From mok at bic.mni.mcgill.ca Wed Mar 1 01:45:42 2006 From: mok at bic.mni.mcgill.ca (Kelvin Mok) Date: Wed, 01 Mar 2006 01:45:42 -0500 Subject: [MINC-users] Failure of nu-estimate on older t1-weighted brain data. In-Reply-To: References: Message-ID: <44054316.9030106@bic.mni.mcgill.ca> Hi Najma, Using the same quarantine, I received errors running nu_estimate in the past as well. The errors were different and potentially caused by memory leak (or lack of memory?) within function nu_estimate_np_and_em - but I never encountered them again. Not sure if this helps. Kelvin Najmeh Khalili M. wrote: > I agree that using an ICBM mask on a native data is not reasonable, but it > worked for most of the cases. However, what is more important is that you > can nu_correct this same data without any mask! > > No, I am not using the standard install! Perhaps Yasser can comment on the > quarantine that Dale built for new version of CIVET. I ran PMP on ACES > cluster. More informed comments about machines and the installation > of tools? Perhaps from Andrew, Jason, Yasser, Dale??? > > N. > > On Tue, 28 Feb 2006, Alex ZIJDENBOS wrote: > > >>I'm not sure what could be going on here; Najma sent me some of the >>data she used and I ran it through nu_correct v1.10 just fine. I'm not >>sure why essentially the same version of n3 would behave differently >>on these data. Are you using a standard install, or a quarantined >>version? The CachedArray error seems to indicate a failure in creating >>a temporary file - that could be a machine resource problem (out of >>/tmp space?). >> >>As for the masking, it seems you are trying to mask a native file with >>a stereotaxic mask, which is likely to produce unexpected results ;) I >>thought N3 checked at least that the sampling lattice of the source >>file and mask are the same - it *should* exit gracefully on something >>like this. >> >>-- A >> >>On Tue, Feb 28, 2006 at 07:18:25PM -0500, Najmeh Khalili M. wrote: >> >>>Greetings, >>> >>>I am trying to perform N3 on t1-data of healthy older brains and I >>>encounter two error messages. (nu_estimate, version 1.10) >>> >>>First, I got the following error for N=50 data sets: >>> >>> Assertion failed at line 742 in file templates/CachedArray.cc >>> nu_estimate_np_and_em: crashed while running volume_stats (termination >>>status=256) >>> >>>Next, I used an ICBM mask; succeeded in non-uniformity correction of N=45 >>>data sets, but failed in 5 with : >>> >>> Direction cosines of mask.mnc and /tmp/native_t1.mnc do not match >>> Failed to shrink mask volume. >>> nu_estimate: crashed while running nu_estimate_np_and_em (termination >>> status=65280) >>> >>>The data dimension in the failed cases is identical to those that have >>>succeeded. The data quality and the brain structure in failing cases is >>>not visually different. I have not seen this problem in younger brains. >>> >>>Has someone else experienced such errors and can any one give an >>>explanation of what the cause of this might be, please? >>> >>>Best, >>>Najma >>> >>> >>>_______________________________________________ >>>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 elo at neurorx.com Wed Mar 1 09:26:55 2006 From: elo at neurorx.com (Ernest Lo) Date: Wed, 1 Mar 2006 09:26:55 -0500 (EST) Subject: [MINC-users] nonlinear registration in minc In-Reply-To: Message-ID: Hello, I would like to perform a nonlinear registration of one image to another. In fact it is the same patient, but there is some minor distortion in one of the scans (that is affecting our tissue segmentation results). So I'm looking for a registration technique that will not only align the images but correct for the distortion. I have experimented with minctracc -nonlinear and mritoself with no success. I don't have much experience in this area but it seems to me that a good nonlinear reg algorithm should be able to easily align these two images. Would anyone know of a good way to do this, in terms of parameter settings, scripts, commands, etc.? I have access to a couple of tools as well - nlfit_xcorr.pl and nlfit_smr.pl - but these require various model files in addition to the target image (blur levels etc.), which I don't know how to generate. Any advice in this area would be appreciated as well. Thanks! Ernest Lo NeuroRX Research Montreal, Canada From jason at bic.mni.mcgill.ca Wed Mar 1 10:14:24 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 01 Mar 2006 10:14:24 -0500 Subject: [MINC-users] nonlinear registration in minc In-Reply-To: References: Message-ID: <4405BA50.7060304@bic.mni.mcgill.ca> Ernest Lo wrote: >Hello, > >I would like to perform a nonlinear registration of one image to another. >In fact it is the same patient, but there is some minor distortion in one >of the scans (that is affecting our tissue segmentation results). So I'm >looking for a registration technique that will not only align the images >but correct for the distortion. > >I have experimented with minctracc -nonlinear and mritoself with no >success. I don't have much experience in this area but it seems to me >that a good nonlinear reg algorithm should be able to easily align these >two images. Would anyone know of a good way to do this, in terms of >parameter settings, scripts, commands, etc.? > >I have access to a couple of tools as well - nlfit_xcorr.pl and >nlfit_smr.pl - but these require various model files in addition to the >target image (blur levels etc.), which I don't know how to generate. Any >advice in this area would be appreciated as well. > > There are, as far as I know, no convenient scripts available for subject to subject non-linear registration. So you'll have to use minctracc itself. The basic options you want are: -nonlinear: erm, I'm sure you can figure out what this option does. -xcorr: objective function -step: 3 values for the spacing of the deformation grid. -simplex: size of search area. -lattice_diameter: width of sub-lattice (three values) -iterations: number of iterations. There are more that might be useful (weight, stiffness, etc.), but those should get you started. Also note that a hierarchical process often gives the best results: i.e. align two blurred versions first, then use the -transform option to minctracc to initialize a second registration at less blurring, and so on. Good luck, Jason >Thanks! > > >Ernest Lo >NeuroRX Research >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 Wed Mar 1 16:14:27 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 2 Mar 2006 07:14:27 +1000 Subject: [MINC-users] nonlinear registration in minc In-Reply-To: <4405BA50.7060304@bic.mni.mcgill.ca> References: <4405BA50.7060304@bic.mni.mcgill.ca> Message-ID: > >I would like to perform a nonlinear registration of one image to another. > >In fact it is the same patient, but there is some minor distortion in one > >of the scans (that is affecting our tissue segmentation results). So I'm > >looking for a registration technique that will not only align the images > >but correct for the distortion. > There are, as far as I know, no convenient scripts available for subject > to subject non-linear registration. So you'll have to use minctracc > itself. The basic options you want are: > > -nonlinear: erm, I'm sure you can figure out what this option does. > -xcorr: objective function > -step: 3 values for the spacing of the deformation grid. > -simplex: size of search area. > -lattice_diameter: width of sub-lattice (three values) > -iterations: number of iterations. Hi Ernest, Jason is right, there is no officially blessed script for doing this, but of course I do have one myself that you are welcome to use. You may have to modify the first part (config) of the script for your application but it generally does a good job as is. This script does all the required blurring and hierarchical fitting that you will need. I have attached it. -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From amatos at mrs.mni.mcgill.ca Wed Mar 1 16:40:24 2006 From: amatos at mrs.mni.mcgill.ca (Andre Matos) Date: Wed, 01 Mar 2006 16:40:24 -0500 Subject: [MINC-users] nonlinear registration in minc In-Reply-To: Message-ID: Hi Ernest, Did you speak with Sridar or Louis Collins regarding this? We have some nonlinear transformations done in the lab and Patricia (from Louis lab) did for us. Andre On 3/1/06 9:26 AM, "Ernest Lo" wrote: > Hello, > > I would like to perform a nonlinear registration of one image to another. > In fact it is the same patient, but there is some minor distortion in one > of the scans (that is affecting our tissue segmentation results). So I'm > looking for a registration technique that will not only align the images > but correct for the distortion. > > I have experimented with minctracc -nonlinear and mritoself with no > success. I don't have much experience in this area but it seems to me > that a good nonlinear reg algorithm should be able to easily align these > two images. Would anyone know of a good way to do this, in terms of > parameter settings, scripts, commands, etc.? > > I have access to a couple of tools as well - nlfit_xcorr.pl and > nlfit_smr.pl - but these require various model files in addition to the > target image (blur levels etc.), which I don't know how to generate. Any > advice in this area would be appreciated as well. > > Thanks! > > > Ernest