From a.janke at gmail.com Fri Jul 8 00:25:37 2011 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 8 Jul 2011 14:25:37 +1000 Subject: [MINC-users] brain-view In-Reply-To: References: Message-ID: Hi Emily, I have talked to Jason Lerch (the Author) and yes brain-view is still maintained. I have been building an older release for a while that is broken with later QT releases. Suffice to say I will be have a crack at building you a new .deb version tonight. For reference, the latest version of brain-view can be found here (in source form). https://launchpad.net/brain-view Thanks a On Fri, Jul 8, 2011 at 10:24, Emily Segal wrote: > Hi minc-users, > Is brain-view no longer being supported? I would like to install brain-view > but there does not seem to be an up-to-date package available that works > with my OS. I am running Ubuntu 10.04. > Please let me know what I can do to get it up and running. > Thanks, > Emily > From pgravel at bic.mni.mcgill.ca Thu Jul 14 03:00:08 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 14 Jul 2011 03:00:08 -0400 (EDT) Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: References: Message-ID: Dear all, Would anyone know if it is possible to run minctracc on 2D minc volumes? I am running some 2D simulations in different orientations and I would like to estimate some transformations using minctracc (I would like to avoid the need to create 3D volumes if possible). I have tried it but to no avail, i.e. the output xfm file contains nan values (please see below for output). Any suggestions would be greatly appreciated. Best Regards, Paul _________________________________ [2D_MINC] 218% minctracc -clobber -mi -lsq6 xtrue_rot45deg.mnc xtrue_target_0deg.mnc xtrue_45deg2_0deg.xfm COG of v1: -0.800728 3.766018 0.000000 COG of v2: 3.196798 2.931377 0.000000 [trans] = 3.997526 -0.834641 0.000000 WARNING: source volume not UNSIGNED_BYTE, will do conversion now. WARNING: target volume not UNSIGNED_BYTE, will do conversion now. out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.8491=F 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T 0.0000=T 0.0000=T 0.0000=T Initial objective function val = 10000000000.00000000 Final objective function value = 10000000000.00000000 [2D_MINC] 221% xfm2param xtrue_45deg2_0deg.xfm after parameter extraction -center 0.00000 0.00000 0.00000 -translation nan nan nan -rotation nan nan nan -scale nan nan nan -shear nan nan nan [2D_MINC] 222% mincinfo xtrue_rot45deg.mnc file: xtrue_rot45deg.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 1 -1.21875 -0 yspace 256 1.21875 -155.391 xspace 256 1.21875 -155.391 [2D_MINC] 223% mincinfo xtrue_target_0deg.mnc file: xtrue_target_0deg.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 1 -1.21875 -0 yspace 256 1.21875 -155.391 xspace 256 1.21875 -155.391 From mallar.chak at gmail.com Thu Jul 14 04:31:11 2011 From: mallar.chak at gmail.com (Mallar Chakravarty) Date: Thu, 14 Jul 2011 04:31:11 -0400 Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: References: Message-ID: Hi Paul, It?s tricky to get minctracc to work on 2D slices in linear mode. I would suggest using the -w_translations and -w_rotations options that you basically ?turn off? the out of plane components by using an absurdly small value. mallar On Thu, Jul 14, 2011 at 3:00 AM, Paul GRAVEL wrote: > Dear all, > > Would anyone know if it is possible to run minctracc on 2D minc volumes? > > I am running some 2D simulations in different orientations and I would like > to estimate some transformations using minctracc (I would like to avoid the > need to create 3D volumes if possible). I have tried it but to no avail, > i.e. the output xfm file contains nan values (please see below for output). > > Any suggestions would be greatly appreciated. > > Best Regards, > > Paul > ______________________________**___ > > [2D_MINC] 218% minctracc -clobber -mi -lsq6 xtrue_rot45deg.mnc > xtrue_target_0deg.mnc xtrue_45deg2_0deg.xfm > > COG of v1: -0.800728 3.766018 0.000000 > COG of v2: 3.196798 2.931377 0.000000 > [trans] = 3.997526 -0.834641 0.000000 > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.8491=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > Initial objective function val = 10000000000.00000000 > Final objective function value = 10000000000.00000000 > > [2D_MINC] 221% xfm2param xtrue_45deg2_0deg.xfm > after parameter extraction > -center 0.00000 