From mark at invivonmr.uu.nl Mon Jan 8 08:56:49 2007 From: mark at invivonmr.uu.nl (mark@invivonmr.uu.nl) Date: Mon, 8 Jan 2007 14:56:49 +0100 (CET) Subject: [MINC-users] [Insight-users]Trouble making MINC2.0.11 Message-ID: <63462.131.211.146.8.1168264609.squirrel@www.invivonmr.uu.nl> Hello, I'm currently trying to install MINC2.0.11 on my PC equipped with solaris 2.9, but during the compilation of the sources I get an error message on linking the ecattominc files. I have installed the NetCDF 3.6.1 package and the configure runs properly. The message is as follows: /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -o ecattominc conversion/ecattominc/ecattominc.o conversion/ecattominc/insertblood.o conversion/ecattominc/ecat_file.o conversion/ecattominc/machine_indep.o libvolume_io2.la libminc2.la -lnetcdf -lm gcc -g -O2 -o ecattominc conversion/ecattominc/ecattominc.o conversion/ecattominc/insertblood.o conversion/ecattominc/ecat_file.o conversion/ecattominc/machine_indep.o ./.libs/libvolume_io2.a ./.libs/libminc2.a -lnetcdf -lm Undefined first referenced symbol in file ntohl conversion/ecattominc/machine_indep.o ntohs conversion/ecattominc/machine_indep.o ld: fatal: Symbol referencing errors. No output written to ecattominc Does anybody know what I'm doing wrong? Thnx a lot! Mark From mark at invivonmr.uu.nl Mon Jan 8 09:04:41 2007 From: mark at invivonmr.uu.nl (Mark Bouts) Date: Mon, 08 Jan 2007 15:04:41 +0100 Subject: [MINC-users] [Insight-users]Trouble making MINC2.0.11 In-Reply-To: <63462.131.211.146.8.1168264609.squirrel@www.invivonmr.uu.nl> References: <63462.131.211.146.8.1168264609.squirrel@www.invivonmr.uu.nl> Message-ID: <45A24F79.2020000@invivonmr.uu.nl> Sorry it should be solaris 9.2 of course Mark mark at invivonmr.uu.nl wrote: > Hello, > > I'm currently trying to install MINC2.0.11 on my PC equipped with solaris > 2.9, but during the compilation of the sources I get an error message on > linking the ecattominc files. I have installed the NetCDF 3.6.1 package > and the configure runs properly. > > The message is as follows: > > /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -o ecattominc > conversion/ecattominc/ecattominc.o conversion/ecattominc/insertblood.o > conversion/ecattominc/ecat_file.o conversion/ecattominc/machine_indep.o > libvolume_io2.la libminc2.la -lnetcdf -lm > gcc -g -O2 -o ecattominc conversion/ecattominc/ecattominc.o > conversion/ecattominc/insertblood.o conversion/ecattominc/ecat_file.o > conversion/ecattominc/machine_indep.o ./.libs/libvolume_io2.a > ./.libs/libminc2.a -lnetcdf -lm > Undefined first referenced > symbol in file > ntohl conversion/ecattominc/machine_indep.o > ntohs conversion/ecattominc/machine_indep.o > ld: fatal: Symbol referencing errors. No output written to ecattominc > > Does anybody know what I'm doing wrong? > > Thnx a lot! > > Mark > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From Paul.Rasser at newcastle.edu.au Tue Jan 9 00:20:32 2007 From: Paul.Rasser at newcastle.edu.au (Paul Rasser) Date: Tue, 09 Jan 2007 16:20:32 +1100 Subject: [MINC-users] spm2xfm Message-ID: <45A3C2480200001F00002F88@WINDOMPRD00.newcastle.edu.au> I've been trying to use spm2xfm on OS X and I'm getting: Can't exec "mat1dump": No such file or directory is mat1dump available? Also, could someone please tell me what version(s) of spm, spm2xfm will be compatible with? Thanks, Paul Rasser From lasse at hst.aau.dk Tue Jan 9 03:07:01 2007 From: lasse at hst.aau.dk (=?ISO-8859-1?Q?Lasse_Riis_=D8stergaard?=) Date: Tue, 09 Jan 2007 09:07:01 +0100 Subject: [MINC-users] [Insight-users]Trouble making MINC2.0.11 In-Reply-To: <45A24F79.2020000@invivonmr.uu.nl> References: <63462.131.211.146.8.1168264609.squirrel@www.invivonmr.uu.nl> <45A24F79.2020000@invivonmr.uu.nl> Message-ID: <45A34D25.8050401@hst.aau.dk> You have to add -lsocket to the list of libraries names when linking. Lasse Mark Bouts wrote: > Sorry it should be solaris 9.2 of course > > Mark > > mark at invivonmr.uu.nl wrote: > >> Hello, >> >> I'm currently trying to install MINC2.0.11 on my PC equipped with solaris >> 2.9, but during the compilation of the sources I get an error message on >> linking the ecattominc files. I have installed the NetCDF 3.6.1 package >> and the configure runs properly. >> >> The message is as follows: >> >> /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -o ecattominc >> conversion/ecattominc/ecattominc.o conversion/ecattominc/insertblood.o >> conversion/ecattominc/ecat_file.o conversion/ecattominc/machine_indep.o >> libvolume_io2.la libminc2.la -lnetcdf -lm >> gcc -g -O2 -o ecattominc conversion/ecattominc/ecattominc.o >> conversion/ecattominc/insertblood.o conversion/ecattominc/ecat_file.o >> conversion/ecattominc/machine_indep.o ./.libs/libvolume_io2.a >> ./.libs/libminc2.a -lnetcdf -lm >> Undefined first referenced >> symbol in file >> ntohl conversion/ecattominc/machine_indep.o >> ntohs conversion/ecattominc/machine_indep.o >> ld: fatal: Symbol referencing errors. No output written to ecattominc >> >> Does anybody know what I'm doing wrong? >> >> Thnx a lot! >> >> Mark >> >> _______________________________________________ >> 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 a.janke at gmail.com Tue Jan 9 06:34:51 2007 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 9 Jan 2007 21:34:51 +1000 Subject: [MINC-users] spm2xfm In-Reply-To: <45A3C2480200001F00002F88@WINDOMPRD00.newcastle.edu.au> References: <45A3C2480200001F00002F88@WINDOMPRD00.newcastle.edu.au> Message-ID: Hi Paul, spm2xfm was an old perl hack that I wrote long ago somewhere just after the Pre-Cambrian era. As such I would guess it would really only work for SPM up untill about SPM99. mat1dump can be found here: http://a.janke.googlepages.com/ If you are using a later version of SPM you may be better of to just use nii2mnc. a On 1/9/07, Paul Rasser wrote: > I've been trying to use spm2xfm on OS X and I'm getting: > > Can't exec "mat1dump": No such file or directory > > is mat1dump available? > > Also, could someone please tell me what version(s) of spm, spm2xfm will > be compatible with? > > Thanks, > Paul Rasser > > > > _______________________________________________ > 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 ernestplo at gmail.com Thu Jan 11 09:29:30 2007 From: ernestplo at gmail.com (Ernest Lo) Date: Thu, 11 Jan 2007 09:29:30 -0500 Subject: [MINC-users] Fwd: Minc to Analyze issue In-Reply-To: References: Message-ID: Hello, I have been following this issue and have a few basic questions, which if anyone might have insight on, would be greatly appreciated: 1. It seems that the mnc2nii and nii2mnc are the preferred scripts to convert between minc and analyze formats. Can these scripts use and produce analyze (i.e. *.img and *.hdr) format files in addition to nifti (*.nii) format files? 2. We currently make use of the scripts minc2analyze and analyze2minc to perform conversions, I believe that are part of the minc tools. How would these scripts compare with mnc2nii and nii2mnc? 3. I currently need to align two analyze format images. I first convert them to minc format and then run an algorithm that produces the xfms. Next I convert the xfm files to .mat format. However the .mat transforms do not align the original analyze format images. I'm guessing that this is a result of the missing direction cosine information that pertains to analyze format images. However I would like to know if there is a way to convert from analyze to minc with no changes to alignment. Thanks, Ernest Lo Montreal Neurological Institute Montreal, Canada From ernestplo at gmail.com Thu Jan 11 10:00:27 2007 From: ernestplo at gmail.com (Ernest Lo) Date: Thu, 11 Jan 2007 10:00:27 -0500 Subject: [MINC-users] xfm to mat ?? Message-ID: Hello, Does anyone have experience or knowledge with converting .xfm (for minc) files to .mat (for analyze) files? >From my understanding, the mat files appear to be a simple text file containing a 4x4 matrix. The first three columns represent the rotational, scale and shear elements. The last column represents the translational components. The bottom (fourth) row always consists of 0 0 0 1 and makes the matrix square. Therefore placing the first three rows of this matrix after the header information of an .xfm file should translate this .mat into a .xfm useable for minc images. Does this sound correct? Thank you, Ernest Lo Montreal Neurological Institute Montreal, Canada From pgravel at bic.mni.mcgill.ca Thu Jan 11 13:25:01 2007 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 11 Jan 2007 13:25:01 -0500 Subject: [MINC-users] Modifying Minc Header Message-ID: Dear All, It is probably a basic question, but here it is. How