Lo > NeuroRX Research > Montreal, Canada > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Andre Matos amatos at mrs.mni.mcgill.ca From pgravel at bic.mni.mcgill.ca Wed Mar 1 21:29:20 2006 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Wed, 1 Mar 2006 21:29:20 -0500 Subject: [MINC-users] Creating a dynamic MINC file Message-ID: Hi All, Pardon my ignorance, but how could I create a minc file from scratch with frame duration of (in min): 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85 and the following properties: -orientation transverse -type short -valid_range -32768 32767 -xstep 2 -ystep 2 -zstep 6.5 -xstart -127 -ystart -127 -zstart -45.5 -size 30 15 128 128 -xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1 I was able to use a combination of micreateimage and mincresample to get the above properties, however I was not able to insert the frame duration. Thanks in advance, Best Regards, Paul From sylvain at bic.mni.mcgill.ca Thu Mar 2 13:50:46 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Thu, 2 Mar 2006 13:50:46 -0500 Subject: [MINC-users] Creating a dynamic MINC file In-Reply-To: Message-ID: Hi Paul, I believe that with mincconcat -concat_dimension time -widthlist '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85' frame1.mnc frame2.mnc ... frame30.mnc out.mnc it should do the trick. Sylvain On Wed, 1 Mar 2006, Paul GRAVEL wrote: > Hi All, > > Pardon my ignorance, but how could I create a minc file from scratch > with frame duration of (in min): > > 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85 > > and the following properties: > > -orientation transverse > -type short > -valid_range -32768 32767 > -xstep 2 -ystep 2 -zstep 6.5 > -xstart -127 -ystart -127 -zstart -45.5 > -size 30 15 128 128 > -xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1 > > I was able to use a combination of micreateimage and mincresample to get > the above properties, however I was not able to insert the frame duration. > > Thanks in advance, > > Best Regards, > > Paul > > > _______________________________________________ > 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) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 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 elo at neurorx.com Thu Mar 2 14:58:53 2006 From: elo at neurorx.com (Ernest Lo) Date: Thu, 2 Mar 2006 14:58:53 -0500 (EST) Subject: [MINC-users] nonlinear registration in minc In-Reply-To: Message-ID: Hello, Thank you all very much for your advice and help (including any pending suggestions as well :). I am in the process of assimilating all the information and trying out the different methods. Ernest Lo NeuroRX Research Montreal, Canada > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Mar 2006 07:14:27 +1000 > From: "Andrew Janke" > Subject: Re: [MINC-users] nonlinear registration in minc > To: "MINC users mailing list" > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > >I would like to perform a nonlinear registration of one image to another. > > >In fact it is the same patient, but there is some minor distortion in one > > >of the scans (that is affecting our tissue segmentation results). So I'm > > >looking for a registration technique that will not only align the images > > >but correct for the distortion. > > > There are, as far as I know, no convenient scripts available for subject > > to subject non-linear registration. So you'll have to use minctracc > > itself. The basic options you want are: > > > > -nonlinear: erm, I'm sure you can figure out what this option does. > > -xcorr: objective function > > -step: 3 values for the spacing of the deformation grid. > > -simplex: size of search area. > > -lattice_diameter: width of sub-lattice (three values) > > -iterations: number of iterations. > > Hi Ernest, > > Jason is right, there is no officially blessed script for doing this, > but of course I do have one myself that you are welcome to use. You > may have to modify the first part (config) of the script for your > application but it generally does a good job as is. This script does > all the required blurring and hierarchical fitting that you will need. > > I have attached it. > > > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > ------------------------------ > > Message: 2 > Date: Wed, 01 Mar 2006 16:40:24 -0500 > From: Andre Matos > Subject: Re: [MINC-users] nonlinear registration in minc > To: MINC users mailing list > Message-ID: > Content-Type: text/plain; charset="US-ASCII" > > Hi Ernest, > > Did you speak with Sridar or Louis Collins regarding this? We have some > nonlinear transformations done in the lab and Patricia (from Louis lab) did > for us. > > Andre > > > On 3/1/06 9:26 AM, "Ernest Lo" wrote: > > > Hello, > > > > I would like to perform a nonlinear registration of one image to another. > > In fact it is the same patient, but there is some minor distortion in one > > of the scans (that is affecting our tissue segmentation results). So I'm > > looking for a registration technique that will not only align the images > > but correct for the distortion. > > > > I have experimented with minctracc -nonlinear and mritoself with no > > success. I don't have much experience in this area but it seems to me > > that a good nonlinear reg algorithm should be able to easily align these > > two images. Would anyone know of a good way to do this, in terms of > > parameter settings, scripts, commands, etc.? > > > > I have access to a couple of tools as well - nlfit_xcorr.pl and > > nlfit_smr.pl - but these require various model files in addition to the > > target image (blur levels etc.), which I don't know how to generate. Any > > advice in this area would be appreciated as well. > > > > Thanks! > > > > > > Ernest Lo > > NeuroRX Research > > Montreal, Canada > > > > > > > > > > _______________________________________________ > > 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 Mar 7 00:33:13 2006 From: Paul.Rasser at newcastle.edu.au (Paul Rasser) Date: Tue, 07 Mar 2006 16:33:13 +1100 Subject: [MINC-users] MacOS packages faulty? Message-ID: Both the packages below failed to install on 10.4.4 http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz Paul. >>> dale at bic.mni.mcgill.ca 02/25/06 1:47 PM >>> Hello, I am displease to inform you all that I believe the packages listed below to be faulty... Since I do not have a 10.4 system I will need a volunteer. Someone with a MacOS 10.4 system; download and install anyone of them if it fails there are all probably broken. Please be careful to read the error message at the end!!! http://packages.bic.mni.mcgill.ca/osx/classify-1.0.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/glim-image-1.1.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/inormalize-0.99.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/mincblob-1.2.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98s.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/register-1.3.6.pkg.tar.gz NOTE: It looks like they have been broken for a while. Even the ones on my backup from a month-ago are bad. They look to have been corrupted in the transfer. I am sorry for the pain this may have cause. I will try to have it rectified shortly. PS: My last official day is Tuesday :) Cheers! dale _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From se at hst.aau.dk Tue Mar 14 10:49:11 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Tue, 14 Mar 2006 16:49:11 +0100 Subject: [MINC-users] Bug in mni_autoreg-0.98v ? Message-ID: <4416E5F7.1090407@hst.aau.dk> I just installed the latest autoreg (0.98v) and noticed a change in autocrop, which included a dependency on the method "split_path" being exported by the MNI::FileUtilities perl module from the mni_perllib. Because of this autocrop fails, as the "split_path" method is exported by the MNI::PathUtilities module. By removing the split_path dependency autocrop runs fine. Am I missing something, or is this a bug? Sry if this is somewhat OT. Best Regards Simon Eskildsen -- Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) From o.winz at fz-juelich.de Tue Mar 14 12:15:30 2006 From: o.winz at fz-juelich.de (Oliver Winz) Date: Tue, 14 Mar 2006 18:15:30 +0100 Subject: [MINC-users] Bug in mni_autoreg-0.98v ? In-Reply-To: References: Message-ID: <4416FA32.8000404@fz-juelich.de> Hi Simon, i have the same bug today on a Mac OS 10.4 system. Please can you explain me how to remove the split_path dependency. Greetings, Oliver > > I just installed the latest autoreg (0.98v) and noticed a change in > autocrop, which included a dependency on the method "split_path" being > exported by the MNI::FileUtilities perl module from the mni_perllib. > Because of this autocrop fails, as the "split_path" method is exported > by the MNI::PathUtilities module. By removing the split_path dependency > autocrop runs fine. Am I missing something, or is this a bug? > Sry if this is somewhat OT. > > Best Regards > Simon Eskildsen > > -- Oliver Winz, M.Sc. Molecular Neuroimaging Group Institute of Medicine (IME) Research Centre Juelich D - 52425 Juelich Germany Phone: +49 2461 61-6493 Web: http://www.fz-juelich.de/ime/mni Location: Building 15.9, Room 3010 From a.janke at gmail.com Tue Mar 14 17:10:36 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 15 Mar 2006 