From Michel.Audette at medizin.uni-leipzig.de Tue Feb 13 09:21:50 2007 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Tue, 13 Feb 2007 15:21:50 +0100 Subject: [MINC-users] VTK, ITK-based support for MINC _and_ tag files In-Reply-To: Message-ID: <160E3DD4FB702C4CB860C65186686E69015F189D@MRZS152229.medizin.uni-leipzig.de> Hi everyone, my institute is adopting a VTK and ITK-based platform for manipulating and visualizing image volumes, OpenMAF, and I was wondering what is available, either in this platform, in IGSTK, or any other based on VTK and ITK, that can support tag files, along with MINC volumes. I would like to use something of that nature, in a manner consistent with David MacDonald's Display program functionality, and build in an interface for more meaningful labels. I know that there are Minc readers and writers in VTK and ITK. Any thoughts? Cheers, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Philipp-Rosenthal-Strasse 55 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From pgravel at bic.mni.mcgill.ca Thu Feb 15 15:30:30 2007 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 15 Feb 2007 15:30:30 -0500 Subject: [MINC-users] Question micreateimage Message-ID: Dear All, Is there a way to use micreateimage (under UNIX), or newimage (emma tools), without supplying a parent MINC file? Thanks in advance! Best Regards, Paul From a.janke at gmail.com Thu Feb 15 18:49:47 2007 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 16 Feb 2007 10:49:47 +1100 Subject: [MINC-users] VTK, ITK-based support for MINC _and_ tag files In-Reply-To: <160E3DD4FB702C4CB860C65186686E69015F189D@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E69015F189D@MRZS152229.medizin.uni-leipzig.de> Message-ID: Hi Michel, I don't know of an OpenMAF interface or project. But it does look interesting. I presume you would build upon one of the existing VTK readers for MINC (of which there are two!). The best contact for the most officially supported one (given that Louis Collins of the BIC's group uses it) was written by Simon Drouin and is now supported by Anka Kochanowska who works for Louis. Perhaps it will be worth sending her an email. a On 2/14/07, Audette, Michel wrote: > > Hi everyone, > > my institute is adopting a VTK and ITK-based platform for manipulating > and visualizing image volumes, OpenMAF, and I was wondering what is > available, either in this platform, in IGSTK, or any other based on VTK > and ITK, that can support tag files, along with MINC volumes. I would > like to use something of that nature, in a manner consistent with David > MacDonald's Display program functionality, and build in an interface for > more meaningful labels. > > I know that there are Minc readers and writers in VTK and ITK. > > Any thoughts? > > Cheers, > > Michel > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Philipp-Rosenthal-Strasse 55 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sean at rogue-research.com Fri Feb 16 11:24:14 2007 From: sean at rogue-research.com (Sean McBride) Date: Fri, 16 Feb 2007 11:24:14 -0500 Subject: [MINC-users] VTK, ITK-based support for MINC _and_ tag files In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69015F189D@MRZS152229.medizin.uni-leipzig.de> Message-ID: <20070216162414.1367426774@smtp1.sympatico.ca> On 2007-02-16 10:49, Andrew Janke said: >I don't know of an OpenMAF interface or project. But it does look >interesting. I presume you would build upon one of the existing VTK >readers for MINC (of which there are two!). There are 2? I know of vtkMINCImageReader, a part of VTK 5: Could you provide a link to the other? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From mishkin at bic.mni.mcgill.ca Tue Feb 20 14:05:09 2007 From: mishkin at bic.mni.mcgill.ca (Mishkin DERAKHSHAN) Date: Tue, 20 Feb 2007 14:05:09 -0500 Subject: [MINC-users] Display Vi property and float datatype In-Reply-To: References: Message-ID: I've been trying to wrap my head around the Display Vl problem for quite some time. I wrote my explanation of how Vx and Vl are calculated in Display versus how they are calculated in volume_io, but it would be great if someone who truly understood what was going on could edit the page. http://wiki.bic.mni.mcgill.ca/index.php/RealVsVoxelValue mishkin On Sat, 27 Jan 2007, Jason Lerch wrote: > Display (and register) load files as byte files. So the only way to > work around this problem is to convert your volume to byte first - > then the values will be consistent across Display and whatever other > program you are using. > > Jason > > On 27-Jan-07, at 9:11 PM, Soren Christensen wrote: > > > Hi, > > I have a MINC file of floats with discrete values 0-2-4-6 etc. > > When viewed in Display the values appear as 0-1.904 - 4.024 - 5.92 > > etc. > > The actual values in the file appear to be ok. as they are 2-4-6 > > when loaded > > into Matlab via EMMA, and also mincmath can identify the values of > > 2 (and > > not 1.904) - so it seems to be related to Display and not the > > actual file > > content. > > Is there a way to change how Display calculates the Vi values? > > It is a problem since I'd like to set a threshold for ROI > > segmentation in > > Display. > > > > Thanks, > > Soren > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jharlap at bic.mni.mcgill.ca Wed Feb 21 15:44:22 2007 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Wed, 21 Feb 2007 15:44:22 -0500 Subject: [MINC-users] Display Vi property and float datatype In-Reply-To: References: Message-ID: <20070221204422.GA4118728@bic.mni.mcgill.ca> Hi Mishkin, I took a quick look and made a few minor edits, but the section that seems most needing editing makes some claims that I cannot find basis for. Where in the code of Display do you find it dividing by 255 to do voxel to value conversion? From what I see, it always (correctly) uses volume_io's convert_voxel_to_value and convert_value_to_voxel. Also, you should take into account that not all mincs are native (from scanner), so your statements about voxel values always being integers is not strictly correct. For an easy example, try: mincmath -double -div -const 2 test.mnc You'll then see voxel values that step by 0.5 rather than 1. Obviously this is a very artificial example, but probability maps stored as MINCs will likely exhibit this behaviour. Out of curiousity, which Alex do you refer to in your page? Cheers, J On Tue, Feb 20, 2007 at 02:05:09PM -0500, Mishkin DERAKHSHAN wrote: > I've been trying to wrap my head around the Display Vl problem for quite > some time. I wrote my explanation of how Vx and Vl are calculated in > Display versus how they are calculated in volume_io, but it would be great > if someone who truly understood what was going on could edit the page. > > http://wiki.bic.mni.mcgill.ca/index.php/RealVsVoxelValue > > mishkin > > On Sat, 27 Jan 2007, Jason Lerch wrote: > > > Display (and register) load files as byte files. So the only way to > > work around this problem is to convert your volume to byte first - > > then the values will be consistent across Display and whatever other > > program you are using. > > > > Jason > > > > On 27-Jan-07, at 9:11 PM, Soren Christensen wrote: > > > > > Hi, > > > I have a MINC file of floats with discrete values 0-2-4-6 etc. > > > When viewed in Display the values appear as 0-1.904 - 4.024 - 5.92 > > > etc. > > > The actual values in the file appear to be ok. as they are 2-4-6 > > > when loaded > > > into Matlab via EMMA, and also mincmath can identify the values of > > > 2 (and > > > not 1.904) - so it seems to be related to Display and not the > > > actual file > > > content. > > > Is there a way to change how Display calculates the Vi values? > > > It is a problem since I'd like to set a threshold for ROI > > > segmentation in > > > Display. > > > > > > Thanks, > > > Soren > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From thomas_mansi at yahoo.fr Wed Feb 21 16:10:57 2007 From: thomas_mansi at yahoo.fr (Thomas Mansi) Date: Wed, 21 Feb 2007 22:10:57 +0100 Subject: [MINC-users] Non-linear registration of two 2D slices Message-ID: <45DCB561.8030704@yahoo.fr> Dear MINC-users, Knowing the efficiency of the minc-tools to co-register two 3D volumes, I was wondering if it was possible to apply minctracc or any other tool to efficiently co-register two 2D slices, non-linearly. Concretely, I am trying