From sylvain at bic.mni.mcgill.ca Tue Sep 2 08:48:16 2008 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 2 Sep 2008 08:48:16 -0400 (EDT) Subject: [MINC-users] get_meansd_voi In-Reply-To: References: Message-ID: get_meansd_voi is part of 'dot' which has not yet been released for linux and for which there is no ETA. It has dependencies on some of dot's custom libraries and is written in perl so you could hack your way into building your own by removing the dependencies - login to yorick. S On Thu, 28 Aug 2008, Marc BOUFFARD wrote: > Hello, where can I get an executable for get_meansd_voi? I would like to > use it to extract some values using a Linux system. > > Marc > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.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 212 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 A.T.Reid at science.ru.nl Tue Sep 2 11:20:49 2008 From: A.T.Reid at science.ru.nl (Andrew Reid) Date: Tue, 02 Sep 2008 17:20:49 +0200 Subject: [MINC-users] Estimating tissue volume from PVEs Message-ID: <48BD59D1.5030707@science.ru.nl> Hello, I want to get an estimate of tissue volume from the PVE volumes in my minc directories. As far as I can tell, this requires that I: 1. Mask with the brain mask (using Perl): $mask = $subject_dir."/".$sname."/mask/".$prefix.$sname."_brain_mask.mnc"; `mincmath -mult ${volume} ${mask} ${temp_vol}`; 2. Resample with the inverse of the linear talairach transform: $transform = $subject_dir."/".$sname."/transforms/linear/".$prefix.$sname."_t1_tal.xfm"; `mincresample -transformation ${transform} -tfm_input_sampling -invert_transformation ${temp_vol} ${temp_trans}`; 3. Calculate tissue volumes. For this I bin the volume into ranges of size 0.1, and multiply the resulting sum by the mid-point of the bin, adding two bins for [0:0.01] = 0 and [0.99:1] = 1. Then I sum the resulting values. `mincstats -volume -quiet -range 0.0,0.01,0.01,0.1,0.1,0.2,0.2,0.3,0.3,0.4,0.4,0.5,0.5,0.6,0.6,0.7,0.7,0.8,0.8,0.9,0.9,0.99,0.99,1.0 ${temp_trans} | tee ${temp_file}`; My questions are: 1. Is this the correct way to apply the inverse transform? I get a weird result in that the mean native GM volume actually decreases with respect to that obtained from the original volumes in talairach space, but the mean native WM and CSF volumes increase. This is confusing, given that it is a linear transform, which I believe should deform in a globally proportional way. 2. Is there a better (more continuous) way to calculate volume than my step #3? The binning method essentially smooths the data, instead of simply summing the PVE values from all voxels. Thanks! -- Andrew Reid Department of Cognitive Neuroscience Radboud University Nijmegen Medical Centre Postbus 9101, 6500 HB Nijmegen The Netherlands phone +31 24 3666171 web www.neuropi.org From a.janke at gmail.com Tue Sep 2 19:34:37 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 3 Sep 2008 09:34:37 +1000 Subject: [MINC-users] Estimating tissue volume from PVEs In-Reply-To: <48BD59D1.5030707@science.ru.nl> References: <48BD59D1.5030707@science.ru.nl> Message-ID: Hi Andrew, 2008/9/3 Andrew Reid : > I want to get an estimate of tissue volume from the PVE volumes in my > minc directories. As far as I can tell, this requires that I: > > 1. Mask with the brain mask (using Perl): > $mask = $subject_dir."/".$sname."/mask/".$prefix.$sname."_brain_mask.mnc"; > `mincmath -mult ${volume} ${mask} ${temp_vol}`; > > 2. Resample with the inverse of the linear talairach transform: > $transform = > $subject_dir."/".$sname."/transforms/linear/".$prefix.$sname."_t1_tal.xfm"; > `mincresample -transformation ${transform} -tfm_input_sampling > -invert_transformation ${temp_vol} ${temp_trans}`; > > 3. Calculate tissue volumes. For this I bin the volume into ranges of > size 0.1, and multiply the resulting sum by the mid-point of the bin, > adding two bins for [0:0.01] = 0 and [0.99:1] = 1. Then I sum the > resulting values. > > My questions are: > 1. Is this the correct way to apply the inverse transform? Yes, as far as I can see. > I get a weird > result in that the mean native GM volume actually decreases with respect > to that obtained from the original volumes in talairach space, but the > mean native WM and CSF volumes increase. This is confusing, given that > it is a linear transform, which I believe should deform in a globally > proportional way. That is correct, it should be proportional. perhaps there is something else askew further down the track in the volume calculations. > 2. Is there a better (more continuous) way to calculate volume than my > step #3? The binning method essentially smooths the data, instead of > simply summing the PVE values from all voxels. Hrm, If I can grok what you are doing correctly why not just this? minccalc -expression "(A[0] < 0.01) ? 0 : ((A[0] > 0.99) ? 1 : A[0])" ${temp_trans} ${temp_trans}.clamped mincstats -sum ${temp_trans}.clamped At which stage you will have to multiply the result of the mincstats call by the volume of a single voxel and possibly include a mask if you want the volume of a particular chunk and/or your ${temp_trans} is not a single structure already. -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From Michel.Audette at medizin.uni-leipzig.de Thu Sep 18 06:23:04 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 18 Sep 2008 12:23:04 +0200 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows Message-ID: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Hi all, I'm seeing some Windows MS VC++ 2003 compilation errors related to enums in volume_io/basic.h and multidim.h . Please forgive the German, and go by the error code. This seems to be related to keywords that are redefined or reused in enums. G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\multidim.h(44): error C2365: 'DOUBLE': Erneute Definition; vorherige Definition war 'Typedef' C:\Programme\Microsoft Visual Studio .NET 2003\Vc7\PlatformSDK\Include\WTypes.h(387): Siehe Deklaration von 'DOUBLE' G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\basic.h(66): error C2143: Syntaxfehler: Es fehlt ';' vor 'constant' (this is related to the use of the word ERROR in an enum) Is there a release that deals with errors like this, or a workaround? Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From a.janke at gmail.com Thu Sep 18 20:37:41 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 18 Sep 2008 17:37:41 -0700 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: Hrm, I thought we had made all such things private now. The plan was to add a VIO_ prefix to all such things. There is a #define that turns this 'on' but I am currently mobile so can't dig it up. Here's hoping someone else will chime in with it. a On 9/18/08, Audette, Michel wrote: > Hi all, > > > > I'm seeing some Windows MS VC++ 2003 compilation errors related to enums in > volume_io/basic.h and multidim.h . > > > > Please forgive the German, and go by the error code. This seems to be > related to keywords that are redefined or reused in enums. > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\multidim.h(44): > error C2365: 'DOUBLE': Erneute Definition; vorherige Definition war > 'Typedef' > > C:\Programme\Microsoft Visual Studio .NET > 2003\Vc7\PlatformSDK\Include\WTypes.h(387): Siehe Deklaration von 'DOUBLE' > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\basic.h(66): > error C2143: Syntaxfehler: Es fehlt ';' vor 'constant' > > (this is related to the use of the word ERROR in an enum) > > > > Is there a release that deals with errors like this, or a workaround? > > > > Best wishes, > > > > Michel > > > > Michel Audette, Ph.D. > > Innovation Center Computer Assisted Surgery (ICCAS) > > Semmelweisstra?e 14 > > Leipzig, Germany > > Phone: ++49 (0) 341 / 97 - 1 20 13 > > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Thu Sep 18 21:20:42 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 18 Sep 2008 18:20:42 -0700 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: > There is a #define that turns this 'on' but I am currently mobile so > can't dig it up. Found it. Check that "VIO_PREFIX_NAMES" is defined as 1. If it is then we have some work to do.. :) -- Andrew Janke(a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sylvain at bic.mni.mcgill.ca Fri Sep 19 08:52:05 2008 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Fri, 19 Sep 2008 08:52:05 -0400 (EDT) Subject: [MINC-users] PET CT registration ... Message-ID: Hello, I've had a request from a researcher who would like to scan a patient at our (PET) facilities but this patient cannot have a MRI (he has a clip) - hence he would have a CT (at the MNI