0.00000 0.00000 > -translation nan nan nan > -rotation nan nan nan > -scale nan nan nan > -shear nan nan nan > > [2D_MINC] 222% mincinfo xtrue_rot45deg.mnc > file: xtrue_rot45deg.mnc > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 1 -1.21875 -0 > yspace 256 1.21875 -155.391 > xspace 256 1.21875 -155.391 > > [2D_MINC] 223% mincinfo xtrue_target_0deg.mnc > file: xtrue_target_0deg.mnc > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 1 -1.21875 -0 > yspace 256 1.21875 -155.391 > xspace 256 1.21875 -155.391 > > ______________________________**_________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users > From sorench at gmail.com Thu Jul 14 05:09:56 2011 From: sorench at gmail.com (Soren Christensen) Date: Thu, 14 Jul 2011 19:09:56 +1000 Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: References: Message-ID: Hi Paul, Adding to that, you may want to try padding with two all-zero slices in each z-extreme (on top of what Mallar suggested). I had to do that to force and in-plane registration only. It was a tip from Andrew. Cheers Soren On Thu, Jul 14, 2011 at 6:31 PM, Mallar Chakravarty wrote: > Hi Paul, > > It?s tricky to get minctracc to work on 2D slices in linear mode. I would > suggest using the -w_translations and -w_rotations options that you > basically ?turn off? the out of plane components by using an absurdly small > value. > > mallar > > On Thu, Jul 14, 2011 at 3:00 AM, Paul GRAVEL >wrote: > > > Dear all, > > > > Would anyone know if it is possible to run minctracc on 2D minc volumes? > > > > I am running some 2D simulations in different orientations and I would > like > > to estimate some transformations using minctracc (I would like to avoid > the > > need to create 3D volumes if possible). I have tried it but to no avail, > > i.e. the output xfm file contains nan values (please see below for > output). > > > > Any suggestions would be greatly appreciated. > > > > Best Regards, > > > > Paul > > ______________________________**___ > > > > [2D_MINC] 218% minctracc -clobber -mi -lsq6 xtrue_rot45deg.mnc > > xtrue_target_0deg.mnc xtrue_45deg2_0deg.xfm > > > > COG of v1: -0.800728 3.766018 0.000000 > > COG of v2: 3.196798 2.931377 0.000000 > > [trans] = 3.997526 -0.834641 0.000000 > > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.8491=F 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > > 0.0000=T 0.0000=T 0.0000=T > > Initial objective function val = 10000000000.00000000 > > Final objective function value = 10000000000.00000000 > > > > [2D_MINC] 221% xfm2param xtrue_45deg2_0deg.xfm > > after parameter extraction > > -center 0.00000 0.00000 0.00000 > > -translation nan nan nan > > -rotation nan nan nan > > -scale nan nan nan > > -shear nan nan nan > > > > [2D_MINC] 222% mincinfo xtrue_rot45deg.mnc > > file: xtrue_rot45deg.mnc > > image: signed__ short -32768 to 32767 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 1 -1.21875 -0 > > yspace 256 1.21875 -155.391 > > xspace 256 1.21875 -155.391 > > > > [2D_MINC] 223% mincinfo xtrue_target_0deg.mnc > > file: xtrue_target_0deg.mnc > > image: signed__ short -32768 to 32767 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 1 -1.21875 -0 > > yspace 256 1.21875 -155.391 > > xspace 256 1.21875 -155.391 > > > > ______________________________**_________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users< > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users> > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Jul 14 06:28:58 2011 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 14 Jul 2011 20:28:58 +1000 Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: References: Message-ID: > Soren said: > ?Adding to that, you may want to try padding with two all-zero slices in > each z-extreme (on top of what Mallar suggested). > I had to do that to force and in-plane registration only. > Mallar said: >> It?s tricky to get minctracc to work on 2D slices in linear mode. ?I would >> suggest using the -w_translations and -w_rotations options that you >> basically ?turn off? the out of plane components by using an absurdly small >> value. I'll bow to Mallars experience with this here... But to add a bit of "practicality" here's how I would approach using this advice. First, remember that minctracc expects a 3D volume, so let's give it one. Make your z slice big and thick so that rotations out of plane are penalised by