Phone: +61 7 3365 4100 > Uni of Qld. (Australia) Home: +61 7 3297 6167 > > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > ======================================================== Jon Harald Kaspersen Tel: +47 73 59 75 89 Ph.D. Mechanical Engineering Mob: +47 93 03 65 90 Senior Scientist Pager +47 96 84 29 94 SINTEF Unimed - Ultralyd Fax: +47 73 59 78 73 N-7465 Trondheim NORWAY e-mail: Jon.H.Kaspersen@unimed.sintef.no WEB: http://www.us.unimed.sintef.no/ ======================================================== --Apple-Mail-2-1004772112 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Andrew, this is great ! Do, you by any chance know the output format from GE Advantage Workstation (Adv 3D XR), a multi angle angio (and thereby 3D) ? It is supposed to be some sort of Dicom format, but I have not been able to read it (or understand it). Regards Jon On Wednesday, August 7, 2002, at 08:37 AM, Andrew Janke wrote: Morning all. A few of you out there might also have a Siemens Sonata (or any siemens scanner that uses IDEA and MOSAIC as output, as such I'm offering a few perl scripts (and wrappers to dicom_to_minc) available for others. http://www.cmr.uq.edu.au/~rotor/software/progs/siemens_conversion/ There should be 3 files: siemens_dcmdir_rename - pads IMA file numbers with 0's to ensure the shell sorts them correctly siemens_dcmdir2mnc - convert a series of IMA files to minc. this script is capable of separating patient series into separate files. siemens_raw2mnc - An initial stab at converting siemens RHP (Raw Handling Package) .raw files to MINC. use -help for more info. I did mail these out a while back to a few here, but I've made a few changes since then. Let us know if you have any problems. Andrew Janke e-mail: rotor@cmr.uq.edu.au PhD Candidate http://www.cmr.uq.edu.au/~rotor/ Centre for Magnetic Resonance Phone: +61 7 3365 4100 Uni of Qld. (Australia) Home: +61 7 3297 6167 _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users ======================================================== Jon Harald Kaspersen Tel: +47 73 59 75 89 Ph.D. Mechanical Engineering Mob: +47 93 03 65 90 Senior Scientist Pager +47 96 84 29 94 SINTEF Unimed - Ultralyd Fax: +47 73 59 78 73 N-7465 Trondheim NORWAY e-mail: Jon.H.Kaspersen@unimed.sintef.no WEB: 1A1A,1A1A,FFFFhttp://www.us.unimed.sintef.no/ ======================================================== --Apple-Mail-2-1004772112-- From minc-users@bic.mni.mcgill.ca Wed Aug 7 23:47:23 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Thu, 8 Aug 2002 08:47:23 +1000 Subject: [MINC-users] Siemens conversion. In-Reply-To: <71B62796-A9D4-11D6-8763-00039364CC7A@sintef.no> Message-ID: On Wed, 7 Aug 2002, Jon Harald Kaspersen wrote: > Do, you by any chance know the output format from GE Advantage > Workstation (Adv 3D XR), a multi angle angio (and thereby 3D) ? > It is supposed to be some sort of Dicom format, but I have not been > able to read it (or understand it). Have you tried: http://www.bic.mni.mcgill.ca/users/neelin/distrib/minc_converters/ge/ Peter Neelin of the mni wrote a number of GE converters a while back. There is a Readme file in that directory that should shed a bit more light. Andrew Janke e-mail: rotor@cmr.uq.edu.au PhD Candidate http://www.cmr.uq.edu.au/~rotor/ Centre for Magnetic Resonance Phone: +61 7 3365 4100 Uni of Qld. (Australia) Home: +61 7 3297 6167 From minc-users@bic.mni.mcgill.ca Wed Aug 14 17:37:34 2002 From: minc-users@bic.mni.mcgill.ca (Kate HANRATTY) Date: Wed, 14 Aug 2002 12:37:34 -0400 Subject: [MINC-users] concatenating and separating T2/PD MR volumes Message-ID: <20020814123734.B984817@shadow.bic.mni.mcgill.ca> [apologies to those who are subscribed to both lists] Hi, I have a series of 8 T2/PD files (in minc format) that I would like to transform in to two .mnc files: one T2 volume and one PD volume. Can someone tell me the recipe? The images were acquired on the Siemens Sonata 1.5 T scanner at the MNI and I used Rick Hoge's script dcm2mnc to generate the minc files. Thanks in advance for any advice you can offer. Kate. -- Kate Hanratty Tel 343-6111 xt 4615 Dep. de psychologie, U. de M. Fax 343-5787 F-484 Pavillon Marie-Victorin katherine.hanratty@umontreal.ca From minc-users@bic.mni.mcgill.ca Tue Aug 20 11:10:05 2002 From: minc-users@bic.mni.mcgill.ca (Anders Rodell) Date: Tue, 20 Aug 2002 12:10:05 +0200 (CEST) Subject: [MINC-users] mystery conversion Message-ID: Hi MINC folks I have received some dynamic and summed minc images scanned on an ecat 953-B pet scanner. The