to register a 2D Nissl-stained histological section to a 2D high-resolution T1-MRI slice. I tried nlpfit and minctracc (with and without masks) but I didn't get any satisfactory results. Moreover, -mi and -xcorr options gave exactly the same results, which is quite strange, isn't it? Do you know a way to non-linearly register two 2D slices? BicWiki says that there is a -2D-non-lin option that can be given to minctracc. But it seems to have disappeared since my version of the program does not recognise it (0.99.2). Many thanks in advance for your help, Best regards, Thomas Mansi ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From acveilleux at mrs.mni.mcgill.ca Thu Feb 22 00:43:38 2007 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 22 Feb 2007 00:43:38 -0500 Subject: [MINC-users] Display Vi property and float datatype In-Reply-To: <20070221204422.GA4118728@bic.mni.mcgill.ca>; from jharlap@bic.mni.mcgill.ca on Wed, Feb 21, 2007 at 03:44:22PM -0500 References: <20070221204422.GA4118728@bic.mni.mcgill.ca> Message-ID: <20070222004338.B18689@mrs.mni.mcgill.ca> On Wed, Feb 21, 2007 at 03:44:22PM -0500, Jonathan HARLAP wrote: > > You'll then see voxel values that step by 0.5 rather than 1. > Obviously this is a very artificial example, but probability maps > stored as MINCs will likely exhibit this behaviour. > > Out of curiousity, which Alex do you refer to in your page? That would probably be me. The general purpose computer geek and most definately not any other Alex you might be thinking of (who'd probably know better then my half-blind guesses.) Alex From a.janke at gmail.com Tue Feb 27 17:31:15 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 28 Feb 2007 09:31:15 +1100 Subject: [MINC-users] Non-linear registration of two 2D slices In-Reply-To: <45DCB561.8030704@yahoo.fr> References: <45DCB561.8030704@yahoo.fr> Message-ID: Thomas, Have a talk to Mallar Chakravarty in Louis Lab, he is the one in the BIC who has spent vast amounts of time on this. (And has it working very well). In essence you just need to set a bunch of parameters via the C/L. Andrew On 2/22/07, Thomas Mansi wrote: > Dear MINC-users, > > Knowing the efficiency of the minc-tools to co-register two 3D volumes, > I was wondering if it was possible to apply minctracc or any other tool > to efficiently co-register two 2D slices, non-linearly. > > Concretely, I am trying to register a 2D Nissl-stained histological > section to a 2D high-resolution T1-MRI slice. I tried nlpfit and > minctracc (with and without masks) but I didn't get any satisfactory > results. Moreover, -mi and -xcorr options gave exactly the same results, > which is quite strange, isn't it? > > Do you know a way to non-linearly register two 2D slices? BicWiki says > that there is a -2D-non-lin option that can be given to minctracc. But > it seems to have disappeared since my version of the program does not > recognise it (0.99.2). > > Many thanks in advance for your help, > Best regards, > > Thomas Mansi > > > > > > ___________________________________________________________________________ > Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. > http://fr.mail.yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sorench at gmail.com Wed Feb 28 01:16:13 2007 From: sorench at gmail.com (Soren Christensen) Date: Wed, 28 Feb 2007 17:16:13 +1100 Subject: [MINC-users] piping mincmath Message-ID: Hi, Is there away to pipe intermediate results from mincmath calculations? fx: mincmath -add -const 1 tge4.mnc | mincmath -mult -const 3 test.mnc The help page says: -filelist: Specify the name of a file containing input file names (- for stdin). But I have trouble making this work. Thanks Soren From a.janke at gmail.com Wed Feb 28 01:21:30 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 28 Feb 2007 17:21:30 +1100 Subject: [MINC-users] piping mincmath In-Reply-To: References: Message-ID: In sort no. This is due to the way that netCDF has a define and data mode that is not at all amenable to pipes. Now with the change to HDF with minc2.0 in theory it should now be possible but I have not (and likely will not!) have the time to implement it. The -filelist option you speak of is