minctracc: (beware! minc_modify_header modifies your file in place!) $ minc_modify_header -dinsert zspace:step 20 xtrue_rot45deg.mnc Then add a "blank" slice either side to further penalise minctracc for doing out of plane rotations: $ mincreshape -dimrange zspace=-1,3 xtrue_rot45deg.mnc expanded.mnc And not run minctracc using the arguments that Mallar suggests: $ minctracc -lsq6 -w_translations 1 1 0.0001 \ -w_rotations 0.00001 0.00001 0.017453 \ expanded.mnc expanded2.mnc out.xfm (you will have to apply the same treatment to your target file to make expanded2.mnc) Let us know how it goes, this seems to be a recurring question so it'd be nice to put this up on wikibooks somewhere if this recipie works well. Thanks a From claude at bic.mni.mcgill.ca Thu Jul 14 08:26:18 2011 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Thu, 14 Jul 2011 08:26:18 -0400 Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: Message-ID: <201107141226.p6ECQIvu005366@cassio.bic.mni.mcgill.ca> Hi Paul, I have demonstrated the capabilities of minctracc to run in 2D mode on histology slices (volume N x M x 1 - 1 slice thickness) in linear and non-linear mode. You need your slice to be in x,y plane, account for weights and lattice size in z-direction, and finally mincblur in 2D. If I recall, don't include shear (lsq12) in your linear registration. The rest works. Shear may work too but I haven't figured it out completely. You need to give a non-zero (+ve ??) voxel thickness in the z-direction and have the 2 slices at the same z start. Seems that the latter is done. Perhaps you can drop by my office next time you go breathing at the corner of BTRC. :-) We'll try it out on your demo mnc file below. Claude > Dear all, > > Would anyone know if it is possible to run minctracc on 2D minc volumes? > > I am running some 2D simulations in different orientations and I would > like to estimate some transformations using minctracc (I would like to > avoid the need to create 3D volumes if possible). I have tried it but to > no avail, i.e. the output xfm file contains nan values (please see below > for output). > > Any suggestions would be greatly appreciated. > > Best Regards, > > Paul > _________________________________ > > [2D_MINC] 218% minctracc -clobber -mi -lsq6 xtrue_rot45deg.mnc xtrue_target_0deg.mnc xtrue_45deg2_0deg.xfm > > COG of v1: -0.800728 3.766018 0.000000 > COG of v2: 3.196798 2.931377 0.000000 > [trans] = 3.997526 -0.834641 0.000000 > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.8491=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.6164=F 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.4418=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > out : nan=F nan=F 1.5000=T 1.0000=T 1.0000=T 1.0000=T > 0.0000=T 0.0000=T 0.0000=T > Initial objective function val = 10000000000.00000000 > Final objective function value = 10000000000.00000000 > > [2D_MINC] 221% xfm2param xtrue_45deg2_0deg.xfm > after parameter extraction > -center 0.00000 0.00000 0.00000 > -translation nan nan nan > -rotation nan nan nan > -scale nan nan nan > -shear nan nan nan > > [2D_MINC] 222% mincinfo xtrue_rot45deg.mnc > file: xtrue_rot45deg.mnc > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 1 -1.21875 -0 > yspace 256 1.21875 -155.391 > xspace 256 1.21875 -155.391 > > [2D_MINC] 223% mincinfo xtrue_target_0deg.mnc > file: xtrue_target_0deg.mnc > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 1 -1.21875 -0 > yspace 256 1.21875 -155.391 > xspace 256 1.21875 -155.391 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Thu Jul 14 11:35:10 2011 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 14 Jul 2011 11:35:10 -0400 Subject: [MINC-users] Article: Neuroscience runs on GNU/Linux Message-ID: I thought this article might interest some of you http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00008/full From vladimir.fonov at gmail.com Thu Jul 14 11:45:59 2011 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 14 Jul 2011 11:45:59 -0400 Subject: [MINC-users] Article: Neuroscience runs on GNU/Linux In-Reply-To: References: Message-ID: Hello, we (me and Louis) actually met these guys at HBM - they were willing to offer help in maintaining MINC tools in NeuroDebian, provided that we make all the software packages comply with Debian standards. On Thu, Jul 14, 2011 at 11:35 AM, Alex Zijdenbos wrote: > I thought this article might interest