images have an .img extension and 31 slices , and apart from this I dont have additional info about the images. I dont even know the size of the header. Does any of you have a description of this format or even better a converter to MINC. best regards Anders Rodell -- -- Anders Bertil Rodell Aarhus PET Centre, Aarhus University Hospital, Norrebrogade 44, 8000 Aarhus C, phone work: +45 89 49 32 99 phone home: +45 86 99 34 64 email: rodell@pet.auh.dk From minc-users@bic.mni.mcgill.ca Wed Aug 21 04:41:39 2002 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Wed, 21 Aug 2002 13:41:39 +1000 Subject: [MINC-users] mystery conversion In-Reply-To: Message-ID: On Tue, 20 Aug 2002, Anders Rodell wrote: > I have received some dynamic and summed minc images scanned on > an ecat 953-B pet scanner. The images have an .img extension and 31 > slices , and apart from this I dont have additional info about the > images. I dont even know the size of the header. > > Does any of you have a description of this format or even better a > converter to MINC. Have you tried Peter Neelins ECAT to MINC converter? http://www.bic.mni.mcgill.ca/users/neelin/distrib/minc_converters/ecat/ If so, or no luck with it, can you provide a sample? Andrew From Sandra.Bobleter@flinders.edu.au Mon Aug 26 06:30:20 2002 From: Sandra.Bobleter@flinders.edu.au (Sandra Bobleter) Date: Mon, 26 Aug 2002 15:00:20 +0930 Subject: [MINC-users] Remove from mailing list Message-ID: <3D6A4284.32476.1446307B@localhost> ptacl@sigma.sss.flinders.edu.au no longer works here. Please remove them from your mailing list. Sandra Bobleter Computer Support Flinders University From minc-users@bic.mni.mcgill.ca Wed Aug 28 15:09:13 2002 From: minc-users@bic.mni.mcgill.ca (Stephen Smith) Date: Wed, 28 Aug 2002 15:09:13 +0100 (BST) Subject: [MINC-users] minctoraw Message-ID: hello - I've just found a gotcha in "minctoraw -normalise" (which I use to convert to analyze). It seems to me that without the -normalise option you get the "arbitrary" scaling of each slice's intensity, which you clearly don't want in the final raw image - right? So my conversion program has always used the -normalise flag. However I have just discovered that there is still some overall intensity scaling that gets lost this way, because when I compare two MINC files their subtraction makes sense - but when comparing two converted analyze files, they are somehow scaled relative to eachother, so the subtraction is not now sensible.....am I missing something? I have looked for documentation but there is none for minctoraw... Thanks, Steve. Stephen M. Smith Head of Image Analysis, FMRIB Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve From minc-users@bic.mni.mcgill.ca Thu Aug 29 03:08:26 2002 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Wed, 28 Aug 2002 22:08:26 -0400 Subject: [MINC-users] minctoraw In-Reply-To: Message-ID: On Wed, 28 Aug 2002, Stephen Smith wrote: > hello - I've just found a gotcha in "minctoraw -normalise" (which I use to > convert to analyze). It seems to me that without the -normalise option you > get the "arbitrary" scaling of each slice's intensity, which you clearly > don't want in the final raw image - right? So my conversion program has > always used the -normalise flag. However I have just discovered that there > is still some overall intensity scaling that gets lost this way, because > when I compare two MINC files their subtraction makes sense - but when > comparing two converted analyze files, they are somehow scaled relative to > eachother, so the subtraction is not now sensible Yes. I am afraid that I never got around to replacing minctoraw (the original, rather primitive program with the helpful name) with mincextract (the later, more featureful program with a less obvious name). Between being afraid of breaking things and general inertia, I never fixed that problem and so people still end up using the rather limited minctoraw. mincextract has the option -image_range that allows you to specify the normalization of the output data (combined with the valid_range, one can calculate a scale from real values to the dumped voxel values). Note also that mincextract has -normalize turned on by default. You will need to specify the output type, however (probably something like "-short -signed -range 0 4095" for analyze files). If your original data was integer data and that scaling was preserved in the conversion to minc, then you can get the original integer values back with something like mincextract -short -signed -range 0 4095 -image_range 0 4095 file.mnc (completely untested - just working from memory). The important point is that using the same -range and -image_range will give a scaling of 1 and offset of 0 when converting real values back to voxel values. 