09:10:36 +1100 Subject: [MINC-users] Bug in mni_autoreg-0.98v ? In-Reply-To: <4416FA32.8000404@fz-juelich.de> References: <4416FA32.8000404@fz-juelich.de> Message-ID: Thanks for the bug reports. This is a harbinger from previous versions when mni_perllib was included in mni_autoreg. The simple fix is to simply edit autocrop and change the following. ie: from this: use MNI::FileUtilities qw( check_output_dirs split_path ); to use MNI::FileUtilities qw( check_output_dirs ); use MNI::PathUtilities qw( split_path ); a On 3/15/06, Oliver Winz wrote: > Hi Simon, > > i have the same bug today on a Mac OS 10.4 system. > Please can you explain me how to remove the split_path dependency. > > Greetings, > Oliver > > > > I just installed the latest autoreg (0.98v) and noticed a change in > > autocrop, which included a dependency on the method "split_path" being > > exported by the MNI::FileUtilities perl module from the mni_perllib. > > Because of this autocrop fails, as the "split_path" method is exported > > by the MNI::PathUtilities module. By removing the split_path dependency > > autocrop runs fine. Am I missing something, or is this a bug? > > Sry if this is somewhat OT. > > > > Best Regards > > Simon Eskildsen > > > > > > > -- > > Oliver Winz, M.Sc. > > Molecular Neuroimaging Group > > Institute of Medicine (IME) > > Research Centre Juelich > > D - 52425 Juelich > > Germany > > > Phone: +49 2461 61-6493 > > Web: http://www.fz-juelich.de/ime/mni > > Location: Building 15.9, Room 3010 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From se at hst.aau.dk Wed Mar 15 10:04:26 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Wed, 15 Mar 2006 16:04:26 +0100 Subject: [MINC-users] Bug in mni_autoreg-0.98v ? In-Reply-To: References: <4416FA32.8000404@fz-juelich.de> Message-ID: <44182CFA.6020709@hst.aau.dk> Yes, that was also my solution. Since we're correcting the perl scripts, I'm slightly annoyed by the way mritotal handles logging. Somewhere after version 0.98r mritotal has considered stdout as an open filehandle for logging, which means that it is not possible to pipe stdout from mritotal: mritotal mri.mnc mri.xfm > test.log self_announce: if supplied, $log must be an open filehandle at /gruppe/ad_mri/Opteron/pack/bin/mritotal line 571 Removing the following from mritotal solves the problem: &self_announce("STDOUT") if $Verbose && ! -t "STDOUT"; I realize that the filehandle check is in the self_announce function, but i am reluctant to change anything in the mni_perllib. Maybe a commandline option to mritotal for handling logging would be in order? Best regards Simon Eskildsen Andrew Janke wrote: >Thanks for the bug reports. > >This is a harbinger from previous versions when mni_perllib was >included in mni_autoreg. The simple fix is to simply edit autocrop >and change the following. > >ie: from this: > > use MNI::FileUtilities qw( check_output_dirs split_path ); > >to > > use MNI::FileUtilities qw( check_output_dirs ); > use MNI::PathUtilities qw( split_path ); > > >a > >On 3/15/06, Oliver Winz wrote: > > >>Hi Simon, >> >>i have the same bug today on a Mac OS 10.4 system. >>Please can you explain me how to remove the split_path dependency. >> >>Greetings, >>Oliver >> >> >>>I just installed the latest autoreg (0.98v) and noticed a change in >>>autocrop, which included a dependency on the method "split_path" being >>>exported by the MNI::FileUtilities perl module from the mni_perllib. >>>Because of this autocrop fails, as the "split_path" method is exported >>>by the MNI::PathUtilities module. By removing the split_path dependency >>>autocrop runs fine. Am I missing something, or is this a bug? >>>Sry if this is somewhat OT. >>> >>> >>> -- Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) From nikelski at bic.mni.mcgill.ca Wed Mar 15 13:45:16 2006 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Wed, 15 Mar 2006 13:45:16 -0500 Subject: [MINC-users] get_meansd_voi --- problems with PET volumes Message-ID: <441860BC.7000600@bic.mni.mcgill.ca> Hi, I'm trying to extract VOI mean and sd using get_meansd_voi. When I try it using ... >get_meansd_voi pet.mnc 0 0 0 1 0 ... which should get me the value at Talairach (0,0,0), instead, I get >n/a n/a 0 Interestingly, if I try to use a larger roi radius, I get ... [~] 83 >get_meansd_voi pet.mnc 0 0 0 1 3 ncvarget: ncid 3: Index exceeds dimension bound miicv_get: MINC package entry point ncvarget: ncid 3: Index exceeds dimension bound miicv_get: MINC package entry point 0.000 0.000 3 Now, if I try this with the average 305 MRI T1, I get no problems. Perhaps the problem is related to the volume data type? The PET volume I'm using is the usual ... [~] 84 >mincinfo pet.mnc file: pet.mnc image: signed__ short -32000 to 32000 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 63 -2.425 -427.96 yspace 128 2.025 -128.588 xspace 128 2.025 -128.588 Now, I'm certain this has worked before ... and on the same PET volumes. What am I missing? Thanks, -Jim -- E. James 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 nikelski at bic.mni.mcgill.ca Wed Mar 15 14:14:37 2006 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Wed, 15 Mar 2006 14:14:37 -0500 Subject: [MINC-users] get_meansd_voi --- problems with PET volumes In-Reply-To: <20060315185527.GA12696@bic.mni.mcgill.ca> References: <441860BC.7000600@bic.mni.mcgill.ca> <20060315185527.GA12696@bic.mni.mcgill.ca> Message-ID: <4418679D.80501@bic.mni.mcgill.ca> Thanks Alex, Yup, I really should have that 3rd cup of coffee before posting anything. Thanks again. -Jim Alex ZIJDENBOS wrote: > Judging by your volume's start values, I would say that your PET > volume is not in Talairach space at all, and the Talairach (world) > coordinate 0,0,0 is most likely well outside your volume... You should > register/resample to stx space first. > > -- Alex > > On Wed, Mar 15, 2006 at 01:45:16PM -0500, EJ Nikelski wrote: > >>Hi, >> >> I'm trying to extract VOI mean and sd using get_meansd_voi. When I >>try it using ... >> >> >>>get_meansd_voi pet.mnc 0 0 0 1 0 >> >>... which should get me the value at Talairach (0,0,0), instead, I get >> >> >>>n/a n/a 0 >> >> Interestingly, if I try to use a larger roi radius, I get ... >> >>[~] 83 >get_meansd_voi pet.mnc 0 0 0 1 3 >>ncvarget: ncid 3: Index exceeds dimension bound >>miicv_get: MINC package entry point >>ncvarget: ncid 3: Index exceeds dimension bound >>miicv_get: MINC package entry point >>0.000 0.000 3 >> >> Now, if I try this with the average 305 MRI T1, I get no problems. >>Perhaps the problem is related to the volume data type? The PET volume >>I'm using is the usual ... >> >>[~] 84 >mincinfo pet.mnc >>file: pet.mnc >>image: signed__ short -32000 to 32000 >>image dimensions: zspace yspace xspace >> dimension name length step start >> -------------- ------ ---- ----- >> zspace 63 -2.425 -427.96 >> yspace 128 2.025 -128.588 >> xspace 128 2.025 -128.588 >> >> >> Now, I'm certain this has worked before ... and on the same PET >>volumes. What am I missing? >> >> >>Thanks, >> >>-Jim >> >> >>-- >>E. James 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 > > > > From t.ruest.1 at research.gla.ac.uk Thu Mar 16 06:42:18 2006 From: t.ruest.1 at research.gla.ac.uk (Torsten Ruest) Date: Thu, 16 Mar 2006 11:42:18 +0000 Subject: [MINC-users] Problems with Inormalize Message-ID: <44194F1A.70606@research.gla.ac.uk> Dear all, I experienced some problems using inormalize. I wanted to scale the intensity of a MR image according to a "reference" image. However there seems something not being OK with this algorithm: although it displays a normalization factor at the end, it seems not to apply it to the saved image. There is no difference between the intensity non-uniformity corrected image (which I did with N3 just before using inormalize) and the inormalized image. Has anybody experienced the same ? Furthermore, I am wondering on what the scaling in inormalize is based on. Given that the 2 images (reference, and image to be scaled according to the reference) have the same matrix size, but are not in register, would the scale factor be just the same as if the images would be in register (assuming that just rotations and translations would need to be applied to bring them in the same space)? Thank you very much for any suggestions. Regards, Torsten From jason at bic.mni.mcgill.ca Fri Mar 17 09:56:44 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 17 Mar 2006 09:56:44 -0500 Subject: [MINC-users] mincmorph/minc2 bug (with workaround) Message-ID: <441ACE2C.2040001@bic.mni.mcgill.ca> Hi all, it appears that there is a bug in mincmorph (and maybe not only mincmorph) if the following conditions are met: * mincmorph linked against minc2 (I'm using a fairly recent CVS version) * input volume larger than volume_io cache threshold. This causes a segfault along with the message "copy_volume(): copying cached volumes not implemented." The main point of this email is that, if anyone else encounters the same situation, and if your volumes are not truly huge, the segfault can be circumvented by disabling volume caching: export VOLUME_CACHE_THRESHOLD=-1 Cheers, Jason From krista at bic.mni.mcgill.ca Fri Mar 17 13:56:26 2006 From: krista at bic.mni.mcgill.ca (Krista GARVER) Date: Fri, 17 Mar 2006 13:56:26 -0500 Subject: [MINC-users] miwriteimage on