some of you > > http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00008/full > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From pgravel at bic.mni.mcgill.ca Thu Jul 14 13:04:35 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 14 Jul 2011 13:04:35 -0400 (EDT) Subject: [MINC-users] minctracc on 2D volumes? In-Reply-To: References: Message-ID: Dear all, Thank you very much for your replies! Mallar, Soren, and Andrew, I apologies but I will use Claude's approach, hope you don't mind ;-)! Claude has solved the problem (many thanks Claude!). Have a good day! Paul On Thu, 14 Jul 2011, Andrew Janke wrote: >> Soren said: >> ?Adding to that, you may want to try padding with two all-zero slices in >> each z-extreme (on top of what Mallar suggested). >> I had to do that to force and in-plane registration only. > >> Mallar said: >>> It?s tricky to get minctracc to work on 2D slices in linear mode. ?I would >>> suggest using the -w_translations and -w_rotations options that you >>> basically ?turn off? the out of plane components by using an absurdly small >>> value. > > I'll bow to Mallars experience with this here... But to add a bit of > "practicality" here's how I would approach using this advice. > > First, remember that minctracc expects a 3D volume, so let's give it one. > > Make your z slice big and thick so that rotations out of plane > are penalised by minctracc: > (beware! minc_modify_header modifies your file in place!) > > $ minc_modify_header -dinsert zspace:step 20 xtrue_rot45deg.mnc > > Then add a "blank" slice either side to further penalise minctracc for > doing out of plane rotations: > > $ mincreshape -dimrange zspace=-1,3 xtrue_rot45deg.mnc expanded.mnc > > And not run minctracc using the arguments that Mallar suggests: > > $ minctracc -lsq6 -w_translations 1 1 0.0001 \ > -w_rotations 0.00001 0.00001 0.017453 \ > expanded.mnc expanded2.mnc out.xfm > > (you will have to apply the same treatment to your target file to make > expanded2.mnc) > > Let us know how it goes, this seems to be a recurring question so it'd > be nice to put this up on wikibooks somewhere if this recipie works > well. > > Thanks > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From atipirne at stanford.edu Fri Jul 15 17:22:29 2011 From: atipirne at stanford.edu (Aaryani Tipirneni) Date: Fri, 15 Jul 2011 14:22:29 -0700 (PDT) Subject: [MINC-users] xfmconcat Message-ID: <1497518735.61141.1310764949630.JavaMail.root@zm04.stanford.edu> Hi MINC experts, I would like to know what operation does xfmconcat does when I use xfmconcat for two xfm files (i.e., what operation it performs on the trasnformation matrices). I tried looking into the code, but couldn't figure out. If anyone knows please tell me what operation it does on the transformation matrices. Thanks for your time, Aaryani From mallar.chak at gmail.com Sat Jul 16 04:10:08 2011 From: mallar.chak at gmail.com (Mallar Chakravarty) Date: Sat, 16 Jul 2011 09:10:08 +0100 Subject: [MINC-users] xfmconcat In-Reply-To: <1497518735.61141.1310764949630.JavaMail.root@zm04.stanford.edu> References: <1497518735.61141.1310764949630.JavaMail.root@zm04.stanford.edu> Message-ID: Hi Aaryani, It would probably make more sense to look at the guts of the output .xfm file (which is simply a text file). You'll see that the transformations simply get called in the order that you concatenated them in. mallar On Fri, Jul 15, 2011 at 10:22 PM, Aaryani Tipirneni wrote: > Hi MINC experts, > > I would like to know what operation does xfmconcat does when I use > xfmconcat for two xfm files (i.e., what operation it performs on the > trasnformation matrices). I tried looking into the code, but couldn't figure > out. If anyone knows please tell me what operation it does on the > transformation matrices. > > > Thanks for your time, > Aaryani > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Sat Jul 16 08:18:56 2011 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 16 Jul 2011 22:18:56 +1000 Subject: [MINC-users] xfmconcat In-Reply-To: <1497518735.61141.1310764949630.JavaMail.root@zm04.stanford.edu> References: <1497518735.61141.1310764949630.JavaMail.root@zm04.stanford.edu> Message-ID: Hi Aaryani, > I would like to know what operation does xfmconcat does when I use xfmconcat for two xfm files (i.e., what operation it performs on the trasnformation matrices). I tried looking into the code, but couldn't figure out. If anyone knows please tell me what operation it does on the transformation matrices. The operation for two successive transformation matricies is a simple matrix product. http://en.wikipedia.org/wiki/Transformation_matrix#Composing_and_inverting_transformations That said if xfmconcat can't combine two transformations the transformation will simply be listed in order in the .xfm file. This typically happens if the transforms being combined aren't all affine or already a combination of transform types. A good example of this is an output nonlinear transformation from minctracc. In this case the transformation is a combination of a linear affine transformation followed by a grid transform that is expressed in another MINC volume. a From lrisa87 at uw.edu Tue Jul 19 13:59:43 2011 From: lrisa87 at uw.edu (Lisa F. Akiyama) Date: Tue, 19 Jul 2011 10:59:43 -0700 Subject: [MINC-users] fit_stages Message-ID: Hello MINC experts, Could someone explain to me what the numerical values signify when you determine fit_stages (e.g. lin,lin,lin,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3). Thank you. Best, Lisa From a.janke at gmail.com Tue Jul 19 23:55:58 2011 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 20 Jul 2011 13:55:58 +1000 Subject: [MINC-users] fit_stages In-Reply-To: References: Message-ID: Hi Lisa, You are no doubt talking about volgenmodel? If so this argument defines the fitting stages. So if your fit config was this: cai-harold$ cat bin/fit.10-genmodel.conf # ICBM nlin conf @conf = ( {'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, {'step' => 16, 'blur_fwhm' => 8, 'iterations' => 20}, {'step' => 12, 'blur_fwhm' => 6, 'iterations' => 20}, {'step' => 8, 'blur_fwhm' => 4, 'iterations' => 20}, {'step' => 6, 'blur_fwhm' => 3, 'iterations' => 20}, {'step' => 4, 'blur_fwhm' => 2, 'iterations' => 10}, {'step' => 2, 'blur_fwhm' => 1, 'iterations' => 10}, ); Then a -fit_Stages argument of lin,lin,lin,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3 means: * do a 'lin' linear fit of all subjects and make a model. * do two more of the same above. (lin, lin) * do a fit of all subjects using up to line 0 from the fit_config, repeat 3 more times ({'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, * do a fit of all subjects up to line 1 of the fit config x 4 {'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, {'step' => 16, 'blur_fwhm' => 8, 'iterations' => 20}, .... a On 20 July 2011 03:59, Lisa F. Akiyama wrote: > Hello MINC experts, > > Could someone explain to me what the numerical values signify when > you determine fit_stages (e.g. lin,lin,lin,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3). > > Thank you. > > > Best, > Lisa > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From lrisa87 at uw.edu Wed Jul 20 13:38:51 2011 From: lrisa87 at uw.edu (Lisa F. Akiyama) Date: Wed, 20 Jul 2011 10:38:51 -0700 Subject: [MINC-users] fit_stages In-Reply-To: References: Message-ID: Hi Andrew, I had some assumptions about the fit_stages arguments values, but just wanted to clarify. Thank you for the explanation! Best, Lisa On Tue, Jul 19, 2011 at 8:55 PM, Andrew Janke wrote: > Hi Lisa, > > You are no doubt talking about volgenmodel? If so this argument > defines the fitting stages. > > So if your fit config was this: > > cai-harold$ cat bin/fit.10-genmodel.conf > # ICBM nlin conf > > @conf = ( > {'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, > {'step' => 16, 'blur_fwhm' => 8, 'iterations' => 20}, > {'step' => 12, 'blur_fwhm' => 6, 'iterations' => 20}, > {'step' => 8, 'blur_fwhm' => 4, 'iterations' => 20}, > {'step' => 6, 'blur_fwhm' => 3, 'iterations' => 20}, > {'step' => 4, 'blur_fwhm' => 2, 'iterations' => 10}, > {'step' => 2, 'blur_fwhm' => 1, 'iterations' => 10}, > ); > > Then a -fit_Stages argument of lin,lin,lin,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3 > means: > > * do a 'lin' linear fit of all subjects and make a model. > * do two more of the same above. (lin, lin) > > * do a fit of all subjects using up to line 0 from the fit_config, > repeat 3 more times > ({'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, > > * do a fit of all subjects up to line 1 of the fit config x 4 > {'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20}, > {'step' => 16, 'blur_fwhm' => 8, 'iterations' => 20}, > > .... > > > a > > On 20 July 2011 03:59, Lisa