regarding a large number of input files if you were adding them all for example and hit the limit of ncargs. The situation you describe however was the main mitigating factor for me to write minccalc. You can do it as such: minccalc -expression '(A[0] + 1) * 3' tge4.mnc test.mnc (Presuming I can grok what you are trying to do correctly!) a On 2/28/07, Soren Christensen wrote: > Hi, > Is there away to pipe intermediate results from mincmath calculations? > fx: > mincmath -add -const 1 tge4.mnc | mincmath -mult -const 3 test.mnc > > The help page says: > -filelist: Specify the name of a file containing input file > names (- for stdin). > > But I have trouble making this work. > > Thanks > Soren > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sorench at gmail.com Wed Feb 28 01:27:54 2007 From: sorench at gmail.com (Soren Christensen) Date: Wed, 28 Feb 2007 17:27:54 +1100 Subject: [MINC-users] piping mincmath In-Reply-To: References: Message-ID: Thanks Andrew, Wasn't aware of minccalc but will start using that in stead! Cheers Soren On 2/28/07, Andrew Janke wrote: > > In sort no. > > This is due to the way that netCDF has a define and data mode that is > not at all amenable to pipes. Now with the change to HDF with minc2.0 > in theory it should now be possible but I have not (and likely will > not!) have the time to implement it. > > The -filelist option you speak of is regarding a large number of input > files if you were adding them all for example and hit the limit of > ncargs. > > The situation you describe however was the main mitigating factor for > me to write minccalc. You can do it as such: > > minccalc -expression '(A[0] + 1) * 3' tge4.mnc test.mnc > > (Presuming I can grok what you are trying to do correctly!) > > > a > > On 2/28/07, Soren Christensen wrote: > > Hi, > > Is there away to pipe intermediate results from mincmath calculations? > > fx: > > mincmath -add -const 1 tge4.mnc | mincmath -mult -const 3 test.mnc > > > > The help page says: > > -filelist: Specify the name of a file containing input file > > names (- for stdin). > > > > But I have trouble making this work. > > > > Thanks > > Soren > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Wed Feb 28 23:20:45 2007 From: sorench at gmail.com (Soren Christensen) Date: Thu, 1 Mar 2007 15:20:45 +1100 Subject: [MINC-users] permuting dimension Message-ID: Hi, Is there an easy way to permute dimension of a minc file or is it necessary to extract the raw data and re-generate the file. I have a few perfusion dicom data sets where it seems the dicom header is simply wrong - so i get something like this: dimension name length step start -------------- ------ ---- ----- time 40 unknown unknown yspace 12 9.1 -123.327 zspace 128 -1.875 -16.2219 xspace 128 -1.875 -120.938 yspace and zspace are swapped around (z is indeed the lowest res dimention) so basically my question is how do I unswap them in the easiest way? Thanks Soren From a.janke at gmail.com Wed Feb 28 23:24:09 2007 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 1 Mar 2007 15:24:09 +1100 Subject: [MINC-users] permuting dimension In-Reply-To: References: Message-ID: Two methods... 1. (what you suggest, minctoraw and then back in). 2. Evil tricks with mincedit using the editor argument in which you specify the editor as sed or the likes. ie: mincedit foo.mnc "sed -e 's/xspace/yspace/'" Note that I haven't checked the above! And of course you will need to use an intermediate step to swap dimensions. a On 3/1/07, Soren Christensen wrote: > Hi, > Is there an easy way to permute dimension of a minc file or is it necessary > to extract the raw data and re-generate the file. > I have a few perfusion dicom data sets where it seems the dicom header is > simply wrong - so i get something like this: > dimension name length step start > -------------- ------ ---- ----- > time 40 unknown unknown > yspace 12 9.1 -123.327 > zspace 128 -1.875 -16.2219 > xspace 128 -1.875 -120.938 > > yspace and zspace are swapped around (z is indeed the lowest res dimention) > so basically my question is how do I unswap them in the easiest way? > > Thanks > Soren > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883