would someone add a variable in the header of a minc file? For example, I am currently running an analysis in PET and I would like to be able to add the parameters used for the analysis, e.g. No. of Basis Functions, Boundaries of iterations, etc., to the header of the resulting *.mnc file. Then I would like to be able to extract these parameters/variables by using either mincheader or something like: mincinfo -attvalue:analysis_params. Is this possible? Thanking you in advance. Best Regards, Paul From jason at bic.mni.mcgill.ca Thu Jan 11 15:14:37 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 11 Jan 2007 15:14:37 -0500 Subject: [MINC-users] Modifying Minc Header In-Reply-To: References: Message-ID: <45A69AAD.9040106@bic.mni.mcgill.ca> Paul GRAVEL wrote: > Dear All, > > It is probably a basic question, but here it is. > > How would someone add a variable in the header of a minc file? For > example, I am currently running an analysis in PET and I would like to be > able to add the parameters used for the analysis, e.g. No. of Basis > Functions, Boundaries of iterations, etc., to the header of the resulting > *.mnc file. Then I would like to be able to extract these > parameters/variables by using either mincheader or something like: > mincinfo -attvalue:analysis_params. Is this possible? > Yup: minc_modify_header -sinsert :globalvar="blah blah" filename.mnc Use -dinsert for double precision numbers rather than strings (which is -sinsert), and of course you might want a different variable than :globalvar. Jason > Thanking you in advance. > > Best Regards, > > Paul > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Fri Jan 12 03:03:41 2007 From: sorench at gmail.com (Soren Christensen) Date: Fri, 12 Jan 2007 19:03:41 +1100 Subject: [MINC-users] xfm to mat ?? In-Reply-To: References: Message-ID: Hi Ernest, I don't think doing this is straigtforward. The XFM that is estimated using the MNI tools refers to the coordinate system in your minc file. (Defined by the direction cosines, the stepsizes and the origo (startpoints) information. When converting to an Analyze 7.5 file you loose the cosines and the startpoints. As such I think you would need to apply another xfm and a translation for your xfm file to work in the Analyze coord system. Is there a reason you cannot apply the transform (transform and resample like target) in MINC and then go back to Analyze? An alternative could be to change the MINC header to reflrect the analyze coord system (voxel based) prior to co-registration to force the xfm to refer to this frame of reference. Soren On 1/12/07, Ernest Lo wrote: > Hello, > > Does anyone have experience or knowledge with converting .xfm (for minc) > files to .mat (for analyze) files? > > >From my understanding, the mat files appear to be a simple text file > containing a 4x4 matrix. The first three > columns represent the rotational, scale and shear elements. The last column > represents the translational > components. The bottom (fourth) row always consists of 0 0 0 1 and makes > the matrix square. Therefore > placing the first three rows of this matrix after the header information of > an .xfm file should translate this > .mat into a .xfm useable for minc images. Does this sound correct? > > Thank you, > > > Ernest Lo > Montreal Neurological Institute > Montreal, Canada > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Fri Jan 12 06:20:30 2007 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 12 Jan 2007 21:20:30 +1000 Subject: [MINC-users] Fwd: Minc to Analyze issue In-Reply-To: References: Message-ID: > 1. It seems that the mnc2nii and nii2mnc are the preferred scripts to > convert between minc and analyze formats. > Can these scripts use and produce analyze (i.e. *.img and *.hdr) format > files in addition to nifti (*.nii) format > files? Yes, use 'mnc2nii -help' to see the various output options. > 2. We currently make use of the scripts minc2analyze and analyze2minc to > perform conversions, I believe that are > part of the minc tools. How would these scripts compare with mnc2nii and > nii2mnc? minc2analyze? If you mean mnc2ana || ana2mnc then they are now old unsupported perl scripts of mine that may produce the same results and may not dependant on where your "analyze" file came from. > 3. I currently need to align two analyze format images. I first