pc Message-ID: Hi all. I am new to fmristat and am running into an annoying problem. I'm using matlab on my pc to run fmristat scripts and I keep getting hung up on 'miwriteimage', which is being called by another program and not explicitly written into my script. Specifically, it says there is an error because miwriteimage can't open the temporary file for writing. I am not sure what to do as it appears like the program should create its own temporary file and I am administrator on the computer, so it shouldn't be a permissions issue. Does anyone know what I'm doing wrong? Thanks. From mok at bic.mni.mcgill.ca Fri Mar 17 14:01:56 2006 From: mok at bic.mni.mcgill.ca (Kelvin Mok) Date: Fri, 17 Mar 2006 14:01:56 -0500 Subject: [MINC-users] miwriteimage on pc In-Reply-To: References: Message-ID: <441B07A4.5020705@bic.mni.mcgill.ca> Hi Krista, It maybe cranky and giving you the message because the path to the temporary file does not exist. Ie, the folder hasn't been created. Although I'm not sure if this helps since, as you said the program is deciding the temp folder. Kelvin Krista GARVER wrote: > Hi all. > > I am new to fmristat and am running into an annoying problem. > I'm using matlab on my pc to run fmristat scripts and I keep getting hung > up on 'miwriteimage', which is being called by another program and not > explicitly written into my script. Specifically, it says there is an > error because miwriteimage can't open the temporary file for writing. I > am not sure what to do as it appears like the program should create its > own temporary file and I am administrator on the computer, so it > shouldn't be a permissions issue. Does anyone know what I'm doing wrong? > > Thanks. > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From krista at bic.mni.mcgill.ca Fri Mar 17 14:16:43 2006 From: krista at bic.mni.mcgill.ca (Krista GARVER) Date: Fri, 17 Mar 2006 14:16:43 -0500 Subject: [MINC-users] miwriteimage on pc (fwd) Message-ID: Thanks. I thought that might be the problem also, but I can't figure out how to change the directory that it is looking for. I altered the miwriteimage script, but it didn't seem to make any difference. Do you know how to change where it is trying to put a tmp file? ---------- Forwarded message ---------- Date: Fri, 17 Mar 2006 14:01:56 -0500 From: Kelvin Mok Reply-To: MINC users mailing list To: MINC users mailing list Subject: Re: [MINC-users] miwriteimage on pc Hi Krista, It maybe cranky and giving you the message because the path to the temporary file does not exist. Ie, the folder hasn't been created. Although I'm not sure if this helps since, as you said the program is deciding the temp folder. Kelvin Krista GARVER wrote: > Hi all. > > I am new to fmristat and am running into an annoying problem. > I'm using matlab on my pc to run fmristat scripts and I keep getting hung > up on 'miwriteimage', which is being called by another program and not > explicitly written into my script. Specifically, it says there is an > error because miwriteimage can't open the temporary file for writing. I > am not sure what to do as it appears like the program should create its > own temporary file and I am administrator on the computer, so it > shouldn't be a permissions issue. Does anyone know what I'm doing wrong? > > Thanks. > > > > _______________________________________________ > 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 Fri Mar 17 14:22:04 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri, 17 Mar 2006 14:22:04 -0500 Subject: [MINC-users] miwriteimage on pc (fwd) In-Reply-To: References: Message-ID: <441B0C5C.1090701@bic.mni.mcgill.ca> Just a guess, but try setting an environment variable TMPDIR to wherever you want it to put temp files. In unix if you use csh or tcsh as your shell, it's as simple as "setenv TMPDIR /tmp" If you use bash then "export TMPDIR=/tmp" If you're in Windows, then you can look at this FAQ to see how to do it... http://www.chem.gla.ac.uk/~louis/software/faq/q1.html Cheers, Jon Krista GARVER wrote: > Thanks. I thought that might be the problem also, but I can't figure out > how to change the directory that it is looking for. I altered the > miwriteimage script, but it didn't seem to make any difference. Do you > know how to change where it is trying to put a tmp file? > > > > ---------- Forwarded message ---------- > Date: Fri, 17 Mar 2006 14:01:56 -0500 > From: Kelvin Mok > Reply-To: MINC users mailing list > To: MINC users mailing list > Subject: Re: [MINC-users] miwriteimage on pc > > Hi Krista, > > It maybe cranky and giving you the message because the path to the > temporary file does not exist. Ie, the folder hasn't been created. > > Although I'm not sure if this helps since, as you said the program is > deciding the temp folder. > > Kelvin > > Krista GARVER wrote: > >>Hi all. >> >>I am new to fmristat and am running into an annoying problem. >>I'm using matlab on my pc to run fmristat scripts and I keep getting hung >>up on 'miwriteimage', which is being called by another program and not >>explicitly written into my script. Specifically, it says there is an >>error because miwriteimage can't open the temporary file for writing. I >>am not sure what to do as it appears like the program should create its >>own temporary file and I am administrator on the computer, so it >>shouldn't be a permissions issue. Does anyone know what I'm doing wrong? >> >>Thanks. >> >> >> >>_______________________________________________ >>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 mferre at bic.mni.mcgill.ca Fri Mar 17 14:39:22 2006 From: mferre at bic.mni.mcgill.ca (Michael Ferreira) Date: Fri, 17 Mar 2006 14:39:22 -0500 Subject: [MINC-users] miwriteimage on pc In-Reply-To: References: Message-ID: <441B106A.9090904@bic.mni.mcgill.ca> If you're in Windows, emma expects "c:\tmp" to exist. There is a short paragraph of instructions right at the top of the fmristat webpage: http://www.math.mcgill.ca/keith/fmristat/ I should mention though that lately, several users have reported problems running fmristat/emma in Windows XP. mike Krista GARVER wrote: > Thanks. I thought that might be the problem also, but I can't figure out > how to change the directory that it is looking for. I altered the > miwriteimage script, but it didn't seem to make any difference. Do you > know how to change where it is trying to put a tmp file? > > > > ---------- Forwarded message ---------- > Date: Fri, 17 Mar 2006 14:01:56 -0500 > From: Kelvin Mok > Reply-To: MINC users mailing list > To: MINC users mailing list > Subject: Re: [MINC-users] miwriteimage on pc > > Hi Krista, > > It maybe cranky and giving you the message because the path to the > temporary file does not exist. Ie, the folder hasn't been created. > > Although I'm not sure if this helps since, as you said the program is > deciding the temp folder. > > Kelvin > > Krista GARVER wrote: > >>Hi all. >> >>I am new to fmristat and am running into an annoying problem. >>I'm using matlab on my pc to run fmristat scripts and I keep getting hung >>up on 'miwriteimage', which is being called by another program and not >>explicitly written into my script. Specifically, it says there is an >>error because miwriteimage can't open the temporary file for writing. I >>am not sure what to do as it appears like the program should create its >>own temporary file and I am administrator on the computer, so it >>shouldn't be a permissions issue. Does anyone know what I'm doing wrong? >> >>Thanks. >> >> >> >>_______________________________________________ >>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 lau at bic.mni.mcgill.ca Fri Mar 17 15:37:54 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Fri, 17 Mar 2006 15:37:54 -0500 Subject: [MINC-users] Register clipping on widescreen laptop Message-ID: Hey all, Has anyone else run into the problem of clipping in the third (rightmost) column of frames in Register (when the application window is maximized)? It seems to clip off at exactly where you would expect the proportion of a "normal" screen resolution to be... 10x7, 12x10, etc). I have two screenshots: 1. http://www.bic.mni.mcgill.ca/~lau/img/register_ws_clip.jpg Register maximized, and clipping 2. http://www.bic.mni.mcgill.ca/~lau/img/register_ws_noclip.jpg Register not maximized, and the third frame looks fine. version 1.3.6 in Ubuntu (Debian-based) Linux (1280x768 resolution). Any ideas? cheers, jonathan From krista at bic.mni.mcgill.ca Tue Mar 21 12:22:55 2006 From: krista at bic.mni.mcgill.ca (Krista GARVER) Date: Tue, 21 Mar 2006 12:22:55 -0500 Subject: [MINC-users] divide a dataset into chunks Message-ID: hello. is there a tool for dividing a dataset into pieces? for example, how would i take a dataset with 208 timepoints, cut off the first 8, and divide the remaining 200 timepoints into 4 datasets of 50 timespoints each? thanks, krista From atsuko at bic.mni.mcgill.ca Tue Mar 21 12:49:25 2006 From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano) Date: Tue, 21 Mar 2006 17:49:25 -0000 Subject: [MINC-users] cavum vergae In-Reply-To: Message-ID: <000201c6955a$bb28db10$53b2ce84@quark> Hello all, Does anybody have any experience with treating MRI images with cavum septi pellucidi and cavum vergae? I tried to transfer the subject's MRI into MNI space using mritotal, but so far, I couldn't success it. Even if I use the -nonlinear option, these cavities are remained. Best, Atsuko Nagano From louis.collins at mcgill.ca Tue Mar 21 13:33:59 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 21 Mar 2006 13:33:59 -0500 Subject: [MINC-users] divide a dataset into chunks In-Reply-To: References: Message-ID: <67cca52a73e1db09429712d9de11e1f4@mcgill.ca> krista, the command is mincreshape: mincreshape volume.mnc -dimrange time=8,50 output.mnc will do what you like if the time dimension is coded as 'time'. use 'mincinfo volume.mnc' to see what the dimension name is called. (it could be vector_dimension, in which case the command becomes: mincreshape volume.mnc -dimrange vector_dimension=8,50 output.mnc good luck, -Louis On Mar 21, 2006, at 12:22 PM, Krista GARVER wrote: > hello. > > is there a tool for dividing a dataset into pieces? for example, how > would i take a dataset with 208 timepoints, cut off the first 8, and > divide the remaining 200 timepoints into 4 datasets of 50 timespoints > each? > > thanks, > krista > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From louis.collins at mcgill.ca Tue Mar 21 13:42:54 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 21 Mar 2006 13:42:54 -0500 Subject: [MINC-users] cavum vergae In-Reply-To: <000201c6955a$bb28db10$53b2ce84@quark> References: <000201c6955a$bb28db10$53b2ce84@quark> Message-ID: <5def3ed237724618c7b80bd5b8adeb5e@mcgill.ca> Atsuko, mritotal should be able to work (bring the data/brain into stereotaxic space) in linear mode, even with a cavum vergae. Tests have shown mritotal to work even in cases with hemispherectomy. however, if you want to map the data into stereotaxic space using a non-linear mapping to remove the enlarged septum, I don't think that it will work. The non-linear warping is not strong enough to achieve the level of deformation needed _and_ the warping procedure needs a 1-1 correspondance between volumes, and in this case, the septum is split in the patient and is a single membrane in the target. -Louis On Jun 21, 2006, at 1:47 PM, Atsuko Nagano wrote: > Hello all, > > Does anybody have any experience with treating MRI images with cavum > septi pellucidi and cavum vergae? > > I tried to transfer the subject's MRI into MNI space using mritotal, > but > so far, I couldn't success it. Even if I use the -nonlinear option, > these cavities are remained. > > Best, > > Atsuko Nagano > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From tpb1 at ualberta.ca Thu Mar 23 13:23:06 2006 From: tpb1 at ualberta.ca (tpb1@ualberta.ca) Date: Thu, 23 Mar 2006 11:23:06 -0700 Subject: [MINC-users] Z-axis flipping or rotation Message-ID: <20060323112306.fza6m7k7jkows0k8@webmail.ualberta.ca> I have a brain that is upside down and I need to orient it properly. I looked in conglomerate and minctools, and it looks like mincreshape should do the trick, but when I try: mincreshape +zdirection p3.mnc p3_zflip.mnc, the following prints out: Copying chunks:................................................................. ...............................................................Done. But the output file is not changed at all. What am I doing wrong? Thanks, Thomas From jason at bic.mni.mcgill.ca Thu Mar 23 13:31:39 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 23 Mar 2006 13:31:39 -0500 Subject: [MINC-users] Z-axis flipping or rotation In-Reply-To: <20060323112306.fza6m7k7jkows0k8@webmail.ualberta.ca> References: <20060323112306.fza6m7k7jkows0k8@webmail.ualberta.ca> Message-ID: <4422E98B.7070304@bic.mni.mcgill.ca> I think the combination of param2xfm and mincresample is actually what you want. Run something like the following: param2xfm -rotation 0 0 180 rotation.xfm mincresample -tfm_input_sampling file.mnc -transform rotation.xfm output.mnc You'll have to experiment with getting the right rotations for your case. Jason tpb1 at ualberta.ca wrote: >I have a brain that is upside down and I need to orient it properly. I >looked in conglomerate and minctools, and it looks like mincreshape >should do the trick, but when I try: >mincreshape +zdirection p3.mnc p3_zflip.mnc, the following prints out: >Copying >chunks:................................................................. >...............................................................Done. > >But the output file is not changed at all. What am I doing wrong? > >Thanks, >Thomas > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From louis.collins at mcgill.ca Fri Mar 24 08:24:47 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Fri, 24 Mar 2006 08:24:47 -0500 Subject: [MINC-users] Z-axis flipping or rotation In-Reply-To: <4422E98B.7070304@bic.mni.mcgill.ca> References: <20060323112306.fza6m7k7jkows0k8@webmail.ualberta.ca> <4422E98B.7070304@bic.mni.mcgill.ca> Message-ID: rotation by 180 degrees might be good, but again might not - this may change left/right in the image. If the data is pointing down, and left is on left, then you'lll need to mirror the image with a negative scale factor on y: param2xfm -scale 1 -1 1 flip.xfm again, you'll have to experiment with the mincresample to get the data in the right place. -Louis On Mar 23, 2006, at 1:31 PM, Jason Lerch wrote: > I think the combination of param2xfm and mincresample is actually what > you want. Run something like the following: > > param2xfm -rotation 0 0 180 rotation.xfm > mincresample -tfm_input_sampling file.mnc -transform rotation.xfm > output.mnc > > You'll have to experiment with getting the right rotations for your > case. > > Jason > > tpb1 at ualberta.ca wrote: > >> I have a brain that is upside down and I need to orient it properly. >> I >> looked in conglomerate and minctools, and it looks like mincreshape >> should do the trick, but when I try: >> mincreshape +zdirection p3.mnc p3_zflip.mnc, the following prints out: >> Copying >> chunks:............................................................... >> .. >> ...............................................................Done. >> >> But the output file is not changed at all. What am I doing wrong? >> >> Thanks, >> Thomas >> >> _______________________________________________ >> 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 mansi at bic.mni.mcgill.ca Wed Mar 29 13:25:57 2006 From: mansi at bic.mni.mcgill.ca (Thomas Mansi) Date: Wed, 29 Mar 2006 20:25:57 +0200 Subject: [MINC-users] Strange problem with mritoself Message-ID: <442AD135.50608@bic.mni.mcgill.ca> Dear all, I'm using mni_autoreg0.98r and I'm having a very strange problem. Maybe you could help me. I want to coregister a T2 axial MRI to a T1 MRI (intrasubject), by doing the following: $ mritoself -lsq9 -mi -far -clobber \ -model icbm_avg_152_t1_tal_lin_symmetric \ -modeldir /usr/local/mni/data/models/ \ -mask target -target_talxfm xfms/patient_t1_to_tal.xfm \ proc/patient_t2ax_clamp.mnc.gz \ proc/patient_t1_clamp.mnc.gz \ xfms/patient_t2ax_to_t1.xfm However, though this command works with our newly acquired (and isotropic) MRI (from the Siemens machine), I get the following error on some older anisotropic images: [mritoself] [mansi at Toshiba:/cygdrive/e/Documents/NOEL/temp/FCD-mspec] [2006-03-28 19:44:45] /usr/local/mni/bin/minctracc -clobber /tmp/mritoself_3804/patient_t2ax_clamp_crop.mnc /tmp/mritoself_3804/patient_t1_clamp_crop.mnc /tmp/mritoself_3804/patient_t2ax_to_t1_tmp1.xfm -est_center -est_translations -lsq9 -mi -groups 256 -threshold 100 0 -model_mask /tmp/mritoself_3804/patient_t1_clamp_mask.mnc -step 7.3 7.3 7.3 -simplex 10 COG of v1: -0.076698 28.486593 23.346405 COG of v2: 0.285103 16.833281 29.833879 [trans] = 0.361800 -11.653313 6.487474 Only center & trans required, now returning from init_transformation slice lim 17 0 row lim 32 0 col lim 32 0 thresh = 100.00000 0.00000 No voxels were found in volume 1 with value above threshold (100.000000). Error in /usr/local/mni/bin/minctracc in file init_lattice.c, line 545 Cannot calculate size of volume 1 .mritoself: crashed while running minctracc (exit status=65280) I don't really understand what's going on here. The source MRI are first nu-corrected using N3 (nu_correct patient_t2ax.mnc patient_t2ax_nuc.mnc) and then clamped (grey level intensities clamped between 0 and 100). Of course, the target T1 MRI has already been coregistered to Talairach space. Minctracc seems to invert the min/max intensity values ... The problem happens on my Cygwin system (laptop with windows XP) but also on Linux and SGI machines. It seems to be related to the input images, since the program works very well with recent volumes and some oldest ones, but fails with others... Did I miss something? Must I upgrade my mni_autoreg? Many thanks in advance for your help! Best regards, Thomas Mansi ___________________________________________________________________________ Nouveau : t?l?phonez moins cher avec Yahoo! Messenger ! D?couvez les tarifs exceptionnels pour appeler la France et l'international. T?l?chargez sur http://fr.messenger.yahoo.com From jason at bic.mni.mcgill.ca Wed Mar 29 14:15:51 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 29 Mar 2006 14:15:51 -0500 Subject: [MINC-users] Strange problem with mritoself In-Reply-To: <442AD135.50608@bic.mni.mcgill.ca> References: <442AD135.50608@bic.mni.mcgill.ca> Message-ID: <442ADCE7.5060300@bic.mni.mcgill.ca> Try either mritoself -nothreshold or mritoself -threshold and rerun it on your old images. Mritoself is dying at the automatic thresholding stage, which is often unnecessary for getting a good fit. Cheers, Jason Thomas Mansi wrote: >Dear all, > >I'm using mni_autoreg0.98r and I'm having a very strange problem. Maybe >you could help me. > >I want to coregister a T2 axial MRI to a T1 MRI (intrasubject), by doing >the following: > >$ mritoself -lsq9 -mi -far -clobber \ >-model icbm_avg_152_t1_tal_lin_symmetric \ >-modeldir /usr/local/mni/data/models/ \ >-mask target -target_talxfm xfms/patient_t1_to_tal.xfm \ >proc/patient_t2ax_clamp.mnc.gz \ >proc/patient_t1_clamp.mnc.gz \ >xfms/patient_t2ax_to_t1.xfm > >However, though this command works with our newly acquired (and >isotropic) MRI (from the Siemens machine), I get the following error on >some older anisotropic images: > >[mritoself] [mansi at Toshiba:/cygdrive/e/Documents/NOEL/temp/FCD-mspec] >[2006-03-28 19:44:45] /usr/local/mni/bin/minctracc -clobber >/tmp/mritoself_3804/patient_t2ax_clamp_crop.mnc >/tmp/mritoself_3804/patient_t1_clamp_crop.mnc >/tmp/mritoself_3804/patient_t2ax_to_t1_tmp1.xfm -est_center >-est_translations -lsq9 -mi -groups 256 -threshold 100 0 -model_mask >/tmp/mritoself_3804/patient_t1_clamp_mask.mnc -step 7.3 7.3 7.3 -simplex 10 >COG of v1: -0.076698 28.486593 23.346405 >COG of v2: 0.285103 16.833281 29.833879 > [trans] = 0.361800 -11.653313 6.487474 >Only center & trans required, now returning from init_transformation >slice lim 17 0 >row lim 32 0 >col lim 32 0 >thresh = 100.00000 0.00000 >No voxels were found in volume 1 with value above threshold (100.000000). >Error in /usr/local/mni/bin/minctracc in file init_lattice.c, line 545 >Cannot calculate size of volume 1 >.mritoself: crashed while running minctracc (exit status=65280) > >I don't really understand what's going on here. The source MRI are first >nu-corrected using N3 (nu_correct patient_t2ax.mnc patient_t2ax_nuc.mnc) >and then clamped (grey level intensities clamped between 0 and 100). Of >course, the target T1 MRI has already been coregistered to Talairach >space. Minctracc seems to invert the min/max intensity values ... > >The problem happens on my Cygwin system (laptop with windows XP) but >also on Linux and SGI machines. It seems to be related to the input >images, since the program works very well with recent volumes and some >oldest ones, but fails with others... Did I miss something? Must I >upgrade my mni_autoreg? > >Many thanks in advance for your help! > >Best regards, >Thomas Mansi > > > > > > >___________________________________________________________________________ >Nouveau : t?l?phonez moins cher avec Yahoo! Messenger ! D?couvez les tarifs exceptionnels pour appeler la France et l'international. >T?l?chargez sur http://fr.messenger.yahoo.com >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From citrog at gmail.com Thu Mar 30 21:00:29 2006 From: citrog at gmail.com (Gil Citro) Date: Thu, 30 Mar 2006 21:00:29 -0500 Subject: [MINC-users] Problem Installing MINC 2.0.09 Message-ID: <9c80f12d0603301800u2762af13ge6f058404e196b57@mail.gmail.com> I'm trying to install MINC 2.0.09 on an AMD64 box running Debian 3.1r0a and am having some trouble. When I run ./configure --enable-64bits it says configure: error: cannot find required library hdf5 and does not generate a Makefile. The config.log is attached. If it try apt-get install hdf5-tools it tells me the most recent version is already installed. Any suggestions would be appreciated. Thanks, Gil From a.janke at gmail.com Thu Mar 30 21:24:02 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 30 Mar 2006 21:24:02 -0500 Subject: [MINC-users] Problem Installing MINC 2.0.09 In-Reply-To: <9c80f12d0603301800u2762af13ge6f058404e196b57@mail.gmail.com> References: <9c80f12d0603301800u2762af13ge6f058404e196b57@mail.gmail.com> Message-ID: Hi Gil, You will also need to install the development hdf package. (hdf5-dev IIRC). a On 3/30/06, Gil Citro wrote: > I'm trying to install MINC 2.0.09 on an AMD64 box running Debian > 3.1r0a and am having some trouble. > > When I run ./configure --enable-64bits it says > > configure: error: cannot find required library hdf5 > > and does not generate a Makefile. The config.log is attached. > > If it try apt-get install hdf5-tools it tells me the most recent > version is already installed. > > Any suggestions would be appreciated. > > Thanks, > Gil > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From ed.gronenschild at mi.unimaas.nl Fri Mar 31 09:58:48 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Fri, 31 Mar 2006 16:58:48 +0200 Subject: [MINC-users] classify - how to? Message-ID: <3680797A-8A3F-4B0A-8D1F-49E60415287C@mi.unimaas.nl> Hi, I want to use classify_clean such that the classified output file does not include the extracranial tissue and the cerebellum. Which options should I use? Ed From jason at bic.mni.mcgill.ca Fri Mar 31 10:44:59 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 31 Mar 2006 10:44:59 -0500 Subject: [MINC-users] classify - how to? In-Reply-To: <3680797A-8A3F-4B0A-8D1F-49E60415287C@mi.unimaas.nl> References: <3680797A-8A3F-4B0A-8D1F-49E60415287C@mi.unimaas.nl> Message-ID: <442D4E7B.9070102@bic.mni.mcgill.ca> Ed Gronenschild wrote: >Hi, > >I want to use classify_clean such that the classified output file >does not include the extracranial tissue and the cerebellum. >Which options should I use? > > There is not option to do this inside classify_clean - you'll need to mask your data either before or after the classification. This can be done using either a manual mask or the cortical_surface or mincbet programs. Cheers, Jason >Ed > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From runa at medphys.ucl.ac.uk Fri Mar 31 15:28:22 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Fri, 31 Mar 2006 21:28:22 +0100 Subject: [MINC-users] INU correction In-Reply-To: <442D4E7B.9070102@bic.mni.mcgill.ca> References: <3680797A-8A3F-4B0A-8D1F-49E60415287C@mi.unimaas.nl> <3680797A-8A3F-4B0A-8D1F-49E60415287C@mi.unimaas.nl> Message-ID: <5.2.0.9.0.20060331212139.036afdd8@pop3-server> Hi, I am using nu_correct command for INU correction on analyze image. but it seems to me that there are some slices the intensity has not been corrected. Can it be happen? the command line I was used: nu_correct -clobber -iterations 100 -stop 2.e-5 t1_in.mnc t1_nu.mnc it is stopped after 16 iteration. Please let me know. Many thanks, Runa At 10:44 31/03/2006 -0500, you wrote: >Ed Gronenschild wrote: > > >Hi, > > > >I want to use classify_clean such that the classified output file > >does not include the extracranial tissue and the cerebellum. > >Which options should I use? > > > > >There is not option to do this inside classify_clean - you'll need to >mask your data either before or after the classification. This can be >done using either a manual mask or the cortical_surface or mincbet programs. > >Cheers, > >Jason > > >Ed > > > >_______________________________________________ > >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 Yours sincerely, Runa From citrog at gmail.com Fri Mar 31 17:32:35 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 17:32:35 -0500 Subject: [MINC-users] Problem compiling ray_trace Message-ID: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> I'm trying to compile ray_trace and it appears to compile, but when I run it I get this error. output_rgb_file(): cannot write image files. Recompile bicpl with an image library, then relink this application. bipcl also is compiled seemingly without errors. Can anyone suggest a fix for this problem? Thanks! Gil Citro From acveilleux at mrs.mni.mcgill.ca Fri Mar 31 17:36:04 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 31 Mar 2006 17:36:04 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>; from citrog@gmail.com on Fri, Mar 31, 2006 at 05:32:35PM -0500 References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> Message-ID: <20060331173604.C667@mrs.mni.mcgill.ca> Are you compiling on SGI? It expects a specific SGI image library when compiling bicpl. Alex On Fri, Mar 31, 2006 at 05:32:35PM -0500, Gil Citro wrote: > Date: Fri, 31 Mar 2006 17:32:35 -0500 > From: "Gil Citro" > To: "MINC Users List" > Subject: [MINC-users] Problem compiling ray_trace > > I'm trying to compile ray_trace and it appears to compile, but when I > run it I get this error. > > output_rgb_file(): cannot write image files. > Recompile bicpl with an image library, then relink this application. > > bipcl also is compiled seemingly without errors. Can anyone suggest a > fix for this problem? Thanks! > > Gil Citro > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From acveilleux at mrs.mni.mcgill.ca Fri Mar 31 17:40:06 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 31 Mar 2006 17:40:06 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>; from citrog@gmail.com on Fri, Mar 31, 2006 at 05:32:35PM -0500 References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> Message-ID: <20060331174006.A17125@mrs.mni.mcgill.ca> You might want to try recompiling bicpl passing --with-image-ppm to configure. Alex On Fri, Mar 31, 2006 at 05:32:35PM -0500, Gil Citro wrote: > Date: Fri, 31 Mar 2006 17:32:35 -0500 > From: "Gil Citro" > To: "MINC Users List" > Subject: [MINC-users] Problem compiling ray_trace > > I'm trying to compile ray_trace and it appears to compile, but when I > run it I get this error. > > output_rgb_file(): cannot write image files. > Recompile bicpl with an image library, then relink this application. > > bipcl also is compiled seemingly without errors. Can anyone suggest a > fix for this problem? Thanks! > > Gil Citro > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From citrog at gmail.com Fri Mar 31 18:05:54 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 18:05:54 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <20060331174006.A17125@mrs.mni.mcgill.ca> References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> <20060331174006.A17125@mrs.mni.mcgill.ca> Message-ID: <9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com> I'm compiling under Debian 3.1r0a for AMD64, but it was a network install and some things might be missing. Is there something I could try to apt-get? I tried passing -with-image-ppm to configure, and it terminated saying configure: error: cannot find required header Thanks, Gil On 3/31/06, Alexandre CARMEL-VEILLEUX wrote: > Are you compiling on SGI? It expects a specific SGI image library > when compiling bicpl. > You might want to try recompiling bicpl passing --with-image-ppm to > configure. > From acveilleux at mrs.mni.mcgill.ca Fri Mar 31 18:11:31 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 31 Mar 2006 18:11:31 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com>; from citrog@gmail.com on Fri, Mar 31, 2006 at 06:05:54PM -0500 References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> <20060331174006.A17125@mrs.mni.mcgill.ca> <9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com> Message-ID: <20060331181131.A17807@mrs.mni.mcgill.ca> libppm is provided by the netpbnm and netpbm=dev packages, I belive. Alex On Fri, Mar 31, 2006 at 06:05:54PM -0500, Gil Citro wrote: > Date: Fri, 31 Mar 2006 18:05:54 -0500 > From: "Gil Citro" > To: "MINC users mailing list" > Subject: Re: [MINC-users] Problem compiling ray_trace > > I'm compiling under Debian 3.1r0a for AMD64, but it was a network > install and some things might be missing. Is there something I could > try to apt-get? > > I tried passing -with-image-ppm to configure, and it terminated saying > > configure: error: cannot find required header > > Thanks, > Gil > > On 3/31/06, Alexandre CARMEL-VEILLEUX wrote: > > > Are you compiling on SGI? It expects a specific SGI image library > > when compiling bicpl. > > > You might want to try recompiling bicpl passing --with-image-ppm to > > configure. > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From citrog at gmail.com Fri Mar 31 18:13:01 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 18:13:01 -0500 Subject: [MINC-users] Problem compiling xdisp-4.5 Message-ID: <9c80f12d0603311513g2637cfebqaa80ed24825b7321@mail.gmail.com> Sorry for the multiple posts for help, I've mostly compiled all the MNI software, but am having trouble with just a few packages. When I try to make xdisp-4.5 I get an error about a missing EZ.h header. I've tried searching to see what package provides that header and I've tried apt-cache search ez and I've installed everything that looked remotely relevant, but make still can't find the EZ.h header. Does anyone know where I should look for it? This is Debian 3.1r0a on AMD64. Thanks. Gil make all-recursive make[1]: Entering directory `/usr/local/mni/xdisp-4.5' Making all in olgx make[2]: Entering directory `/usr/local/mni/xdisp-4.5/olgx' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/usr/local/mni/xdisp-4.5/olgx' make[2]: Entering directory `/usr/local/mni/xdisp-4.5' if gcc -DHAVE_CONFIG_H -I. -I. -I. -Iolgx -IEZWGL-1.50/include -I/usr/X11R6/include -g -O2 -MT xdisp-xdisp.o -MD -MP -MF ".deps/xdisp-xdisp.Tpo" -c -o xdisp-xdisp.o `test -f 'xdisp.c' || echo './'`xdisp.c; \ then mv -f ".deps/xdisp-xdisp.Tpo" ".deps/xdisp-xdisp.Po"; else rm -f ".deps/xdisp-xdisp.Tpo"; exit 1; fi In file included from xdisp.c:16: xdisp.h:75:16: EZ.h: No such file or directory In file included from xdisp.c:16: xdisp.h:120: error: syntax error before '*' token xdisp.h:127: warning: data definition has no type or storage class xdisp.c: In function `main': xdisp.c:382: warning: assignment makes pointer from integer without a cast make[2]: *** [xdisp-xdisp.o] Error 1 make[2]: Leaving directory `/usr/local/mni/xdisp-4.5' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/mni/xdisp-4.5' make: *** [all] Error 2 From acveilleux at mrs.mni.mcgill.ca Fri Mar 31 18:16:15 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 31 Mar 2006 18:16:15 -0500 Subject: [MINC-users] Problem compiling xdisp-4.5 In-Reply-To: <9c80f12d0603311513g2637cfebqaa80ed24825b7321@mail.gmail.com>; from citrog@gmail.com on Fri, Mar 31, 2006 at 06:13:01PM -0500 References: <9c80f12d0603311513g2637cfebqaa80ed24825b7321@mail.gmail.com> Message-ID: <20060331181615.B17807@mrs.mni.mcgill.ca> Download ftp://ftp.ma.utexas.edu/pub/mzou/EZWGL-1.50-src.tar.gz Unpack it in the xdisp directory. Compile it. Compile xdisp. Alex On Fri, Mar 31, 2006 at 06:13:01PM -0500, Gil Citro wrote: > Date: Fri, 31 Mar 2006 18:13:01 -0500 > From: "Gil Citro" > To: "MINC Users List" > Subject: [MINC-users] Problem compiling xdisp-4.5 > > Sorry for the multiple posts for help, I've mostly compiled all the > MNI software, but am having trouble with just a few packages. When I > try to make xdisp-4.5 I get an error about a missing EZ.h header. > I've tried searching to see what package provides that header and I've > tried apt-cache search ez and I've installed everything that looked > remotely relevant, but make still can't find the EZ.h header. Does > anyone know where I should look for it? This is Debian 3.1r0a on > AMD64. Thanks. > > Gil > > make all-recursive > make[1]: Entering directory `/usr/local/mni/xdisp-4.5' > Making all in olgx > make[2]: Entering directory `/usr/local/mni/xdisp-4.5/olgx' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory `/usr/local/mni/xdisp-4.5/olgx' > make[2]: Entering directory `/usr/local/mni/xdisp-4.5' > if gcc -DHAVE_CONFIG_H -I. -I. -I. -Iolgx -IEZWGL-1.50/include > -I/usr/X11R6/include -g -O2 -MT xdisp-xdisp.o -MD -MP -MF > ".deps/xdisp-xdisp.Tpo" -c -o xdisp-xdisp.o `test -f 'xdisp.c' || echo > './'`xdisp.c; \ > then mv -f ".deps/xdisp-xdisp.Tpo" ".deps/xdisp-xdisp.Po"; else rm -f > ".deps/xdisp-xdisp.Tpo"; exit 1; fi > In file included from xdisp.c:16: > xdisp.h:75:16: EZ.h: No such file or directory > In file included from xdisp.c:16: > xdisp.h:120: error: syntax error before '*' token > xdisp.h:127: warning: data definition has no type or storage class > xdisp.c: In function `main': > xdisp.c:382: warning: assignment makes pointer from integer without a cast > make[2]: *** [xdisp-xdisp.o] Error 1 > make[2]: Leaving directory `/usr/local/mni/xdisp-4.5' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/mni/xdisp-4.5' > make: *** [all] Error 2 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From citrog at gmail.com Fri Mar 31 18:29:59 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 18:29:59 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <20060331181131.A17807@mrs.mni.mcgill.ca> References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> <20060331174006.A17125@mrs.mni.mcgill.ca> <9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com> <20060331181131.A17807@mrs.mni.mcgill.ca> Message-ID: <9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com> On 3/31/06, Alexandre CARMEL-VEILLEUX wrote: > libppm is provided by the netpbnm and netpbm=dev packages, > I belive. > > Alex > netpbm is the newest version. netpbm-dev is a virtual package, and libnetpbm10-dev is installed to provude it. When I pass --with-image-ppm to configure when compiling bicpl-1.4.2 is still says From citrog at gmail.com Fri Mar 31 18:50:12 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 18:50:12 -0500 Subject: [MINC-users] Problem compiling ray_trace In-Reply-To: <9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com> References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com> <20060331174006.A17125@mrs.mni.mcgill.ca> <9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com> <20060331181131.A17807@mrs.mni.mcgill.ca> <9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com> Message-ID: <9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com> (Sorry for the last message, I sent too soon) On 3/31/06, Alexandre CARMEL-VEILLEUX wrote: > > libppm is provided by the netpbnm and netpbm=dev packages, > > I belive. > > > > Alex > > > netpbm is the newest version. netpbm-dev is a virtual package, and libnetpbm10-dev is installed to provude it. When I pass --with-image-ppm to configure when compiling bicpl-1.4.2 is still says configure: error: cannot find required header, but if I pass --with-image-netpbm it configures and compiles without error. However, when I then try to configure and compile ray_trace it configures without error but gives the following error when being compiled undefined reference to `ppm_writeppminit` (see below) If I compile bicpl without --with-image-netpbm I don't get this error when compiling ray_trace, but then I have the original problem I reported. It looks to me like I'm missing some libraries having to do with pixmaps, so I did apt-cache search pixmap, and apt-get install for the packages below, but no change. libgd-gd2-perl libgd2-xpm libgd2-xpm-dev libgdchart-gd2-xpm libgdchart-gd2-xpm-dev libgd-tools libxpm-dev libxpm4 libxpm4-dbg Compiling bicpl with --with-image-ppm goves the same error, and --with-image-netpbm gives no error until I compile ray_trace. Thanks for all the help so far. If anyone has any other ideas I'd greatly appreciate it. Gil make all-recursive make[1]: Entering directory `/usr/local/mni/ray_trace-1.0' Making all in Graphics make[2]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics' Making all in GLUT_windows make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics/GLUT_windows'make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics/GLUT_windows' Making all in G_graphics make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics/G_graphics' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics/G_graphics' Making all in OpenGL_graphics make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics/OpenGL_graphics' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics/OpenGL_graphics' make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics' make[2]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics' make[2]: Entering directory `/usr/local/mni/ray_trace-1.0' /bin/sh ./libtool --mode=link gcc -g -O2 -o ray_trace ray_trace.o intersect.o trace.o volume.o Graphics/libbicgl.a -lbicpl -lvolume_io -lminc -lnetcdf -lm mkdir .libs gcc -g -O2 -o ray_trace ray_trace.o intersect.o trace.o volume.o Graphics/libbicgl.a -lbicpl /usr/lib/libvolume_io.so /usr/lib/libminc.so -lnetcdf -lm /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x3e): In function `input_rgb_file': /usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:31: undefined reference to `ppm_readppminit' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x4b):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:33: undefined reference to `pm_allocrow' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xa2):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:46: undefined reference to `ppm_readppmrow' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xb6):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:56: undefined reference to `pm_freerow' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1c3): In function `output_rgb_file':/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:97: undefined reference to `ppm_writeppminit' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1d1):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:100: undefined reference to `pm_allocrow' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x20c):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:118: undefined reference to `ppm_writeppmrow' /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x219):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:121: undefined reference to `pm_freerow' collect2: ld returned 1 exit status make[2]: *** [ray_trace] Error 1 make[2]: Leaving directory `/usr/local/mni/ray_trace-1.0' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/mni/ray_trace-1.0' make: *** [all] Error 2 From citrog at gmail.com Fri Mar 31 19:17:01 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 19:17:01 -0500 Subject: [MINC-users] Problem Installing MINC 2.0.09 In-Reply-To: References: <9c80f12d0603301800u2762af13ge6f058404e196b57@mail.gmail.com> Message-ID: <9c80f12d0603311617g236c262ay49bbfc037a3a4517@mail.gmail.com> Thanks. apt-get install hdf5-serial-dev fixed it. Gil On 3/30/06, Andrew Janke wrote: > Hi Gil, > > You will also need to install the development hdf package. (hdf5-dev IIRC). > > a > > > On 3/30/06, Gil Citro wrote: > > I'm trying to install MINC 2.0.09 on an AMD64 box running Debian > > 3.1r0a and am having some trouble. > > > > When I run ./configure --enable-64bits it says > > > > configure: error: cannot find required library hdf5 > > > > and does not generate a Makefile. The config.log is attached. > > > > If it try apt-get install hdf5-tools it tells me the most recent > > version is already installed. > > > > Any suggestions would be appreciated. > > > > Thanks, > > Gil > > From citrog at gmail.com Fri Mar 31 21:18:18 2006 From: citrog at gmail.com (Gil Citro) Date: Fri, 31 Mar 2006 21:18:18 -0500 Subject: [MINC-users] Problem compiling xdisp-4.5 In-Reply-To: <20060331181615.B17807@mrs.mni.mcgill.ca> References: <9c80f12d0603311513g2637cfebqaa80ed24825b7321@mail.gmail.com> <20060331181615.B17807@mrs.mni.mcgill.ca> Message-ID: <9c80f12d0603311818i4ef56037nced9205a37461af0@mail.gmail.com> Thanks! In case anyone else searches the list in the future with this problem, the solution below worked for me. When compiling EZWGT, I needed to make static and then make install-static rather than make shared and make install-shared. Thanks again for the help! Gil On 3/31/06, Alexandre CARMEL-VEILLEUX wrote: > Download ftp://ftp.ma.utexas.edu/pub/mzou/EZWGL-1.50-src.tar.gz > Unpack it in the xdisp directory. > Compile it. > Compile xdisp. > > Alex > > On Fri, Mar 31, 2006 at 06:13:01PM -0500, Gil Citro wrote: > > Date: Fri, 31 Mar 2006 18:13:01 -0500 > > From: "Gil Citro" > > To: "MINC Users List" > > Subject: [MINC-users] Problem compiling xdisp-4.5 > > > > Sorry for the multiple posts for help, I've mostly compiled all the > > MNI software, but am having trouble with just a few packages. When I > > try to make xdisp-4.5 I get an error about a missing EZ.h header. > > I've tried searching to see what package provides that header and I've > > tried apt-cache search ez and I've installed everything that looked > > remotely relevant, but make still can't find the EZ.h header. Does > > anyone know where I should look for it? This is Debian 3.1r0a on > > AMD64. Thanks. > > > > Gil > > > > make all-recursive > > make[1]: Entering directory `/usr/local/mni/xdisp-4.5' > > Making all in olgx > > make[2]: Entering directory `/usr/local/mni/xdisp-4.5/olgx' > > make[2]: Nothing to be done for `all'. > > make[2]: Leaving directory `/usr/local/mni/xdisp-4.5/olgx' > > make[2]: Entering directory `/usr/local/mni/xdisp-4.5' > > if gcc -DHAVE_CONFIG_H -I. -I. -I. -Iolgx -IEZWGL-1.50/include > > -I/usr/X11R6/include -g -O2 -MT xdisp-xdisp.o -MD -MP -MF > > ".deps/xdisp-xdisp.Tpo" -c -o xdisp-xdisp.o `test -f 'xdisp.c' || echo > > './'`xdisp.c; \ > > then mv -f ".deps/xdisp-xdisp.Tpo" ".deps/xdisp-xdisp.Po"; else rm -f > > ".deps/xdisp-xdisp.Tpo"; exit 1; fi > > In file included from xdisp.c:16: > > xdisp.h:75:16: EZ.h: No such file or directory > > In file included from xdisp.c:16: > > xdisp.h:120: error: syntax error before '*' token > > xdisp.h:127: warning: data definition has no type or storage class > > xdisp.c: In function `main': > > xdisp.c:382: warning: assignment makes pointer from integer without a cast > > make[2]: *** [xdisp-xdisp.o] Error 1 > > make[2]: Leaving directory `/usr/local/mni/xdisp-4.5' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/usr/local/mni/xdisp-4.5' > > make: *** [all] Error 2 > > From dwagne at bic.mni.mcgill.ca Fri Mar 31 22:23:46 2006 From: dwagne at bic.mni.mcgill.ca (Dylan David Wagner) Date: Fri, 31 Mar 2006 22:23:46 -0500 Subject: [MINC-users] distorted tal transformations with 3T data. Message-ID: <442DF242.7060500@bic.mni.mcgill.ca> Hey Minc Users, I've got 100+ mprage 3D MRIs from a Philips 3T scanner, all acquired with identical sequences. I'm attempting to transform them into tal space, but am finding the transformation is distorted for some, but not all, of the images. I've included an anonymyzed dataset on scratch1 (ddw_talsucks) in case anyone wants to poke around. The data were originally in analyze and were converted to minc using nii2mnc. To rule out conversion issues, I went back to the raw dicoms and converted some direct to afni and from there to minc using 3dAFNItoMINC (we don't have a direct dicom 2 minc script here). That didn't help. About 1/3rd of my images (30 out of 110) will not properly convert to tal space, checking both the original analyze header and the new minc header shows no difference in number of slices, step sizes etc. I even double checked the scanning protocols at the scanner and everyone is identical. The *only* difference I can find between files that work and those that don't, is that the working files have an intensity gradient (brighter in the middle) while the non-working files are more uniform. I know, you would expect it to be the other way around, but it's not. The range of intensities is pretty variable across all these files. Tried clamping some of the files with mincmath (0-300) before running mritotal, but that didn't help much. Nu_correct before mritotal on the bad files seems to help a little, but the output is still distorted. The dataset on scratch1 includes 2 "bad" files and 2 "good" files. You can see for yourself that the overall characterisitcs of the images are identical. But check out the resulting bad*_tal.mnc for some wild distortion! 2 more things: we're using a SENSE coil to speed up acquisition, I'm asking around to see if a bad sense reference scan could be causing the variability between "bad" and "good" mris. And secondly, all these images normalize without fail and without distortion in SPM2. Thanks, DDW