presumably or from another facility) a few questions ... Has anyone out there converted CT to minc ? I've never worked or played with CT images before but chances are that some of our in house Dicom-to-minc converters could do the work. Has anyone done PET transmission to CT registration ? thanks in advance, S --- 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 212 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 Jean-Francois.Malouin at bic.mni.mcgill.ca Fri Sep 19 13:37:19 2008 From: Jean-Francois.Malouin at bic.mni.mcgill.ca (Jean-Francois Malouin) Date: Fri, 19 Sep 2008 13:37:19 -0400 Subject: [MINC-users] nu_correct In-Reply-To: References: Message-ID: <20080919173719.GB292866@yorick.bic.mni.mcgill.ca> Help this soul please. jf * Matthew Perry [20080919 13:34]: > *Hi, > > I was hoping you could help me with a problem I've been having with > nu_correct. I have been trying to use nu_correct and the rawtominc for > inhomogeneity correction in my spgr images. The rawtominc conversion comes > out fine since I have been able to confirm the results in the minc display. > > However, when I try to run nu_correct on the now mnc format spgr, it keeps > on giving me an error message. I included the call to nu_correct (in red) > that I used as well as the error message (in blue) that I received after > running it. > > > > > > $ nu_correct -clobber -V1.0 TACO_work.mnc TACO_workout.mnc > Processing:...........................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > function: field_CV() > Field standard deviation not defined > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=65280) > > > Thank you, > Matt* -- < From claude at bic.mni.mcgill.ca Fri Sep 19 13:46:44 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Fri, 19 Sep 2008 13:46:44 -0400 (EDT) Subject: [MINC-users] nu_correct References: Message-ID: <200809191746.m8JHkiiP293635@yorick.bic.mni.mcgill.ca> Hi Matt, It is very difficult to guess the cause of the error. The easiest way would be to place the mnc file on your home page where I can retrieve it so that I can try to reproduce the error here. Hopefully, this is not sensitive data. If you cannot provide data for testing, then try to do a mincstats, mincinfo on the image and send it to me directly. Also indicate on which platform you are running nu_correct. Linux, OS-X, other? version of o/s? Claude > > > > $ nu_correct -clobber -V1.0 TACO_work.mnc TACO_workout.mnc > > Processing:...........................................Done > > Not implemented yet in cache_volume_range_has_changed() > > Not implemented yet in cache_volume_range_has_changed() > > function: field_CV() > > Field standard deviation not defined > > nu_correct: crashed while running nu_estimate_np_and_em (termination > > status=65280) > > > > > > Thank you, > > Matt* > > -- > < > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From mok at bic.mni.mcgill.ca Fri Sep 19 15:57:00 2008 From: mok at bic.mni.mcgill.ca (Kelvin Mok) Date: Fri, 19 Sep 2008 15:57:00 -0400 Subject: [MINC-users] Display and slice plane rendering In-Reply-To: References: Message-ID: <48D4040C.9040901@bic.mni.mcgill.ca> Hi, Revisiting an old topic, Display. I'm having trouble when trying to render a 3D slice into the object window. When I choose the desired plane, then press SliceView(S)/CreateSlice(A)/ToggleSliceVisible(T), the slice fails to appear in the object window. I am able to render the slice into the fourth panel of the 3D window without problem, but I would like to have it in the object window from which I can superimpose onto other objects. If I recall correctly, this can be done. Am I missing something? Thanks in advance, Kelvin Andrew Janke wrote: > Hi Soren, > > Not sure if anyone posted a reply to this so here is how I do this > (when I have to) Display does not have the best documentation! > > First place the cross hairs in the 3D view on a place that you want in > your oblique view. then.. > > 1. Press 's' for Slice View > > 2. Press 'r' to make sure things are visible > > 3. Press 'e' (Pick slice Angle). > > Then click somewhere else in the image that you want in your oblique > view. after a few hacks at this (#3 only) you will get the hang of > it. > > > a > > On 9/10/07, Soren Christensen wrote: > >> Hi, >> I am trying to create a 3D sliceplane rendering from an arbitrary >> slice plane but have problems doing this in Display. >> I: >> 1) turn on the "fourth window" in Display (S-S) >> 2) Toggle on the cut plane in the 3D window (S-Q) and orient it as I want. >> 3) Try to do S-A from the fourth window in order to render the >> arbitrary slice-cut to the 3D window. >> >> Step 3 is where I have the problem. I cannot render the arbitrary >> slice-cut to the 3D window. The other standard view planes render >> fine. >> >> If this functionality is not available using the approach above, is >> there pherhaps another way to achieve it? eg. resampling volume >> differently or so? >> >> Thanks >> Soren >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> > > > -- ----------------------------------------------------------------- Kelvin Mok (mok at bic.mni.mcgill.ca) McConnell Brain Imaging Centre - Montreal Neurological Institute 514-398-6447 ____________________________________________________________________ From mok at bic.mni.mcgill.ca Fri Sep 19 16:54:22 2008 From: mok at bic.mni.mcgill.ca (Kelvin Mok) Date: Fri, 19 Sep 2008 16:54:22 -0400 Subject: [MINC-users] Display and slice plane rendering Message-ID: Hi, Revisiting an old topic, Display. I'm having trouble when trying to render a 3D slice into the object window. When I choose the desired plane, then press SliceView(S)/CreateSlice(A)/ToggleSliceVisible(T), the slice fails to appear in the object window. I am able to render the slice into the fourth panel of the 3D window without problem, but I would like to have it in the object window from which I can superimpose onto other objects. If I recall correctly, this can be done. Am I missing something? Thanks in advance, Kelvin Andrew Janke wrote: > Hi Soren, > > Not sure if anyone posted a reply to this so here is how I do this > (when I have to) Display does not have the best documentation! > > First place the cross hairs in the 3D view on a place that you want in > your oblique view. then.. > > 1. Press 's' for Slice View > > 2. Press 'r' to make sure things are visible > > 3. Press 'e' (Pick slice Angle). > > Then click somewhere else in the image that you want in your oblique > view. after a few hacks at this (#3 only) you will get the hang of > it. > > > a > > On 9/10/07, Soren Christensen wrote: > >> Hi, >> I am trying to create a 3D sliceplane rendering from an arbitrary >> slice plane but have problems doing this in Display. >> I: >> 1) turn on the "fourth window" in Display (S-S) >> 2) Toggle on the cut plane in the 3D window (S-Q) and orient it as I want. >> 3) Try to do S-A from the fourth window in order to render the >> arbitrary slice-cut to the 3D window. >> >> Step 3 is where I have the problem. I cannot render the arbitrary >> slice-cut to the 3D window. The other standard view planes render >> fine. >> >> If this functionality is not available using the approach above, is >> there pherhaps another way to achieve it? eg. resampling volume >> differently or so? >> >> Thanks >> Soren >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> > > > From steve at sumost.ca Mon Sep 22 03:17:22 2008 From: steve at sumost.ca (Steven Robbins) Date: Mon, 22 Sep 2008 02:17:22 -0500 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: <20080922071722.GB25520@sumost.ca> On Thu, Sep 18, 2008 at 06:20:42PM -0700, Andrew Janke wrote: > > There is a #define that turns this 'on' but I am currently mobile so > > can't dig it up. > > Found it. > > Check that "VIO_PREFIX_NAMES" is defined as 1. > > If it is then we have some work to do.. :) It's not going to help. The offending code (below, from basic.h) is NOT conditional on VIO_PREFIX_NAMES. typedef enum { OK, ERROR, INTERNAL_ERROR, END_OF_FILE, QUIT } VIO_Status; The enum VIO_Data_types in multidim.h, which has the offending enum value "DOUBLE", is similar. In the past, I've worked around this kind of problem by partitioning my code so that a given file never needs to include conflicting headers. Some things to try: * Move includes from the .h file into the .c file. * If you need a type in the .h that is only passed around by pointers, you can use a forward declaration to avoid #including the header defining it. * Creating a type that encapsulates the volume_io type can help achieve the first two points. Cheers, -Steve From Michel.Audette at medizin.uni-leipzig.de Mon Sep 22 03:37:14 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Mon, 22 Sep 2008 09:37:14 +0200 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E69024252F8@MRZS152229.medizin.uni-leipzig.de> Hi Andrew, you were right about this #define. I had it set to 0. Hopefully everything compiles (under way). I suspect that it would be set to 1 by default by now. Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke Sent: September 19, 2008 2:38 AM To: MINC users mailing list Subject: Re: [MINC-users] redefinitions in volume_io/basic.h,multidim.h causing compilation errors on Windows Hrm, I thought we had made all such things private now. The plan was to add a VIO_ prefix to all such things. There is a #define that turns this 'on' but I am currently mobile so can't dig it up. Here's hoping someone else will chime in with it. a On 9/18/08, Audette, Michel wrote: > Hi all, > > > > I'm seeing some Windows MS VC++ 2003 compilation errors related to enums in > volume_io/basic.h and multidim.h . > > > > Please forgive the German, and go by the error code. This seems to be > related to keywords that are redefined or reused in enums. > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\multidim.h(44): > error C2365: 'DOUBLE': Erneute Definition; vorherige Definition war > 'Typedef' > > C:\Programme\Microsoft Visual Studio .NET > 2003\Vc7\PlatformSDK\Include\WTypes.h(387): Siehe Deklaration von 'DOUBLE' > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\basic.h(66): > error C2143: Syntaxfehler: Es fehlt ';' vor 'constant' > > (this is related to the use of the word ERROR in an enum) > > > > Is there a release that deals with errors like this, or a workaround? > > > > Best wishes, > > > > Michel > > > > Michel Audette, Ph.D. > > Innovation Center Computer Assisted Surgery (ICCAS) > > Semmelweisstra?e 14 > > Leipzig, Germany > > Phone: ++49 (0) 341 / 97 - 1 20 13 > > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From Michel.Audette at medizin.uni-leipzig.de Mon Sep 22 05:09:04 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Mon, 22 Sep 2008 11:09:04 +0200 Subject: [MINC-users] PET CT registration ... In-Reply-To: References: Message-ID: <160E3DD4FB702C4CB860C65186686E6902425303@MRZS152229.medizin.uni-leipzig.de> Sylvain, I've worked with CT images in minc format. I'm pretty sure that dicom3_to_minc worked robustly, but I have not tried dcm2mnc recently with these data sets. I have not worked with PET however. Not sure if this helps in any way. Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Sylvain Milot Sent: September 19, 2008 2:52 PM To: minc-users at bic.mni.mcgill.ca Subject: [MINC-users] PET CT registration ... Hello, I've had a request from a researcher who would like to scan a patient at our (PET) facilities but this patient cannot have a MRI (he has a clip) - hence he would have a CT (at the MNI presumably or from another facility) a few questions ... Has anyone out there converted CT to minc ? I've never worked or played with CT images before but chances are that some of our in house Dicom-to-minc converters could do the work. Has anyone done PET transmission to CT registration ? thanks in advance, S --- 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 212 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 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From rupe.brooks at gmail.com Mon Sep 22 07:56:09 2008 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Mon, 22 Sep 2008 07:56:09 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: hi Michel, Are you actually rebuilding the MINC library under windows? As I'm sure you know, I managed to build it natively under windows but with a certain amout of pain. It sounds like you got past this specific problem, but if others are interested maybe its time to re-discuss building MINC on windows. It would be great to have the support integrated right in the source, with minimal pain necessary. So far, my experience was that to build it natively, i had to make minor mods to hdf_convenience.c to adhere to ANSI c, standards (variable declarations), and i forcibly removed the dll_exports and built it statically. I got minc2 and volume_io to build, and more than half of the minc tools. However, those that require flex/bison, and the conversion build tree I was never successful with. Of course, one can build it under cygwin, but this has the disadvantage of requiring cygwin, and requiring anything else built against it to also use cygwin. Rupert On Thu, Sep 18, 2008 at 6:23 AM, Audette, Michel wrote: > Hi all, > > > > I'm seeing some Windows MS VC++ 2003 compilation errors related to enums in volume_io/basic.h and multidim.h . > > > > Please forgive the German, and go by the error code. This seems to be related to keywords that are redefined or reused in enums. > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\multidim.h(44): error C2365: 'DOUBLE': Erneute Definition; vorherige Definition war 'Typedef' > > C:\Programme\Microsoft Visual Studio .NET 2003\Vc7\PlatformSDK\Include\WTypes.h(387): Siehe Deklaration von 'DOUBLE' > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\basic.h(66): error C2143: Syntaxfehler: Es fehlt ';' vor 'constant' > > (this is related to the use of the word ERROR in an enum) > > > > Is there a release that deals with errors like this, or a workaround? > > > > Best wishes, > > > > Michel > > > > Michel Audette, Ph.D. > > Innovation Center Computer Assisted Surgery (ICCAS) > > Semmelweisstra?e 14 > > Leipzig, Germany > > Phone: ++49 (0) 341 / 97 - 1 20 13 > > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks From Michel.Audette at medizin.uni-leipzig.de Mon Sep 22 08:06:12 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Mon, 22 Sep 2008 14:06:12 +0200 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E690242530F@MRZS152229.medizin.uni-leipzig.de> Hi Rupert, nice to hear from you. I'm not trying anything fancy. I would just like to link with the dlls that I got from the BIC website, under MS VC++ 2003, and the compiler does not like some of the header files that I'm including... Based on your text, it sounds like you know more about this issue than anyone else in MINCland. Is there a wiki that you could annotate, if you could manage to find the time? Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Rupert Brooks Sent: September 22, 2008 1:56 PM To: MINC users mailing list Subject: Re: [MINC-users] redefinitions in volume_io/basic.h,multidim.h causing compilation errors on Windows hi Michel, Are you actually rebuilding the MINC library under windows? As I'm sure you know, I managed to build it natively under windows but with a certain amout of pain. It sounds like you got past this specific problem, but if others are interested maybe its time to re-discuss building MINC on windows. It would be great to have the support integrated right in the source, with minimal pain necessary. So far, my experience was that to build it natively, i had to make minor mods to hdf_convenience.c to adhere to ANSI c, standards (variable declarations), and i forcibly removed the dll_exports and built it statically. I got minc2 and volume_io to build, and more than half of the minc tools. However, those that require flex/bison, and the conversion build tree I was never successful with. Of course, one can build it under cygwin, but this has the disadvantage of requiring cygwin, and requiring anything else built against it to also use cygwin. Rupert On Thu, Sep 18, 2008 at 6:23 AM, Audette, Michel wrote: > Hi all, > > > > I'm seeing some Windows MS VC++ 2003 compilation errors related to enums in volume_io/basic.h and multidim.h . > > > > Please forgive the German, and go by the error code. This seems to be related to keywords that are redefined or reused in enums. > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\multidim.h(44): error C2365: 'DOUBLE': Erneute Definition; vorherige Definition war 'Typedef' > > C:\Programme\Microsoft Visual Studio .NET 2003\Vc7\PlatformSDK\Include\WTypes.h(387): Siehe Deklaration von 'DOUBLE' > > > > G:\windows\srcMAF\maf\openMAF22\Libraries\MINC\include\volume_io\basic.h(66): error C2143: Syntaxfehler: Es fehlt ';' vor 'constant' > > (this is related to the use of the word ERROR in an enum) > > > > Is there a release that deals with errors like this, or a workaround? > > > > Best wishes, > > > > Michel > > > > Michel Audette, Ph.D. > > Innovation Center Computer Assisted Surgery (ICCAS) > > Semmelweisstra?e 14 > > Leipzig, Germany > > Phone: ++49 (0) 341 / 97 - 1 20 13 > > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Mon Sep 22 17:30:37 2008 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 23 Sep 2008 07:30:37 +1000 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: Hi Rupert, > So far, my experience was that to build it natively, i had to make > minor mods to hdf_convenience.c to adhere to ANSI c, standards > (variable declarations), and i forcibly removed the dll_exports and > built it statically. I got minc2 and volume_io to build, and more > than half of the minc tools. However, those that require flex/bison, > and the conversion build tree I was never successful with. By all means send the diffs and I will integrate them into CVS where possible. There have already been a number of Win32 specific changes made from previous work of Leila Baghdadi and Bert Vincent. At one state there even was a stand alone .exe MINC installer (perish the thought! :) -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From rupe.brooks at gmail.com Tue Sep 23 09:12:37 2008 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 23 Sep 2008 09:12:37 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: Ok - So heres my adventurous tale of building MINC tools natively on Windows XP with Visual Studio 2005 express. My reason for doing this was that I wanted to be able to read MINC files using the itkMINC2IO. Not surprisingly that requires linking against the minc2 library. For just general use of the minc tools under windows, a cygwin build is probably my recommendation for people. I've put the full set of binaries that I've created on my website for download if people need them. I will make some effort to keep these up to date. http://www.rupertbrooks.ca/code.html I'll try to help out anyone who wants to push this project forward, but i can't spend too much time on it. Day job and all ya know. 1. MINC is dependent on HDF, SZ, Z, and NETCDF. - I got HDF5, SZ and ZLIB from the hdf 5 site. - The NETCDF from unidata did not come with netcdf.h, oddly enough. I used the binary and .h from the 2005 installer package that Leila Baghdadi made. 2. I configured a Visual Studio solution using CMAKE. The CMakeLists file in the minc distribution was modified as described below. The CMAKE settings are: USE_PARSERS=OFF HDF5_LIBRARY=hdf5dll.lib NETCDF_LIBRARY=netcdf.lib SZ_LIBRARY=szlibdll.lib Z_LIBRARY=zlib1.dll I found it was absolutely necessary to build against the DLL versions of things. I would have preferred to build static - my application would have been fat, but i could have passed the binaries around much more easily. Anyway, i never managed to get static linking to these required libraries to work. Turning the parsers off was also necessary. I tried fairly hard to find a flex for windows native builds. The thing is - besides the parser, you need to link against the flex library. This seems to be pretty much ignored by purveyors of native flex tools. Theres a few out there that i tried, and they gave me completely different results for simple programs vs flex on unix, so i abandoned the search. 3. It is necessary to change the hdf_convenience.c to be ANSI compliant. See changes below. This should not interfere with building on any other system. 4. I removed the dll_export stuff in the minc api. I wanted a static build, and i had trouble with the DLL build anyway. 5. I fired up visual studio and build the solution, in both release and debug modes. Due to the use of Debug postfix in the CMake, i end up with minc.lib and mincd.lib for optimized and debug respectively. There are 3 projects that dont build (xfminvert, dcm2mnc, acr_nema). After some investigation, i saw that they made heavy use of POSIX specific calls from unistd.h, etc, and I figured the porting effort was too hard for me. Particularly because i didnt really need these tools. TODO: Theres lots of things that could improve this. Config.h is partly build through CMake tests, mainly due to Andrew, and partly through direct hacks (due to me). Proper testing would be the way to go. Under Unix theres a fair number of compiler warnings. Under Win32, the compiler is freaking out. There are hundreds of warnings. I think that most of these are spurious. Nevertheless i dont like spurious warnings, if for no other reason than they hide the real problems. I also suspect there are some real issues lurking in among the spurious ones. There are no code tests in WIN32. I really think that some serious test scripts and data should be added Rupert CODE CHANGES (apologies for the length of this) diff -d -r minc-2.0.15 cleanunpack/minc-2.0.15 diff -d -r minc-2.0.15/CMakeLists.txt cleanunpack/minc-2.0.15/CMakeLists.txt 1,32c1,31 < # CMakeFiles.txt for the MINC2 library < # < # Andrew Janke - a.janke at gmail.com < CMAKE_MINIMUM_REQUIRED(VERSION 2.6) < PROJECT(libminc2) < < SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules") < < < #ADD_SUBDIRECTORY( testdir ) < #ADD_SUBDIRECTORY( doc ) < < < # Packaging defines < SET(CPACK_GENERATOR TGZ) < SET(CPACK_PACKAGE_VERSION_MAJOR 2) < SET(CPACK_PACKAGE_VERSION_MINOR 0) < SET(CPACK_PACKAGE_VERSION_PATCH 15) < INCLUDE(CPack) < < < SET(PACKAGE "minc") < SET(PACKAGE_BUGREPORT "a.janke at gmail.com") < < SET(PACKAGE_NAME "minc") < SET(PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") < SET(PACKAGE_STRING "${PACKAGE_NAME} ${PACKAGE_VERSION}") < < SET(CMAKE_DEBUG_POSTFIX "d") < < # yes, build as minc2 < SET(MINC2 "1") --- > # CMakeFiles.txt for the MINC2 library > # > # Andrew Janke - a.janke at gmail.com > > PROJECT(libminc2) > > SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules") > > > #ADD_SUBDIRECTORY( testdir ) > #ADD_SUBDIRECTORY( doc ) > > > # Packaging defines > SET(CPACK_GENERATOR TGZ) > SET(CPACK_PACKAGE_VERSION_MAJOR 2) > SET(CPACK_PACKAGE_VERSION_MINOR 0) > SET(CPACK_PACKAGE_VERSION_PATCH 14) > INCLUDE(CPack) > > > SET(PACKAGE "minc") > SET(PACKAGE_BUGREPORT "a.janke at gmail.com") > > SET(PACKAGE_NAME "minc") > SET(PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") > SET(PACKAGE_STRING "${PACKAGE_NAME} ${PACKAGE_VERSION}") > > > # yes, build as minc2 > SET(MINC2 "1") 58,66c57 < INCLUDE_DIRECTORIES( ${NETCDF_INCLUDE_DIR} ${HDF5_INCLUDE_DIR} ${CMAKE_BINARY_DIR}) < FIND_LIBRARY(SZ_LIBRARY NAMES sz libszdll < PATHS /usr/lib DOC "path to the sz library") < FIND_LIBRARY(Z_LIBRARY NAMES z libz < PATHS /usr/lib DOC "path to the z library") < IF(NOT UNIX) < ADD_DEFINITIONS(-D_CRT_SECURE_NO_DEPRECATE -DDLL_NETCDF -D_POSIX_ -D_HDF5USEDLL_ -D_USE_MATH_DEFINES) < #ADD_DEFINITIONS( -D_POSIX_ -D_USE_MATH_DEFINES) < ENDIF(NOT UNIX) --- > INCLUDE_DIRECTORIES( ${NETCDF_INCLUDE_DIR} ${HDF5_INCLUDE_DIR} ) 69c60 < CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/config.h.cmake ${CMAKE_BINARY_DIR}/config.h) --- > CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/config.h.cmake ${CMAKE_SOURCE_DIR}/config.h) 72c63 < CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/epm-header.in ${CMAKE_BINARY_DIR}/epm-header) --- > CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/epm-header.in ${CMAKE_SOURCE_DIR}/epm-header) 118c109 < ADD_LIBRARY(minc2 ${minc1_LIB_SRCS} ${minc2_LIB_SRCS}) --- > ADD_LIBRARY(minc2 STATIC ${minc1_LIB_SRCS} ${minc2_LIB_SRCS}) 173c164 < ADD_LIBRARY(volume_io2 ${volume_io2_LIB_SRCS}) --- > ADD_LIBRARY(volume_io2 STATIC ${volume_io2_LIB_SRCS}) diff -d -r minc-2.0.15/config.h.cmake cleanunpack/minc-2.0.15/config.h.cmake 2,3d1 < #ifndef CONFIG_H_INCG < #define CONFIG_H_INCG 17,49d14 < < #ifdef WIN32 < #undef HAVE_MKSTEMP < #define HAVE_FCNTL_H 1 < #define HAVE_FLOAT_H 1 < #define HAVE_MEMORY_H 1 < #define HAVE_STDINT_H 1 < #define HAVE_STDLIB_H 1 < #define HAVE_STRING_H 1 < #define HAVE_SYS_STAT_H 1 < #define HAVE_SYS_TYPES_H 1 < #define HAVE_TEMPNAM 1 < #define HAVE_TMPNAM 1 < #define STDC_HEADERS 1 < #define sleep(x) _sleep(x) < #define snprintf _snprintf < #define strncasecmp(x,y,z) strnicmp(x,y,z) < #define tempnam(x,y) _tempnam(x,y) < < int __stdcall gethostname(char *name, int namelen); < < /* Quick implmentation of rint() for Intel, since thoughtless Microsoft < * programmers failed to provide us with one... < */ < __inline double rint(double dblvar) < { < __asm fld dblvar < __asm frndint < __asm fst dblvar < return dblvar; < } < #endif < #endif \ No newline at end of file diff -d -r minc-2.0.15/conversion/CMakeLists.txt cleanunpack/minc-2.0.15/conversion/CMakeLists.txt 1,82c1,77 < # CMakeFiles.txt for the MINC2 conversion progs < # < # Andrew Janke - a.janke at gmail.com < < LINK_DIRECTORIES(../) < LINK_LIBRARIES( optimized minc2 debug minc2d ${NETCDF_LIBRARY} ${HDF5_LIBRARY} ${SZ_LIBRARY} ${Z_LIBRARY}) < IF(NOT UNIX) < LINK_LIBRARIES(ws2_32) < ADD_DEFINITIONS(-DDLL_NETCDF -D_POSIX_ -D_HDF5USEDLL_ -D_USE_MATH_DEFINES) < ENDIF(NOT UNIX) < < ADD_DEFINITIONS(-DHAVE_CONFIG_H) < < < # conversion progs (and libraries) < INCLUDE_DIRECTORIES(Acr_nema) < ADD_LIBRARY(acr_nema STATIC < Acr_nema/acr_io.c < Acr_nema/dicom_client_routines.c < Acr_nema/dicom_network.c < Acr_nema/element.c < Acr_nema/file_io.c < Acr_nema/globals.c < Acr_nema/group.c < Acr_nema/message.c < Acr_nema/value_repr.c) < #INSTALL(TARGETS acr_nema DESTINATION lib) < < ADD_EXECUTABLE(dcm2mnc < dcm2mnc/dcm2mnc.c < dcm2mnc/dicom_to_minc.c < dcm2mnc/siemens_to_dicom.c < dcm2mnc/dicom_read.c < dcm2mnc/minc_file.c < dcm2mnc/progress.c < dcm2mnc/string_to_filename.c) < TARGET_LINK_LIBRARIES(dcm2mnc acr_nema ) < < ADD_EXECUTABLE(ecattominc < ecattominc/ecattominc.c < ecattominc/insertblood.c < ecattominc/ecat_file.c < ecattominc/machine_indep.c < ) < ADD_EXECUTABLE(minctoecat < minctoecat/minctoecat.c < minctoecat/ecat_write.c < minctoecat/machine_indep.c < ) < TARGET_LINK_LIBRARIES(minctoecat volume_io2 minc2) < < ADD_EXECUTABLE(mnc2nii < nifti1/mnc2nii.c < nifti1/nifti1_io.c < nifti1/znzlib.c < ) < ADD_EXECUTABLE(nii2mnc < nifti1/nii2mnc.c < nifti1/nifti1_io.c < nifti1/znzlib.c < ) < TARGET_LINK_LIBRARIES(nii2mnc volume_io2 minc2) < < ADD_EXECUTABLE(upet2mnc < micropet/upet2mnc.c < ) < < ADD_EXECUTABLE(vff2mnc < vff2mnc/vff2mnc.c < ) < < < # install progs < INSTALL(TARGETS < dcm2mnc < ecattominc < minctoecat < mnc2nii < nii2mnc < upet2mnc < vff2mnc < DESTINATION bin) --- > # CMakeFiles.txt for the MINC2 conversion progs > # > # Andrew Janke - a.janke at gmail.com > > LINK_DIRECTORIES(../) > LINK_LIBRARIES( minc2 ${NETCDF_LIBRARY} ${HDF5_LIBRARY} ) > ADD_DEFINITIONS(-DHAVE_CONFIG_H) > > > # conversion progs (and libraries) > INCLUDE_DIRECTORIES(Acr_nema) > ADD_LIBRARY(acr_nema STATIC > Acr_nema/acr_io.c > Acr_nema/dicom_client_routines.c > Acr_nema/dicom_network.c > Acr_nema/element.c > Acr_nema/file_io.c > Acr_nema/globals.c > Acr_nema/group.c > Acr_nema/message.c > Acr_nema/value_repr.c) > #INSTALL(TARGETS acr_nema DESTINATION lib) > > ADD_EXECUTABLE(../dcm2mnc > dcm2mnc/dcm2mnc.c > dcm2mnc/dicom_to_minc.c > dcm2mnc/siemens_to_dicom.c > dcm2mnc/dicom_read.c > dcm2mnc/minc_file.c > dcm2mnc/progress.c > dcm2mnc/string_to_filename.c) > TARGET_LINK_LIBRARIES(../dcm2mnc acr_nema ) > > ADD_EXECUTABLE(../ecattominc > ecattominc/ecattominc.c > ecattominc/insertblood.c > ecattominc/ecat_file.c > ecattominc/machine_indep.c > ) > ADD_EXECUTABLE(../minctoecat > minctoecat/minctoecat.c > minctoecat/ecat_write.c > minctoecat/machine_indep.c > ) > TARGET_LINK_LIBRARIES(../minctoecat volume_io2 minc2) > > ADD_EXECUTABLE(../mnc2nii > nifti1/mnc2nii.c > nifti1/nifti1_io.c > nifti1/znzlib.c > ) > ADD_EXECUTABLE(../nii2mnc > nifti1/nii2mnc.c > nifti1/nifti1_io.c > nifti1/znzlib.c > ) > TARGET_LINK_LIBRARIES(../nii2mnc volume_io2 minc2) > > ADD_EXECUTABLE(../upet2mnc > micropet/upet2mnc.c > ) > > ADD_EXECUTABLE(../vff2mnc > vff2mnc/vff2mnc.c > ) > > > # install progs > INSTALL(TARGETS > ../dcm2mnc > ../ecattominc > ../minctoecat > ../mnc2nii > ../nii2mnc > ../upet2mnc > ../vff2mnc > DESTINATION bin) Only in minc-2.0.15: epm-header diff -d -r minc-2.0.15/libsrc/hdf_convenience.c cleanunpack/minc-2.0.15/libsrc/hdf_convenience.c 1266,1267d1265 < hsize_t val; < int unit_size; 1344,1347c1342,1344 < < //hsize_t val; < val = 1; < unit_size = nctypelen( vartype ); --- > > hsize_t val = 1; > int unit_size = nctypelen( vartype ); diff -d -r minc-2.0.15/libsrc/image_conversion.c cleanunpack/minc-2.0.15/libsrc/image_conversion.c 317d316 < int new_icv; 341c340 < //int new_icv; --- > int new_icv; diff -d -r minc-2.0.15/libsrc/minc.h cleanunpack/minc-2.0.15/libsrc/minc.h 465c465 < //#if defined(_MSC_VER) --- > #if defined(_MSC_VER) 469,470c469,470 < //#define MNCAPI __declspec(dllimport) < //#else --- > #define MNCAPI __declspec(dllimport) > #else 472c472 < //#endif /* _MSC_VER not defined */ --- > #endif /* _MSC_VER not defined */ diff -d -r minc-2.0.15/progs/CMakeLists.txt cleanunpack/minc-2.0.15/progs/CMakeLists.txt 9,18c9 < #IF(UNIX) < LINK_LIBRARIES( optimized minc2 debug minc2d ${NETCDF_LIBRARY} ${HDF5_LIBRARY} ${SZ_LIBRARY} ${Z_LIBRARY}) < #ELSE(UNIX) < #LINK_LIBRARIES( minc2 ${NETCDF_LIBRARY} ${HDF5_LIBRARY} szlibdll zlib) < IF(NOT UNIX) < LINK_LIBRARIES(ws2_32) < # winsoc needed for gethostname < ADD_DEFINITIONS(-DDLL_NETCDF -D_POSIX_ -D_HDF5USEDLL_ -D_USE_MATH_DEFINES) < #ADD_DEFINITIONS(-D_POSIX_ -D_USE_MATH_DEFINES) < ENDIF(NOT UNIX) --- > LINK_LIBRARIES( minc2 ${NETCDF_LIBRARY} ${HDF5_LIBRARY} ) 21,22c12,13 < #SET(BISON_FIND_REQUIRED) < #SET(FLEX_FIND_REQUIRED) --- > SET(BISON_FIND_REQUIRED) > SET(FLEX_FIND_REQUIRED) 26,31d16 < IF(BISON_FOUND AND FLEX_FOUND) < SET(USE_PARSERS TRUE CACHE BOOL "Build targets needing flex and bison (minccalc,mincgen)") < ELSE(BISON_FOUND AND FLEX_FOUND) < SET(USE_PARSERS FALSE CACHE BOOL "Build targets needing flex and bison (minccalc,mincgen)") < ENDIF(BISON_FOUND AND FLEX_FOUND) < 33,34c18,19 < ADD_EXECUTABLE(invert_raw_image mincview/invert_raw_image.c) < ADD_EXECUTABLE(mincaverage mincaverage/mincaverage.c) --- > ADD_EXECUTABLE(../invert_raw_image mincview/invert_raw_image.c) > ADD_EXECUTABLE(../mincaverage mincaverage/mincaverage.c) 36,45c21,24 < # these targets require bison and flex to build < IF(USE_PARSERS) < BISON_TARGET(minccalc minccalc/gram.y ${CMAKE_CURRENT_BINARY_DIR}/gram.c COMPILE_FLAGS "--debug") < FLEX_TARGET(minccalc minccalc/lex.l ${CMAKE_CURRENT_BINARY_DIR}/lex.c) < SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/gram.c < PROPERTIES COMPILE_FLAGS "-I${CMAKE_CURRENT_SOURCE_DIR}/minccalc") < SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/lex.c < PROPERTIES COMPILE_FLAGS "-I${CMAKE_CURRENT_SOURCE_DIR}/minccalc") < ADD_EXECUTABLE(minccalc minccalc/minccalc.c < ${CMAKE_CURRENT_BINARY_DIR}/gram.c --- > BISON_TARGET(../minccalc minccalc/gram.y minccalc/gram.c COMPILE_FLAGS "--debug") > FLEX_TARGET(../minccalc minccalc/lex.l minccalc/lex.c) > ADD_EXECUTABLE(../minccalc minccalc/minccalc.c > minccalc/gram.c 48c27 < ${CMAKE_CURRENT_BINARY_DIR}/lex.c --- > minccalc/lex.c 55,77c34,36 < BISON_TARGET(mincgen mincgen/ncgentab.y ${CMAKE_CURRENT_BINARY_DIR}/ncgentab.c) < FLEX_TARGET(mincgen mincgen/ncgenyy.l ${CMAKE_CURRENT_BINARY_DIR}/ncgenyy.c) < SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/ncgentab.c < PROPERTIES COMPILE_FLAGS "-I${CMAKE_CURRENT_SOURCE_DIR}/mincgen") < SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/ncgenyy.c < PROPERTIES COMPILE_FLAGS "-I${CMAKE_CURRENT_SOURCE_DIR}/mincgen") < ADD_EXECUTABLE(mincgen mincgen/main.c < mincgen/escapes.c < mincgen/genlib.c < mincgen/getfill.c < mincgen/init.c < mincgen/load.c < ${CMAKE_CURRENT_BINARY_DIR}/ncgentab.c < ${CMAKE_CURRENT_BINARY_DIR}/ncgenyy.c) < INSTALL(TARGETS < minccalc < mincgen < DESTINATION bin) < ENDIF(USE_PARSERS) < < ADD_EXECUTABLE(mincconcat mincconcat/mincconcat.c) < ADD_EXECUTABLE(mincconvert mincconvert/mincconvert.c) < ADD_EXECUTABLE(minccopy minccopy/minccopy.c) --- > ADD_EXECUTABLE(../mincconcat mincconcat/mincconcat.c) > ADD_EXECUTABLE(../mincconvert mincconvert/mincconvert.c) > ADD_EXECUTABLE(../minccopy minccopy/minccopy.c) 79c38 < ADD_EXECUTABLE(mincdump mincdump/mincdump.c --- > ADD_EXECUTABLE(../mincdump mincdump/mincdump.c 83,86c42,45 < ADD_EXECUTABLE(mincexample1 mincexample/mincexample1.c) < ADD_EXECUTABLE(mincexample2 mincexample/mincexample2.c) < ADD_EXECUTABLE(mincexpand mincexpand/mincexpand.c) < ADD_EXECUTABLE(mincextract mincextract/mincextract.c) --- > ADD_EXECUTABLE(../mincexample1 mincexample/mincexample1.c) > ADD_EXECUTABLE(../mincexample2 mincexample/mincexample2.c) > ADD_EXECUTABLE(../mincexpand mincexpand/mincexpand.c) > ADD_EXECUTABLE(../mincextract mincextract/mincextract.c) 87a47,56 > BISON_TARGET(../mincgen mincgen/ncgentab.y mincgen/nccentab.c) > FLEX_TARGET(../mincgen mincgen/ncgenyy.l mincgen/ncgenyy.c) > ADD_EXECUTABLE(../mincgen mincgen/main.c > mincgen/escapes.c > mincgen/genlib.c > mincgen/getfill.c > mincgen/init.c > mincgen/load.c > mincgen/ncgentab.c > mincgen/ncgenyy.c) 89,94c58,63 < ADD_EXECUTABLE(mincinfo mincinfo/mincinfo.c) < ADD_EXECUTABLE(minclookup minclookup/minclookup.c) < ADD_EXECUTABLE(mincmakescalar mincmakescalar/mincmakescalar.c) < ADD_EXECUTABLE(mincmakevector mincmakevector/mincmakevector.c) < ADD_EXECUTABLE(mincmath mincmath/mincmath.c) < ADD_EXECUTABLE(minc_modify_header minc_modify_header/minc_modify_header.c) --- > ADD_EXECUTABLE(../mincinfo mincinfo/mincinfo.c) > ADD_EXECUTABLE(../minclookup minclookup/minclookup.c) > ADD_EXECUTABLE(../mincmakescalar mincmakescalar/mincmakescalar.c) > ADD_EXECUTABLE(../mincmakevector mincmakevector/mincmakevector.c) > ADD_EXECUTABLE(../mincmath mincmath/mincmath.c) > ADD_EXECUTABLE(../minc_modify_header minc_modify_header/minc_modify_header.c) 96c65 < ADD_EXECUTABLE(mincresample mincresample/mincresample.c --- > ADD_EXECUTABLE(../mincresample mincresample/mincresample.c 99c68 < TARGET_LINK_LIBRARIES(mincresample volume_io2) --- > TARGET_LINK_LIBRARIES(../mincresample volume_io2) 101c70 < ADD_EXECUTABLE(mincreshape mincreshape/mincreshape.c --- > ADD_EXECUTABLE(../mincreshape mincreshape/mincreshape.c 104,106c73,75 < ADD_EXECUTABLE(mincstats mincstats/mincstats.c) < ADD_EXECUTABLE(minctoraw minctoraw/minctoraw.c) < ADD_EXECUTABLE(mincwindow mincwindow/mincwindow.c) --- > ADD_EXECUTABLE(../mincstats mincstats/mincstats.c) > ADD_EXECUTABLE(../minctoraw minctoraw/minctoraw.c) > ADD_EXECUTABLE(../mincwindow mincwindow/mincwindow.c) 108c77 < ADD_EXECUTABLE(rawtominc rawtominc/rawtominc.c --- > ADD_EXECUTABLE(../rawtominc rawtominc/rawtominc.c 111,112c80,81 < ADD_EXECUTABLE(voxeltoworld coordinates/voxeltoworld.c) < TARGET_LINK_LIBRARIES(voxeltoworld volume_io2 minc2) --- > ADD_EXECUTABLE(../voxeltoworld coordinates/voxeltoworld.c) > TARGET_LINK_LIBRARIES(../voxeltoworld volume_io2 minc2) 114,115c83,84 < ADD_EXECUTABLE(worldtovoxel coordinates/worldtovoxel.c) < TARGET_LINK_LIBRARIES(worldtovoxel volume_io2 minc2) --- > ADD_EXECUTABLE(../worldtovoxel coordinates/worldtovoxel.c) > TARGET_LINK_LIBRARIES(../worldtovoxel volume_io2 minc2) 118,119c87,88 < ADD_EXECUTABLE(transformtags xfm/transformtags.c) < TARGET_LINK_LIBRARIES(transformtags volume_io2 minc2) --- > ADD_EXECUTABLE(../transformtags xfm/transformtags.c) > TARGET_LINK_LIBRARIES(../transformtags volume_io2 minc2) 121,122c90,91 < ADD_EXECUTABLE(xfmconcat xfm/xfmconcat.c) < TARGET_LINK_LIBRARIES(xfmconcat volume_io2 minc2) --- > ADD_EXECUTABLE(../xfmconcat xfm/xfmconcat.c) > TARGET_LINK_LIBRARIES(../xfmconcat volume_io2 minc2) 124,125c93,94 < ADD_EXECUTABLE(xfminvert xfm/xfminvert.c) < TARGET_LINK_LIBRARIES(xfminvert volume_io2 minc2) --- > ADD_EXECUTABLE(../xfminvert xfm/xfminvert.c) > TARGET_LINK_LIBRARIES(../xfminvert volume_io2 minc2) 129,157c98,126 < invert_raw_image < mincaverage < # minccalc < mincconcat < mincconvert < minccopy < mincdump < # mincexample1 < # mincexample2 < mincexpand < mincextract < # mincgen < mincinfo < minclookup < mincmakescalar < mincmakevector < mincmath < minc_modify_header < mincresample < mincreshape < mincstats < minctoraw < mincwindow < rawtominc < voxeltoworld < worldtovoxel < transformtags < xfmconcat < xfminvert --- > ../invert_raw_image > ../mincaverage > ../minccalc > ../mincconcat > ../mincconvert > ../minccopy > ../mincdump > # ../mincexample1 > # ../mincexample2 > ../mincexpand > ../mincextract > ../mincgen > ../mincinfo > ../minclookup > ../mincmakescalar > ../mincmakevector > ../mincmath > ../minc_modify_header > ../mincresample > ../mincreshape > ../mincstats > ../minctoraw > ../mincwindow > ../rawtominc > ../voxeltoworld > ../worldtovoxel > ../transformtags > ../xfmconcat > ../xfminvert diff -d -r minc-2.0.15/volume_io/Include/volume_io.h cleanunpack/minc-2.0.15/volume_io/Include/volume_io.h 52,54c52,54 < //#if defined(_MSC_VER) < //#define VIOAPI __declspec(dllimport) < //#else --- > #if defined(_MSC_VER) > #define VIOAPI __declspec(dllimport) > #else 56c56 < //#endif /* _MSC_VER not defined */ --- > #endif /* _MSC_VER not defined */ On Mon, Sep 22, 2008 at 5:30 PM, Andrew Janke wrote: > Hi Rupert, > >> So far, my experience was that to build it natively, i had to make >> minor mods to hdf_convenience.c to adhere to ANSI c, standards >> (variable declarations), and i forcibly removed the dll_exports and >> built it statically. I got minc2 and volume_io to build, and more >> than half of the minc tools. However, those that require flex/bison, >> and the conversion build tree I was never successful with. > > By all means send the diffs and I will integrate them into CVS where > possible. There have already been a number of Win32 specific changes > made from previous work of Leila Baghdadi and Bert Vincent. At one > state there even was a stand alone .exe MINC installer (perish the > thought! :) > > > > -- > Andrew Janke - andrew.janke at anu.edu.au > Department of Geriatric Medicine, ANU > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks From baghdadi at phenogenomics.ca Tue Sep 23 10:04:36 2008 From: baghdadi at phenogenomics.ca (Leila Baghdadi) Date: Tue, 23 Sep 2008 10:04:36 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69024252ED@MRZS152229.medizin.uni-leipzig.de> Message-ID: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20080923/64de08e8/attachment.txt From Michel.Audette at medizin.uni-leipzig.de Tue Sep 23 11:11:53 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Tue, 23 Sep 2008 17:11:53 +0200 Subject: [MINC-users] using Display with large volumes In-Reply-To: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> References: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E690242533D@MRZS152229.medizin.uni-leipzig.de> Dear all, I have some very large volumes of 0.2mm resolution that I would like to hand-segment under Display, and I was wondering if there is a means of running it or compiling it in a manner that minimizes the lag related to processing such large volumes. Any suggestions, beyond cropping? Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From louis.collins at mcgill.ca Tue Sep 23 13:15:33 2008 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 23 Sep 2008 13:15:33 -0400 Subject: [MINC-users] using Display with large volumes In-Reply-To: <160E3DD4FB702C4CB860C65186686E690242533D@MRZS152229.medizin.uni-leipzig.de> References: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> <160E3DD4FB702C4CB860C65186686E690242533D@MRZS152229.medizin.uni-leipzig.de> Message-ID: <8874F65A-8410-4D7D-8DEE-5BF753F6321E@mcgill.ca> at the shell, try setenv VOLUME_CACHE_THRESHOLD -1 you should then be able to load in the entire volume without swapping, if you have enough memory on your machine. Display and register both had some kind of internal limit to the amount of memory used. An SGI throwback perhaps? -Louis On Sep 23, 2008, at 11:11 AM, Audette, Michel wrote: > Dear all, > > I have some very large volumes of 0.2mm resolution that I would like > to hand-segment under Display, and I was wondering if there is a > means of running it or compiling it in a manner that minimizes the > lag related to processing such large volumes. > > Any suggestions, beyond cropping? > > Best wishes, > > Michel > > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Semmelweisstra?e 14 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From rupe.brooks at gmail.com Tue Sep 23 14:30:47 2008 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 23 Sep 2008 14:30:47 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> References: <1222178676.7456.26.camel@mouse30.phenogenomics.ca> Message-ID: Hi Leila, The latest installer that I have seen is 19 July 2005 on the http://www.bic.mni.mcgill.ca/software/minc/ page. I think that was version .08 or .09. If theres a newer one, I'd be interested to try it out. The installer you created worked very well, and I'd like very much for one to be available - makes my life so much easier when my stuff depends on MINC. I'm very curious how you created it - you have a minccalc in there. That requires flex, so i guess you found a good one for Windows? I'm also curious if you had to make adjustments to the CMakeLists like i did to get it to build. What version of Visual Studio? Cheers, Rupert (See, i knew there was people that knew more than me out there :-) On Tue, Sep 23, 2008 at 10:04 AM, Leila Baghdadi wrote: > Hi guys, > > I still have the windows installer and infact I recently updated it. The > main reason for us doing that for the converter vff2mnc which is used > here to create minc2 files from vff. > I used cmake to create all the project files for windows so that was > easy. I found alot of difficulty when I was trying to build some > programs specially the ones using sockets (dicom rountines), I simply > could not find the equivalent headers and functions on windows. > so I decided to build the windows installer with all the programs and > converter (minc2) and I left the rest alone. > Andrew, > I have the windows installer with recent changes which I have committed > to cvs. let me know if you can use it in anyways. > > Leila > On Tue, 2008-09-23 at 07:30 +1000, Andrew Janke wrote: >> Hi Rupert, >> >> > So far, my experience was that to build it natively, i had to make >> > minor mods to hdf_convenience.c to adhere to ANSI c, standards >> > (variable declarations), and i forcibly removed the dll_exports and >> > built it statically. I got minc2 and volume_io to build, and more >> > than half of the minc tools. However, those that require flex/bison, >> > and the conversion build tree I was never successful with. >> >> By all means send the diffs and I will integrate them into CVS where >> possible. There have already been a number of Win32 specific changes >> made from previous work of Leila Baghdadi and Bert Vincent. At one >> state there even was a stand alone .exe MINC installer (perish the >> thought! :) >> >> >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks From baghdadi at phenogenomics.ca Tue Sep 23 15:49:15 2008 From: baghdadi at phenogenomics.ca (Leila Baghdadi) Date: Tue, 23 Sep 2008 15:49:15 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: References: Message-ID: <1222199355.25193.5.camel@mouse30.phenogenomics.ca> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20080923/e62d4d48/attachment.txt From Michel.Audette at medizin.uni-leipzig.de Wed Sep 24 04:29:57 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 24 Sep 2008 10:29:57 +0200 Subject: [MINC-users] using Display with large volumes In-Reply-To: <8874F65A-8410-4D7D-8DEE-5BF753F6321E@mcgill.ca> References: <1222178676.7456.26.camel@mouse30.phenogenomics.ca><160E3DD4FB702C4CB860C65186686E690242533D@MRZS152229.medizin.uni-leipzig.de> <8874F65A-8410-4D7D-8DEE-5BF753F6321E@mcgill.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E6902425343@MRZS152229.medizin.uni-leipzig.de> Hi Louis, thanks for your kind reply. I'll give it a try. Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of D. Louis Collins Sent: September 23, 2008 7:16 PM To: MINC users mailing list Subject: Re: [MINC-users] using Display with large volumes at the shell, try setenv VOLUME_CACHE_THRESHOLD -1 you should then be able to load in the entire volume without swapping, if you have enough memory on your machine. Display and register both had some kind of internal limit to the amount of memory used. An SGI throwback perhaps? -Louis On Sep 23, 2008, at 11:11 AM, Audette, Michel wrote: > Dear all, > > I have some very large volumes of 0.2mm resolution that I would like > to hand-segment under Display, and I was wondering if there is a > means of running it or compiling it in a manner that minimizes the > lag related to processing such large volumes. > > Any suggestions, beyond cropping? > > Best wishes, > > Michel > > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Semmelweisstra?e 14 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From baghdadi at phenogenomics.ca Fri Sep 26 11:44:56 2008 From: baghdadi at phenogenomics.ca (Leila Baghdadi) Date: Fri, 26 Sep 2008 11:44:56 -0400 Subject: [MINC-users] redefinitions in volume_io/basic.h, multidim.h causing compilation errors on Windows In-Reply-To: <8E20326FC656DC4FAED041EF42DD5A5D037BE4D9@skuld.svf.au.dk> References: Message-ID: <1222443896.11249.28.camel@mouse30.phenogenomics.ca> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20080926/b4a1b894/attachment.txt From vladimir.fonov at gmail.com Fri Sep 26 15:52:30 2008 From: vladimir.fonov at gmail.com (Vladimir FONOV) Date: Fri, 26 Sep 2008 15:52:30 -0400 Subject: [MINC-users] MINC2 is not thread safe? Message-ID: <48DD3D7E.60707@gmail.com> Hello All, I was trying to write a small program that would process some minc files in parallel. I am randomly getting one of the following error messags whenever I am trying to read MINC files in parallel: (from MI_icv_chkid): Illegal ICV identifier or HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 0. Back trace follows. #000: H5S.c line 476 in H5Sclose(): not a data space major(01): Function arguments minor(03): Inappropriate type or (from miicv_create): Unable to open file 'XXXXXXX.mnc' So, is the MINC library not multithread safe? I am using MINC1 API , ans reading MINC2 files. Version of the library: libminc: 2.0.15 netcdf : 3.6.1 of Mar 10 2008 13:23:53 $ HDF5 : 1.6.6 -- Best regards, Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com From tejasvinee at gmail.com Fri Sep 26 16:04:52 2008 From: tejasvinee at gmail.com (Tejaswini Ganapathi) Date: Fri, 26 Sep 2008 16:04:52 -0400 Subject: [MINC-users] problem with nu_estimate_np_and_em In-Reply-To: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> References: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> Message-ID: <6ec808c10809261304t235a3e62s90283e5442044d@mail.gmail.com> Hi ! I tried running nu_estimate_np_and_em with the following options : > > $ nu_estimate_np_and_em -normalize_field -save_fields -mask mask.mnc > breast.mnc fields_time.mnc > > I get the following error: > > nu_estimate_np_and_em: couldn't find program "class_statistics" > nu_estimate_np_and_em: couldn't find program "estimate" > add_default_args: warning: adding default arguments for unregistered > program "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 > add_default_args: warning: adding default arguments for unregistered > program "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 > add_default_args: warning: adding default arguments for unregistered > program "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 > add_default_args: warning: adding default arguments for unregistered > program "resample_labels" at /usr/bin/nu_estimate_np_and_em line 1683 > add_default_args: warning: adding default arguments for unregistered > program "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 > spawn: error: program "mincmath" not registered at > /usr/bin/nu_estimate_np_and_em line 673 > > I installed minc and n3 as per instructions. Am i missing some libraries? > Thanks > -- > TG > -- TG From claude at bic.mni.mcgill.ca Fri Sep 26 16:21:13 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Fri, 26 Sep 2008 16:21:13 -0400 (EDT) Subject: [MINC-users] problem with nu_estimate_np_and_em References: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> Message-ID: <200809262021.m8QKLDRk600346@yorick.bic.mni.mcgill.ca> Have you set the PATH accordingly? Or do a "rehash". Are the programs in /usr/bin/? Do a directory listing. File permissions??? > > Hi ! I tried running nu_estimate_np_and_em with the following options : > > > > $ nu_estimate_np_and_em -normalize_field -save_fields -mask mask.mnc > > breast.mnc fields_time.mnc > > > > I get the following error: > > > > nu_estimate_np_and_em: couldn't find program "class_statistics" > > nu_estimate_np_and_em: couldn't find program "estimate" > > add_default_args: warning: adding default arguments for unregistered > > program "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 > > add_default_args: warning: adding default arguments for unregistered > > program "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > > program "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > > program "resample_labels" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > > program "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 > > spawn: error: program "mincmath" not registered at > > /usr/bin/nu_estimate_np_and_em line 673 > > > > I installed minc and n3 as per instructions. Am i missing some libraries? > > Thanks > > -- > > TG > > > > > > -- > TG > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Mon Sep 29 01:04:08 2008 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 29 Sep 2008 15:04:08 +1000 Subject: [MINC-users] MINC2 is not thread safe? In-Reply-To: <48DD3D7E.60707@gmail.com> References: <48DD3D7E.60707@gmail.com> Message-ID: Hi Vlad, (to follow up from our chat so that others know). * I haven't tried this. * It *should* work with the MINC2 API on MINC2 files a > I was trying to write a small program that would process some minc files in > parallel. I am randomly getting one of the following error messags whenever > I am trying to read MINC files in parallel: -- Andrew J (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From tejasvinee at gmail.com Tue Sep 30 15:41:19 2008 From: tejasvinee at gmail.com (Tejaswini Ganapathi) Date: Tue, 30 Sep 2008 15:41:19 -0400 Subject: [MINC-users] problem with nu_estimate_np_and_em In-Reply-To: <200809262021.m8QKLDRk600346@yorick.bic.mni.mcgill.ca> References: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> <200809262021.m8QKLDRk600346@yorick.bic.mni.mcgill.ca> Message-ID: <6ec808c10809301241j1a5cd156qb1a4d5d157de933@mail.gmail.com> Hi Claude, All of my installed files (exe files) are in /usr/bin. Infact nu_correct, nu_estimate and nu_evaluate work fine. I'm having this problem only with nu_estimate_np_and_em Ive tried the following on the shell command line, $ nu_estimate_np_and_em -normalize_field -save_fields -mask mask.mnc breast.mnc fields_time.mnc $ nu_estimate_np_and_em -clobber -normalize_field -initial fieldimages.mnc breastimages.mnc breastfields.imp And I get exactly the same error, nu_estimate_np_and_em: couldn't find program "class_statistics" nu_estimate_np_and_em: couldn't find program "estimate" add_default_args: warning: adding default arguments for unregistered program "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 add_default_args: warning: adding default arguments for unregistered program "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 add_default_args: warning: adding default arguments for unregistered program "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 add_default_args: warning: adding default arguments for unregistered program "resample_labels" at /usr/bin/nu_estimate_np_and_em line 1683 add_default_args: warning: adding default arguments for unregistered program "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 spawn: error: program "mincmath" not registered at /usr/bin/nu_estimate_np_and_em line 673 The file permissions are fine, as the software works for nu_estimate, nu_evaluate and nu_correct. Can you please help me with this? Thanks, TG On Fri, Sep 26, 2008 at 4:21 PM, Claude LEPAGE wrote: > > Have you set the PATH accordingly? Or do a "rehash". Are the programs > in /usr/bin/? Do a directory listing. File permissions??? > > > > > Hi ! I tried running nu_estimate_np_and_em with the following options : > > > > > > $ nu_estimate_np_and_em -normalize_field -save_fields -mask mask.mnc > > > breast.mnc fields_time.mnc > > > > > > I get the following error: > > > > > > nu_estimate_np_and_em: couldn't find program "class_statistics" > > > nu_estimate_np_and_em: couldn't find program "estimate" > > > add_default_args: warning: adding default arguments for unregistered > > > program "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 > > > add_default_args: warning: adding default arguments for unregistered > > > program "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 > > > add_default_args: warning: adding default arguments for unregistered > > > program "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 > > > add_default_args: warning: adding default arguments for unregistered > > > program "resample_labels" at /usr/bin/nu_estimate_np_and_em line 1683 > > > add_default_args: warning: adding default arguments for unregistered > > > program "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 > > > spawn: error: program "mincmath" not registered at > > > /usr/bin/nu_estimate_np_and_em line 673 > > > > > > I installed minc and n3 as per instructions. Am i missing some > libraries? > > > Thanks > > > -- > > > TG > > > > > > > > > > > -- > > TG > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From tejasvinee at gmail.com Tue Sep 30 17:00:17 2008 From: tejasvinee at gmail.com (Tejaswini Ganapathi) Date: Tue, 30 Sep 2008 17:00:17 -0400 Subject: [MINC-users] problem with nu_estimate_np_and_em In-Reply-To: <200809302004.m8UK4gd0059804@yorick.bic.mni.mcgill.ca> References: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> <200809262021.m8QKLDRk600346@yorick.bic.mni.mcgill.ca> <200809302004.m8UK4gd0059804@yorick.bic.mni.mcgill.ca> Message-ID: <6ec808c10809301400w780a88a0x72b4a8959f0f95a@mail.gmail.com> Yes, I am working with MNI. I have installed MNI-N3 v1.10, netcdf v4.0, minc v1.5 on a windows XP system running cygwin, and I got all of them from the MNI site. Is there something obviously wrong because of which nu_estimate_np_and_em doesn't seem to work? Thanks, TG On Tue, Sep 30, 2008 at 4:04 PM, Claude LEPAGE wrote: > Hi, > > Are you working at the BIC/MNI? If so, it will be easier to solve your > problem. If not, it will be very difficult. I don't know what package you > installed, how, where you got it from, on which system. I suspect that > your package is not properly installed or there is some package missing. > MNI software is open source, but I don't provide support for installation. > Sorry. > > Claude > > > > > > > Hi Claude, > > All of my installed files (exe files) are in /usr/bin. Infact nu_correct, > > nu_estimate and nu_evaluate work fine. I'm having this problem only with > > nu_estimate_np_and_em > > > > Ive tried the following on the shell command line, > > $ nu_estimate_np_and_em -normalize_field -save_fields -mask > > mask.mnc breast.mnc fields_time.mnc > > > > $ nu_estimate_np_and_em -clobber -normalize_field -initial > fieldimages.mnc > > breastimages.mnc breastfields.imp > > > > And I get exactly the same error, > > > > nu_estimate_np_and_em: couldn't find program "class_statistics" > > nu_estimate_np_and_em: couldn't find program "estimate" > > add_default_args: warning: adding default arguments for unregistered > program > > "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 > > add_default_args: warning: adding default arguments for unregistered > program > > "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > program > > "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > program > > "resample_labels" at /usr/bin/nu_estimate_np_and_em line 1683 > > add_default_args: warning: adding default arguments for unregistered > program > > "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 > > spawn: error: program "mincmath" not registered at > > /usr/bin/nu_estimate_np_and_em line 673 > > > > The file permissions are fine, as the software works for nu_estimate, > > nu_evaluate and nu_correct. Can you please help me with this? > > > > Thanks, > > TG > > > > > > > > On Fri, Sep 26, 2008 at 4:21 PM, Claude LEPAGE >wrote: > > > > > > > > Have you set the PATH accordingly? Or do a "rehash". Are the programs > > > in /usr/bin/? Do a directory listing. File permissions??? > > > > > > > > > > > Hi ! I tried running nu_estimate_np_and_em with the following options > : > > > > > > > > > > $ nu_estimate_np_and_em -normalize_field -save_fields -mask > mask.mnc > > > > > breast.mnc fields_time.mnc > > > > > > > > > > I get the following error: > > > > > > > > > > nu_estimate_np_and_em: couldn't find program "class_statistics" > > > > > nu_estimate_np_and_em: couldn't find program "estimate" > > > > > add_default_args: warning: adding default arguments for > unregistered > > > > > program "estimate" at /usr/bin/nu_estimate_np_and_em line 1678 > > > > > add_default_args: warning: adding default arguments for > unregistered > > > > > program "spline_smooth" at /usr/bin/nu_estimate_np_and_em line 1683 > > > > > add_default_args: warning: adding default arguments for > unregistered > > > > > program "mincresample" at /usr/bin/nu_estimate_np_and_em line 1683 > > > > > add_default_args: warning: adding default arguments for > unregistered > > > > > program "resample_labels" at /usr/bin/nu_estimate_np_and_em line > 1683 > > > > > add_default_args: warning: adding default arguments for > unregistered > > > > > program "mincmath" at /usr/bin/nu_estimate_np_and_em line 1683 > > > > > spawn: error: program "mincmath" not registered at > > > > > /usr/bin/nu_estimate_np_and_em line 673 > > > > > > > > > > I installed minc and n3 as per instructions. Am i missing some > > > libraries? > > > > > Thanks > > > > > -- > > > > > TG > > > > > > -- Tejaswini Ganapathi Apt #1705 33, Wood Street Toronto, ON M4Y2P8 Ph: +1 647 291 1486 From a.janke at gmail.com Tue Sep 30 20:27:04 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 1 Oct 2008 10:27:04 +1000 Subject: [MINC-users] problem with nu_estimate_np_and_em In-Reply-To: <6ec808c10809301241j1a5cd156qb1a4d5d157de933@mail.gmail.com> References: <6ec808c10809251401o65ef869bsf84e14c4fcccb8d@mail.gmail.com> <200809262021.m8QKLDRk600346@yorick.bic.mni.mcgill.ca> <6ec808c10809301241j1a5cd156qb1a4d5d157de933@mail.gmail.com> Message-ID: Hi, On Wed, Oct 1, 2008 at 5:41 AM, Tejaswini Ganapathi wrote: > All of my installed files (exe files) are in /usr/bin. Infact nu_correct, > nu_estimate and nu_evaluate work fine. I'm having this problem only with > nu_estimate_np_and_em > > Ive tried the following on the shell command line, > $ nu_estimate_np_and_em -normalize_field -save_fields -mask > mask.mnc breast.mnc fields_time.mnc > > nu_estimate_np_and_em: couldn't find program "class_statistics" > nu_estimate_np_and_em: couldn't find program "estimate" I reckon you have hit on a bug. And amusingly I cannot find these two executables that you are talking about on my system (or yorick!) either. I suspect that you are using a little used part of the N3 package that has escaped inspection/execution for a long time. Now we just have to find what these two little programs do, John!? :) -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883