convert > them to minc format and then run an algorithm that produces the xfms. Next > I convert the xfm files to .mat format. However the .mat transforms do not > align the original analyze format images. I'm guessing that this is a > result of the missing direction cosine information that pertains to analyze > format images. However I would like to know if there is > a way to convert from analyze to minc with no changes to alignment. It could be the direction cosiones and it might also be that you are using the spm_defaults type approach to handle left-right flips "radio and neuro" orientation. In which case, all bets are off. My suggestion would be that if you really do want to mess with both analyze and minc would be to register and then resample in MINC before converting back. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From ernestplo at gmail.com Fri Jan 12 10:01:09 2007 From: ernestplo at gmail.com (Ernest Lo) Date: Fri, 12 Jan 2007 10:01:09 -0500 Subject: [MINC-users] Fwd: Minc to Analyze issue Message-ID: Hi Andrew, I had already edited the direction cosine information in the minc image (as per a previous recommendation you made on minc-users): minc_modify_header -dinsert xspace:direction_cosines=1,0,0 foo.mnc etc., so hopefully that is not the problem. With regard to the spm_defaults issue, I am using standard minc and analyze formats -- is there a way to determine if spm_defaults is being used? >>It could be the direction cosiones and it might also be that you are >>using the spm_defaults type approach to handle left-right flips "radio >>and neuro" orientation. In which case, all bets are off. I have been doing a lot of testing, and in one test case, minc2analyze preserves image alignment across format conversion, whereas mnc2nii does not. I can show/send you the images if you like. I'm still trying to figure out where minc2analyze comes from in the context of minc tools. >>minc2analyze? If you mean mnc2ana || ana2mnc then they are now old >>unsupported perl scripts of mine that may produce the same results and >>may not dependant on where your "analyze" file came from. The reason I would like to conserve image alignment across format conversion (in both the images and transforms) is that I am experimenting with using customized pre-processing (in minc format) for Siena (which requires analyze format input). Thanks a lot, Ernest Andrew Janke a.janke at gmail.com Fri Jan 12 06:20:30 EST 2007 * Previous message: [MINC-users] Fwd: Minc to Analyze issue * Next message: [MINC-users] xfm to mat ?? * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > 1. It seems that the mnc2nii and nii2mnc are the preferred scripts to > convert between minc and analyze formats. > Can these scripts use and produce analyze (i.e. *.img and *.hdr) format > files in addition to nifti (*.nii) format > files? Yes, use 'mnc2nii -help' to see the various output options. > 2. We currently make use of the scripts minc2analyze and analyze2minc to > perform conversions, I believe that are > part of the minc tools. How would these scripts compare with mnc2nii and > nii2mnc? minc2analyze? If you mean mnc2ana || ana2mnc then they are now old unsupported perl scripts of mine that may produce the same results and may not dependant on where your "analyze" file came from. > 3. I currently need to align two analyze format images. I first convert > them to minc format and then run an algorithm that produces the xfms. Next > I convert the xfm files to .mat format. However the .mat transforms do not > align the original analyze format images. I'm guessing that this is a > result of the missing direction cosine information that pertains to analyze > format images. However I would like to know if there is > a way to convert from analyze to minc with no changes to alignment. It could be the direction cosiones and it might also be that you are using the spm_defaults type approach to handle left-right flips "radio and neuro" orientation. In which case, all bets are off. My suggestion would be that if you really do want to mess with both analyze and minc would be to register and then resample in MINC before converting back. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Fri Jan 12 17:31:34 2007 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 13 Jan 2007 08:31:34 +1000 Subject: [MINC-users] Fwd: Minc to Analyze issue In-Reply-To: References: Message-ID: > With regard to the spm_defaults issue, I am using standard minc and analyze > formats -- is there a way to determine if spm_defaults is being used? Nope. But then spm_defaults is SPM specific and you seem to be using FSL. Meaning you could load your analyze image in SPM and then in FSL and get two (very) different things. > I have been doing a lot of testing, and in one test case, minc2analyze > preserves image alignment across format conversion, whereas mnc2nii does > not. > I can show/send you the images if you like. I'm still trying to figure out > where minc2analyze comes from in the context of minc tools. ! have never used minc2analyze but I do know that steve smith wrote something yonks ago so I presume this is it. > The reason I would like to conserve image alignment across format conversion > (in both the images and transforms) is that I am experimenting with using > customized pre-processing (in minc format) for Siena (which requires analyze > format input). Whenever I have done this in the past, the only consistent way to make this work is to resample everything to the same space (using mincresample) and then convert. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From ed.gronenschild at mi.unimaas.nl Tue Jan 16 04:21:51 2007 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Tue, 16 Jan 2007 10:21:51 +0100 Subject: [MINC-users] Mac & Intel Message-ID: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> Hi, I lost track, but what are the necessary packages I have to download and to install to use the MNI software on a Mac with Intel processor? Regards, Ed From Kent.Conover at concordia.ca Tue Jan 16 09:54:01 2007 From: Kent.Conover at concordia.ca (conover) Date: Tue, 16 Jan 2007 09:54:01 -0500 Subject: [MINC-users] Mac & Intel In-Reply-To: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> References: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> Message-ID: <5EE4A218-2F4B-4E67-8B9D-60389D2C8BFE@concordia.ca> Hi Ed, Here is the URL to the main MINC distribution page: http://www.bic.mni.mcgill.ca/software/minc/ You will likely need fmr_preprocess, which is a Perl script for motion correction. Unfortunately I can't recall where to get it right now. You will need to install some perl routines from CPAN - good luck. Here is the URL to the EMMA home page, unfortunately it appears to be missing a link to a download site: http://www.bic.mni.mcgill.ca/software/emma/ Here is the URL for FMRISTAT: http://www.math.mcgill.ca/keith/fmristat/ Regards and bon chance, Kent On 16-Jan-07, at 4:21 AM, Ed Gronenschild wrote: > Hi, > > I lost track, but what are the necessary packages I have to > download and > to install to use the MNI software on a Mac with Intel processor? > > Regards, > > Ed > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jason at bic.mni.mcgill.ca Tue Jan 16 10:21:33 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 16 Jan 2007 10:21:33 -0500 Subject: [MINC-users] Mac & Intel In-Reply-To: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> References: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> Message-ID: <45ACED7D.8040506@bic.mni.mcgill.ca> Ed Gronenschild wrote: > Hi, > > I lost track, but what are the necessary packages I have to download and > to install to use the MNI software on a Mac with Intel processor? > There's also this for prebuilt binaries: http://www.bic.mni.mcgill.ca/users/jason/mactel Jason > Regards, > > Ed > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From acveilleux at mrs.mni.mcgill.ca Tue Jan 16 11:34:06 2007 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Tue, 16 Jan 2007 11:34:06 -0500 Subject: [MINC-users] Mac & Intel In-Reply-To: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl>; from ed.gronenschild@mi.unimaas.nl on Tue, Jan 16, 2007 at 10:21:51AM +0100 References: <83A9EF5E-5420-4CA8-9AD5-02B7242C8487@mi.unimaas.nl> Message-ID: <20070116113406.C3248@mrs.mni.mcgill.ca> Hello, My usual install process: 1) Install X11 from Mac OS X disk 2) Install the latest Developers Tools from Apple's developers' sites. 3) Install fink or darwinports (I think you can avoid them, but it's useful to get any/all *nix libraries you might be missing. 4) Download and install all the .pkg found in http://packages.bic.mni.mcgill.ca/osx-10.4-intel-beta/ Notice that the "beta" tools have been compiled in October and the non-beta in June. I've had all sorts of problems with the June ones so I recommend you try the beta from October instead. Good luck, Alex On Tue, Jan 16, 2007 at 10:21:51AM +0100, Ed Gronenschild wrote: > To: minc-users at bic.mni.mcgill.ca > From: Ed Gronenschild > Date: Tue, 16 Jan 2007 10:21:51 +0100 > X-Mailer: Apple Mail (2.752.2) > Subject: [MINC-users] Mac & Intel > > Hi, > > I lost track, but what are the necessary packages I have to download and > to install to use the MNI software on a Mac with Intel processor? > > Regards, > > Ed > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From Alexander.Fornito at wh.org.au Tue Jan 23 19:28:40 2007 From: Alexander.Fornito at wh.org.au (Fornito, Alexander) Date: Wed, 24 Jan 2007 11:28:40 +1100 Subject: [MINC-users] CIVET download? Message-ID: Hi, Is it possible for non-MNI researchers to download CIVET? I can't seem to find any links to relevant software download pages. Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito at wh.org.au From nikelski at bic.mni.mcgill.ca Wed Jan 24 11:42:30 2007 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Wed, 24 Jan 2007 11:42:30 -0500 Subject: [MINC-users] print_all_labels? Message-ID: <45B78C76.9020209@bic.mni.mcgill.ca> Hi all, We need to run "print_all_labels" locally (Ubuntu), and I'm looking to find either the source code or a package that contains it. While I can see it on Yorick in mni/bin, it does not appear to be part of the regular mincy tools. Does anyone know where I can find it? Cheers, -Jim -- Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From sylvain at bic.mni.mcgill.ca Wed Jan 24 11:59:52 2007 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed, 24 Jan 2007 11:59:52 -0500 Subject: [MINC-users] print_all_labels? In-Reply-To: <45B78C76.9020209@bic.mni.mcgill.ca> References: <45B78C76.9020209@bic.mni.mcgill.ca> Message-ID: Hello Jim, its part of conglomerate. S On Wed, 24 Jan 2007, EJ Nikelski wrote: > Hi all, > > We need to run "print_all_labels" locally (Ubuntu), and I'm looking > to find either the source code or a package that contains it. While I > can see it on Yorick in mni/bin, it does not appear to be part of the > regular mincy tools. Does anyone know where I can find it? > > Cheers, > > -Jim > > > > -- > Jim Nikelski, Ph.D. > Postdoctoral Research Fellow > Bloomfield Centre for Research in Aging > Lady Davis Institute for Medical Research > Sir Mortimer B. Davis - Jewish General Hospital > McGill University > Tel: (514) 340-8222 x 2298 > Fax: (514) 340-8295 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From sorench at gmail.com Sat Jan 27 21:11:40 2007 From: sorench at gmail.com (Soren Christensen) Date: Sun, 28 Jan 2007 13:11:40 +1100 Subject: [MINC-users] Display Vi property and float datatype Message-ID: 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 From jason at bic.mni.mcgill.ca Sat Jan 27 21:21:28 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Sat, 27 Jan 2007 21:21:28 -0500 Subject: [MINC-users] Display Vi property and float datatype In-Reply-To: References: Message-ID: 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 From sorench at gmail.com Sat Jan 27 22:06:17 2007 From: sorench at gmail.com (Soren Christensen) Date: Sun, 28 Jan 2007 14:06:17 +1100 Subject: [MINC-users] Display Vi property and float datatype In-Reply-To: References: Message-ID: Thanks! I can work my way around it that way. It is a shame that Display the shortcomming of loading bytes since it also puts limits on the resolution of the colormapping. If someone should ever have the time to enhance it, I think that Display with a few add-ons could be one of the best ROI delineation tools out there. In my experience it is a lot faster to use than something like Analyze when dealing with many subjects. Soren On 1/28/07, 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 sean at rogue-research.com Mon Jan 29 13:50:09 2007 From: sean at rogue-research.com (Sean McBride) Date: Mon, 29 Jan 2007 13:50:09 -0500 Subject: [MINC-users] Sample MINC files... Message-ID: <20070129185009.1143951439@smtp1.sympatico.ca> Hi all, Is there any collection of sample MINC files out there? I've looked around the BIC page but found nothing. The reason I'm looking is to test some code that works with MINC files. The NifTI folks for example have this page: With a variety of samples. I'm looking for something like that. 