'Hope this helps. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Thu Aug 29 03:19:52 2002 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Wed, 28 Aug 2002 22:19:52 -0400 Subject: [MINC-users] mystery conversion In-Reply-To: Message-ID: On Wed, 21 Aug 2002, Andrew Janke wrote: > On Tue, 20 Aug 2002, Anders Rodell wrote: > > > I have received some dynamic and summed minc images scanned on > > an ecat 953-B pet scanner. The images have an .img extension and 31 > > slices , and apart from this I dont have additional info about the > > images. I dont even know the size of the header. > > Does any of you have a description of this format or even better a > > converter to MINC. > > Have you tried Peter Neelins ECAT to MINC converter? > http://www.bic.mni.mcgill.ca/users/neelin/distrib/minc_converters/ecat/ My apologies, Anders, for not responding sooner. As Andrew suggests, you might get some help from ecattominc. It has code to support versions of ecat files that predate version 7 (.v) files, but it has had very little testing. Try running dump_ecat_header and see what it produces - it attempts to auto-detect the type of ecat file (in a very primitive way). Let us know whether you have any success with this. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Thu Aug 29 10:26:20 2002 From: minc-users@bic.mni.mcgill.ca (Stephen Smith) Date: Thu, 29 Aug 2002 10:26:20 +0100 (BST) Subject: [MINC-users] minctoraw In-Reply-To: Message-ID: Hi - thanks for the reply, though I couldn't quite follow what the range options are really doing. I have tried that and sadly it gives junk output - most values being set to 32767... The intensity range parts of mincheader are below - does that tell you anything useful about what the options should be to mincextract? Many thanks, Steve. image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ; image-max = 5896592.46886447, 6089528.00976801, 5860417.05494506, 6511574.50549451, 6487457.56288156, 6487457.56288156, 6439223.67765568, 7247141.25518926, 8887093.35286935, 8127409.66056166, 8127409.66056166, 7970649.53357753, 8404754.5006105, 7560661.50915751, 7476252.21001221, 8368579.08669109, 7910357.17704518, 7584778.45177045, 7645070.80830281, 8091234.24664225, 7669187.75091575, 8103292.71794872, 7741538.57875458, 8356520.61538462, 8175643.54578755, 9092087.36507937, 8416812.97191697, 7102439.5995116, 7138615.01343101, 7560661.50915751, 7174790.42735043, 7223024.31257631, 6704510.04639805, 7838006.34920635, 6981854.88644689, 6981854.88644689, 7319492.08302808, 7765655.52136752, 7813889.40659341, 8682099.34065934, 8043000.36141636, 8139468.13186813, 8368579.08669109, 7042147.24297924, 5920709.41147741, 5691598.45665446, 3641658.33455433, 3581365.97802198, 3436664.32234432, 3931061.64590965 ; On Wed, 28 Aug 2002, Peter NEELIN wrote: > On Wed, 28 Aug 2002, Stephen Smith wrote: > > > hello - I've just found a gotcha in "minctoraw -normalise" (which I use to > > convert to analyze). It seems to me that without the -normalise option you > > get the "arbitrary" scaling of each slice's intensity, which you clearly > > don't want in the final raw image - right? So my conversion program has > > always used the -normalise flag. However I have just discovered that there > > is still some overall intensity scaling that gets lost this way, because > > when I compare two MINC files their subtraction makes sense - but when > > comparing two converted analyze files, they are somehow scaled relative to > > eachother, so the subtraction is not now sensible > > Yes. I am afraid that I never got around to replacing minctoraw (the > original, rather primitive program with the helpful name) with mincextract > (the later, more featureful program with a less obvious name). Between > being afraid of breaking things and general inertia, I never fixed > that problem and so people still end up using the rather limited > minctoraw. > > mincextract has the option -image_range that allows you to specify the > normalization of the output data (combined with the valid_range, one can > calculate a scale from real values to the dumped voxel values). Note also > that mincextract has -normalize turned on by default. You will need to > specify the output type, however (probably something like > "-short -signed -range 0 4095" for analyze files). If your original data > was integer data and that scaling was preserved in the conversion to minc, > then you can get the original integer values back with something like > > mincextract -short -signed -range 0 4095 -image_range 0 4095 file.mnc > > (completely untested - just working from memory). The important point is > that using the same -range and -image_range will give a scaling of 1 and > offset of 0 when converting real values back to voxel values. > > 'Hope this helps. > > Peter > ---- > Peter Neelin (neelin@bic.mni.mcgill.ca) > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > Stephen M. Smith Head of Image Analysis, FMRIB Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve From minc-users@bic.mni.mcgill.ca Thu Aug 29 10:41:08 2002 From: minc-users@bic.mni.mcgill.ca (Stephen Smith) Date: Thu, 29 Aug 2002 10:41:08 +0100 (BST) Subject: [MINC-users] minctoraw In-Reply-To: Message-ID: sorry - forgot to add that the MINC images are being created by gyrotominc - I guess it is possible that gyrotominc is doing something nasty to the global intensity scaling? Thanks. On Wed, 28 Aug 2002, Peter NEELIN wrote: > On Wed, 28 Aug 2002, Stephen Smith wrote: > > > hello - I've just found a gotcha in "minctoraw -normalise" (which I use to > > convert to analyze). It seems to me that without the -normalise option you > > get the "arbitrary" scaling of each slice's intensity, which you clearly > > don't want in the final raw image - right? So my conversion program has > > always used the -normalise flag. However I have just discovered that there > > is still some overall intensity scaling that gets lost this way, because > > when I compare two MINC files their subtraction makes sense - but when > > comparing two converted analyze files, they are somehow scaled relative to > > eachother, so the subtraction is not now sensible > > Yes. I am afraid that I never got around to replacing minctoraw (the > original, rather primitive program with the helpful name) with mincextract > (the later, more featureful program with a less obvious name). Between > being afraid of breaking things and general inertia, I never fixed > that problem and so people still end up using the rather limited > minctoraw. > > mincextract has the option -image_range that allows you to specify the > normalization of the output data (combined with the valid_range, one can > calculate a scale from real values to the dumped voxel values). Note also > that mincextract has -normalize turned on by default. You will need to > specify the output type, however (probably something like > "-short -signed -range 0 4095" for analyze files). If your original data > was integer data and that scaling was preserved in the conversion to minc, > then you can get the original integer values back with something like > > mincextract -short -signed -range 0 4095 -image_range 0 4095 file.mnc > > (completely untested - just working from memory). The important point is > that using the same -range and -image_range will give a scaling of 1 and > offset of 0 when converting real values back to voxel values. > > 'Hope this helps. > > Peter > ---- > Peter Neelin (neelin@bic.mni.mcgill.ca) > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > Stephen M. Smith Head of Image Analysis, FMRIB Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve From minc-users@bic.mni.mcgill.ca Fri Aug 30 01:55:01 2002 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Thu, 29 Aug 2002 20:55:01 -0400 Subject: [MINC-users] minctoraw In-Reply-To: Message-ID: On Thu, 29 Aug 2002, Stephen Smith wrote: > sorry - forgot to add that the MINC images are being created by gyrotominc > - I guess it is possible that gyrotominc is doing something nasty to the > global intensity scaling? Nothing nasty - it does what it is meant to do, pass on the scaling information provided by the scanner. Granted, few people actually care in the case of MRI, but some do (or have in the past). Why the Philips likes huge numbers I do not know, but that is what it does. To normalize two of these files, you can find the min and max of the two files' image_minimum and image_maximum variables and use those as argument to -image_range. Alternatively, you could pass on the scaling to the analyze file since it does support scaling. Of course, there is no guarantee that the application using the files will read and use the appropriate values from the header. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca)