From a.janke at gmail.com Mon Sep 6 09:26:02 2010 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 6 Sep 2010 23:26:02 +1000 Subject: [MINC-users] register and Display issues on Nvidia hardware + later versions of Ubuntu/Fedora. In-Reply-To: References: Message-ID: And as a follow up to this: http://packages.bic.mni.mcgill.ca/tgz/Display-1.5.0.tar.gz Updated binary packages will follow shortly. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From pgravel at bic.mni.mcgill.ca Thu Sep 9 10:06:40 2010 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 9 Sep 2010 10:06:40 -0400 (EDT) Subject: [MINC-users] CIVET ? In-Reply-To: References: Message-ID: Dear All, I would like to start using CIVET, but was wondering how to go about it, i.e. can it be used by anyone at the BIC? If so, how does one get setup? Any help will be appreciated. Best Regards, Paul From a.janke at gmail.com Thu Sep 9 10:32:11 2010 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 10 Sep 2010 00:32:11 +1000 Subject: [MINC-users] CIVET ? In-Reply-To: References: Message-ID: Hi Paul, On Fri, Sep 10, 2010 at 00:06, Paul GRAVEL wrote: > I would like to start using CIVET, but was wondering how to go about it, > i.e. can it be used by anyone at the BIC? ?If so, how does one get setup? CIVET is developed by Prof Alan Evans group at the BIC, we don't have a binary package or source code for it as of yet and I don't know of any plans for this. As such, you'd be best to contact Alan directly regarding a version of CIVET. Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From pgravel at bic.mni.mcgill.ca Thu Sep 9 19:49:12 2010 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 9 Sep 2010 19:49:12 -0400 (EDT) Subject: [MINC-users] CIVET ? In-Reply-To: References: Message-ID: Thanks to all who replied! I shall look into your suggestions! Best, Paul On Thu, 9 Sep 2010, Paul GRAVEL wrote: > Dear All, > > I would like to start using CIVET, but was wondering how to go about it, i.e. > can it be used by anyone at the BIC? If so, how does one get setup? > > Any help will be appreciated. > > Best Regards, > > Paul > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From v.popescu at vumc.nl Wed Sep 15 11:32:46 2010 From: v.popescu at vumc.nl (Popescu, V. ) Date: Wed, 15 Sep 2010 17:32:46 +0200 Subject: [MINC-users] N3 problem Message-ID: <6D6611E81E29754A80F752BFCDB5303502AE1D54@vumc-mb02.vumc.nl> Dear all, I have a problem running standard N3. It works perfectly on all scans except for one, and I cannot see any striking difference between that particular scans and the rest from the same protocol. It stops after the first iteration (default=4) and I get the following message: CV of field change: 0.000983288 Transforming slices:............................................Done inputCompactField(): Incorrect number of coefficients Failure reading field file: /data/iac11/aca/onep/veronica/MAGNIMS3DBET/imagesforgrid/theinfamous143/ Manbetset143_noneckN3.imp nu_evaluate: crashed while running evaluate_field (termination status=256) nu_correct: crashed while running nu_evaluate (termination status=256) In the directory I have now besides the original image a . imp file. I would appreciate any suggestions. Thank you! Veronica From vladimir.fonov at gmail.com Wed Sep 15 15:09:04 2010 From: vladimir.fonov at gmail.com (Vladimir Fonov) Date: Wed, 15 Sep 2010 15:09:04 -0400 Subject: [MINC-users] N3 problem In-Reply-To: <6D6611E81E29754A80F752BFCDB5303502AE1D54@vumc-mb02.vumc.nl> References: <6D6611E81E29754A80F752BFCDB5303502AE1D54@vumc-mb02.vumc.nl> Message-ID: Hello, sometimes this kind of a problem is caused by irregular sampling of the minc file (it usually happens due to the glitches in dicom to minc conversion). You can check if it is the case by using mincheader command and searching for irregular word in image dimensions description part ( xspace,yspace,zspace attributes) On Wed, Sep 15, 2010 at 11:32 AM, Popescu, V. wrote: > Dear all, > I have a problem running standard N3. It works perfectly on all scans > except for one, and I cannot see any striking difference between that > particular scans and the rest from the same protocol. It stops after the > first iteration (default=4) and I get the following message: > > CV of field change: 0.000983288 > Transforming slices:............................................Done > inputCompactField(): Incorrect number of coefficients -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From kojinet at bic.mni.mcgill.ca Wed Sep 15 18:49:26 2010 From: kojinet at bic.mni.mcgill.ca (Ji Hyum KO) Date: Wed, 15 Sep 2010 18:49:26 -0400 (EDT) Subject: [MINC-users] mincaverage gives float numbers for integers Message-ID: Hi, What I am trying to do is to combind masks (segmented) that are in five seperate volume. So, volume 1 has grey matter, volume 2 has white matter, volume 3 has striatum, etc... Each volume do not have overlapping voxels. In order to give different integer values, I multiplied the masks with 1, 2, 3, 4 or 5. Then, mincaverage all volume, then mincmath -mult -const 5... The resulted image has weird float values such as 2.0252... How can I make them clean integer values like 2.000000 Best, Ji Hyun From v.popescu at vumc.nl Fri Sep 17 03:35:04 2010 From: v.popescu at vumc.nl (Popescu, V. ) Date: Fri, 17 Sep 2010 09:35:04 +0200 Subject: [MINC-users] N3 problem (Vladimir Fonov) In-Reply-To: Message-ID: <6D6611E81E29754A80F752BFCDB5303502AE1ECB@vumc-mb02.vumc.nl> Dear Vladimir, Thanks for your answer. I ran the mincheader command and I got the following output. It looks fine to me. Plus I converted the image from nifti and not directly from DICOM. netcdf Manbetset143_noneck { dimensions: xspace = 128 ; yspace = 240 ; zspace = 196 ; variables: int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image" ; double xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = 1.20000004768372 ; xspace:start = -74.5828010946915 ; xspace:direction_cosines = -0.995703348275213, 0.0888212777983069, -0.0261844007723182 ; xspace:units = "mm" ; double yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 1. ; yspace:start = -105.174504296302 ; yspace:direction_cosines = 0.08885174879246, 0.996044861809147, -3.43728227382414e-07 ; yspace:units = "mm" ; double zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 1. ; zspace:start = -141.503699403711 ; zspace:direction_cosines = -0.0260808070375557, 0.00232687191043303, 0.999657129805706 ; zspace:units = "mm" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; float image(xspace, yspace, zspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:complete = "true_" ; image:signtype = "signed__" ; image:valid_range = 0.f, 1078.f ; // global attributes: :history = "" ; data: rootvariable = _ ; xspace = 0 ; yspace = 0 ; zspace = 0 ; image-min = _ ; image-max = 1078 ; } Today's Topics: 1. Re: N3 problem (Vladimir Fonov) 2. mincaverage gives float numbers for integers (Ji Hyum KO) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Sep 2010 15:09:04 -0400 From: Vladimir Fonov Subject: Re: [MINC-users] N3 problem To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hello, sometimes this kind of a problem is caused by irregular sampling of the minc file (it usually happens due to the glitches in dicom to minc conversion). You can check if it is the case by using mincheader command and searching for irregular word in image dimensions description part ( xspace,yspace,zspace attributes) On Wed, Sep 15, 2010 at 11:32 AM, Popescu, V. wrote: > Dear all, > I have a problem running standard N3. It works perfectly on all scans > except for one, and I cannot see any striking difference between that > particular scans and the rest from the same protocol. It stops after the > first iteration (default=4) and I get the following message: > > CV of field change: 0.000983288 > Transforming slices:............................................Done > inputCompactField(): Incorrect number of coefficients -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From sorench at gmail.com Mon Sep 27 22:30:07 2010 From: sorench at gmail.com (Soren Christensen) Date: Tue, 28 Sep 2010 12:30:07 +1000 Subject: [MINC-users] compiling Display 1.5.0 Message-ID: Hi, When compiling Display 1.5.0, i get no resulting binary, yet no errors when building. the last 'make' action starts with: /bin/sh ./libtool --tag=CC --mode=link gcc -g -O2 -L/usr/local/lib/ -L/usr/local/hdf5-1.8.5/lib -L/usr/local/mni/lib -o Display dummy.o main/main.o main/display.o ..... lots of .o files If I omit /bin/sh ./libtool --tag=CC --mode=link and start from gcc, then Display builds. Any ideas why this libtool is not working for me? Soren From a.janke at gmail.com Wed Sep 29 02:03:59 2010 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 29 Sep 2010 16:03:59 +1000 Subject: [MINC-users] compiling Display 1.5.0 In-Reply-To: References: Message-ID: On Tue, Sep 28, 2010 at 12:30, Soren Christensen wrote: > ?When compiling Display 1.5.0, i get no resulting binary, yet no > errors when building. > the last 'make' action starts with: > /bin/sh ./libtool --tag=CC ? --mode=link gcc ?-g -O2 > -L/usr/local/lib/ -L/usr/local/hdf5-1.8.5/lib -L/usr/local/mni/lib -o > Display dummy.o main/main.o main/display.o ..... lots of .o files > > If I omit /bin/sh ./libtool --tag=CC ? --mode=link and start from gcc, > then Display builds. Hi Soren, I can't help but I can say that you are not alone. This seems to happen on later versions of libtool (or at least the one that comes with Ubuntu Lynx). The only work-around I have found is to do a 'make install' in a local directory and use that. Andrew From sorench at gmail.com Wed Sep 29 02:10:13 2010 From: sorench at gmail.com (Soren Christensen) Date: Wed, 29 Sep 2010 16:10:13 +1000 Subject: [MINC-users] compiling Display 1.5.0 In-Reply-To: References: Message-ID: Thanks Andrew, Yes not a real problem as it builds ok. Cheers Soren On Wed, Sep 29, 2010 at 4:03 PM, Andrew Janke wrote: > On Tue, Sep 28, 2010 at 12:30, Soren Christensen > wrote: > > When compiling Display 1.5.0, i get no resulting binary, yet no > > errors when building. > > the last 'make' action starts with: > > /bin/sh ./libtool --tag=CC --mode=link gcc -g -O2 > > -L/usr/local/lib/ -L/usr/local/hdf5-1.8.5/lib -L/usr/local/mni/lib -o > > Display dummy.o main/main.o main/display.o ..... lots of .o files > > > > If I omit /bin/sh ./libtool --tag=CC --mode=link and start from gcc, > > then Display builds. > > Hi Soren, > > I can't help but I can say that you are not alone. This seems to > happen on later versions of libtool (or at least the one that comes > with Ubuntu Lynx). The only work-around I have found is to do a 'make > install' in a local directory and use that. > > > Andrew > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Wed Sep 29 13:51:23 2010 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 30 Sep 2010 03:51:23 +1000 Subject: [MINC-users] N3 problem (Vladimir Fonov) In-Reply-To: <6D6611E81E29754A80F752BFCDB5303502AE1ECB@vumc-mb02.vumc.nl> References: <6D6611E81E29754A80F752BFCDB5303502AE1ECB@vumc-mb02.vumc.nl> Message-ID: On Fri, Sep 17, 2010 at 17:35, Popescu, V. wrote: > Dear Vladimir, > Thanks for your answer. > I ran the mincheader command and I got the following output. > It looks fine to me. Plus I converted the image from nifti and not > directly from DICOM. Well from the headers it would seem that this is not the problem this time. (although it often is). Can I ask what version of N3 you are using? There was a long standing bug regarding spline sampling that we fixed a few years back, it only occurred in certain very specific cases of image dimensions and steps. If this is the problem then if you do something as simple as adding one slice in the Z direction: mincreshape -dimrange zspace=0,197 in.mnc out.mnc before running N3 then odds are it should "just work". Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From v.popescu at vumc.nl Thu Sep 30 13:09:10 2010 From: v.popescu at vumc.nl (Popescu, V. ) Date: Thu, 30 Sep 2010 19:09:10 +0200 Subject: [MINC-users] N3 problem (Andrew Janke) In-Reply-To: Message-ID: <6D6611E81E29754A80F752BFCDB5303502BA4129@vumc-mb02.vumc.nl> Dear Andrew, Thank you very much for your help! Now it finally works, with the slice added! And I am using version 1.10. Thanks again! Best wishes, Veronica -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of minc-users-request at bic.mni.mcgill.ca Sent: donderdag 30 september 2010 18:00 To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 62, Issue 9 Send MINC-users mailing list submissions to minc-users at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-users-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." Today's Topics: 1. Re: N3 problem (Vladimir Fonov) (Andrew Janke) ---------------------------------------------------------------------- Message: 1 Date: Thu, 30 Sep 2010 03:51:23 +1000 From: Andrew Janke Subject: Re: [MINC-users] N3 problem (Vladimir Fonov) To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 On Fri, Sep 17, 2010 at 17:35, Popescu, V. wrote: > Dear Vladimir, > Thanks for your answer. > I ran the mincheader command and I got the following output. > It looks fine to me. Plus I converted the image from nifti and not > directly from DICOM. Well from the headers it would seem that this is not the problem this time. (although it often is). Can I ask what version of N3 you are using? There was a long standing bug regarding spline sampling that we fixed a few years back, it only occurred in certain very specific cases of image dimensions and steps. If this is the problem then if you do something as simple as adding one slice in the Z direction: mincreshape -dimrange zspace=0,197 in.mnc out.mnc before running N3 then odds are it should "just work". Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 ------------------------------ _______________________________________________ MINC-users mailing list MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest, Vol 62, Issue 9 *****************************************