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 hjjo at bme.hanyang.ac.kr Mon Jan 29 14:24:48 2007 From: hjjo at bme.hanyang.ac.kr (H.Jo) Date: Tue, 30 Jan 2007 04:24:48 +0900 Subject: [MINC-users] A question about BrainWeb custom simulator Message-ID: <000001c743db$2429da90$6c7d8fb0$@hanyang.ac.kr> Dear MINC Gods and Goddesses: Hi, I've used BrainWeb custom simulator for my simulation studies. Actually, I have a problem using the simulator, that is... I submitted my request about 10 days ago. But, I've got no response from the server. I really wonder whether it works. Who could answer me? Somebody help, please~ - Hang Joon --- Hang Joon Jo, PhD candidate - Tel : 82-2-2220-0697 / Fax : 82-2-2296-5943 Web: http://cna.hanyang.ac.kr Dept. of Medicine (Biomedical Engineering), College of Medicine, Hanyang University Sungdong P.O. Box 55, Seoul, KOREA, 133-605 From a.janke at gmail.com Mon Jan 29 19:37:46 2007 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 30 Jan 2007 11:37:46 +1100 Subject: [MINC-users] CIVET download? In-Reply-To: References: Message-ID: Hi Alex, As of yet CIVET is not available for public download however Prof Alan Evans (the head of the group who developed CIVET) has made it available to groups on a collaborative basis. You'd be best to email him directly. www.bic.mni.mcgill.ca/~alan a On 1/24/07, Fornito, Alexander wrote: > Hi, > Is it possible for non-MNI researchers to download CIVET? I can't seem to find any links to relevant software download pages. > Thanks, > Alex > > Alex Fornito > JN Peters Research Fellow > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne Levels 2 & 3, Alan Gilbert Building > 161 Barry St Carlton South Vic 3053 Australia > Ph: +61 3 8344 1861 > Fax: +61 3 9348 0469 > email: alexander.fornito at wh.org.au > > _______________________________________________ > 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 Alexander.Fornito at wh.org.au Mon Jan 29 21:13:14 2007 From: Alexander.Fornito at wh.org.au (Fornito, Alexander) Date: Tue, 30 Jan 2007 13:13:14 +1100 Subject: [MINC-users] CIVET download? References: Message-ID: ok thanks. Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito at wh.org.au ________________________________ From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke Sent: Tue 1/30/2007 11:37 AM To: MINC users mailing list Subject: Re: [MINC-users] CIVET download? Hi Alex, As of yet CIVET is not available for public download however Prof Alan Evans (the head of the group who developed CIVET) has made it available to groups on a collaborative basis. You'd be best to email him directly. www.bic.mni.mcgill.ca/~alan a On 1/24/07, Fornito, Alexander wrote: > Hi, > Is it possible for non-MNI researchers to download CIVET? I can't seem to find any links to relevant software download pages. > Thanks, > Alex > > Alex Fornito > JN Peters Research Fellow > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne Levels 2 & 3, Alan Gilbert Building > 161 Barry St Carlton South Vic 3053 Australia > Ph: +61 3 8344 1861 > Fax: +61 3 9348 0469 > email: alexander.fornito at wh.org.au > > _______________________________________________ > 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 WARNING: This message originated from outside the Northern/Melbourne/Western Health e-mail network. The sender cannot be validated. Caution is advised. Contact IT Services (+61 3) 9342 8888 for more information. From se at hst.aau.dk Wed Jan 31 03:38:54 2007 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Wed, 31 Jan 2007 09:38:54 +0100 Subject: [MINC-users] Sample MINC files... In-Reply-To: <20070129185009.1143951439@smtp1.sympatico.ca> References: <20070129185009.1143951439@smtp1.sympatico.ca> Message-ID: <45C0559E.3020002@hst.aau.dk> Hi Sean, I guess you can always download samples from Brainweb: http://www.bic.mni.mcgill.ca/brainweb/ Simon Sean McBride wrote: > Hi all, > > Is there any collection of sample MINC files out there? I've looked > around the BIC page but found nothing. The reason I'm looking is to > test some code that works with MINC files. > > The NifTI folks for example have this page: > > > With a variety of samples. I'm looking for something like that. > > Thanks! > >