F. Akiyama wrote: > > Hello MINC experts, > > > > Could someone explain to me what the numerical values signify when > > you determine fit_stages (e.g. > lin,lin,lin,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3). > > > > Thank you. > > > > > > Best, > > Lisa > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From pgravel at bic.mni.mcgill.ca Fri Jul 22 15:51:13 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Fri, 22 Jul 2011 15:51:13 -0400 (EDT) Subject: [MINC-users] mincresample default interpolation method In-Reply-To: References: Message-ID: Dear All, Do you know which interpolation method mincresample is using as default? I am using mincresample version: [2D_MINC] 359% mincresample -version program: 1.5.1 libminc: 1.5.1 netcdf : "3.6.3" of Feb 24 2010 17:27:28 $ Thanks, Paul From vladimir.fonov at gmail.com Fri Jul 22 16:38:23 2011 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 22 Jul 2011 16:38:23 -0400 Subject: [MINC-users] mincresample default interpolation method In-Reply-To: References: Message-ID: Hello, it is trilinear . On Fri, Jul 22, 2011 at 3:51 PM, Paul GRAVEL wrote: > Dear All, > > Do you know which interpolation method mincresample is using as default? > > I am using mincresample version: > > [2D_MINC] 359% mincresample -version > program: 1.5.1 > libminc: 1.5.1 > netcdf : "3.6.3" of Feb 24 2010 17:27:28 $ > > Thanks, > > Paul > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From pgravel at bic.mni.mcgill.ca Fri Jul 22 17:09:29 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Fri, 22 Jul 2011 17:09:29 -0400 (EDT) Subject: [MINC-users] mincresample default interpolation method In-Reply-To: References: Message-ID: Many thanks! P. On Fri, 22 Jul 2011, Vladimir S. FONOV wrote: > Hello, > > it is trilinear . > > > On Fri, Jul 22, 2011 at 3:51 PM, Paul GRAVEL wrote: >> Dear All, >> >> Do you know which interpolation method mincresample is using as default? >> >> I am using mincresample version: >> >> [2D_MINC] 359% mincresample -version >> program: 1.5.1 >> libminc: 1.5.1 >> netcdf : "3.6.3" of Feb 24 2010 17:27:28 $ >> >> Thanks, >> >> Paul >> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > Best regards, > > ?Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From pgravel at bic.mni.mcgill.ca Sun Jul 24 16:00:52 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Sun, 24 Jul 2011 16:00:52 -0400 (EDT) Subject: [MINC-users] Reading and wrting MINC files in C In-Reply-To: References: Message-ID: Hello All, Is there a C procedure/program/library readily available to read/write MINC files in C? Something analogous to what EMMA does in matlab, i.e. getimages/putimages? Thanks, Paul From jason at phenogenomics.ca Sun Jul 24 17:41:49 2011 From: jason at phenogenomics.ca (Jason Lerch) Date: Sun, 24 Jul 2011 17:41:49 -0400 Subject: [MINC-users] Reading and wrting MINC files in C In-Reply-To: References: Message-ID: <932CD359-62F6-419D-9135-549D7E14CE61@phenogenomics.ca> Hi Paul, Yup, a plethora of choice. See the minc2 tutorials that can be found here: http://en.wikibooks.org/wiki/MINC/Tutorials And some C++ tutorials here: http://en.wikibooks.org/wiki/MINC/EZMINC/Tutorial Jason On 2011-07-24, at 4:00 PM, Paul GRAVEL wrote: > Hello All, > > Is there a C procedure/program/library readily available to read/write MINC files in C? Something analogous to what EMMA does in matlab, i.e. getimages/putimages? > > Thanks, > > Paul > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From pgravel at bic.mni.mcgill.ca Sun Jul 24 21:23:43 2011 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Sun, 24 Jul 2011 21:23:43 -0400 (EDT) Subject: [MINC-users] Reading and wrting MINC files in C In-Reply-To: <932CD359-62F6-419D-9135-549D7E14CE61@phenogenomics.ca> References: <932CD359-62F6-419D-9135-549D7E14CE61@phenogenomics.ca> Message-ID: Great; thanks! Paul On Sun, 24 Jul 2011, Jason Lerch wrote: > Hi Paul, > > Yup, a plethora of choice. See the minc2 tutorials that can be found here: > > http://en.wikibooks.org/wiki/MINC/Tutorials > > And some C++ tutorials here: > > http://en.wikibooks.org/wiki/MINC/EZMINC/Tutorial > > Jason > > On 2011-07-24, at 4:00 PM, Paul GRAVEL wrote: > >> Hello All, >> >> Is there a C procedure/program/library readily available to read/write MINC files in C? Something analogous to what EMMA does in matlab, i.e. getimages/putimages? >> >> Thanks, >> >> Paul >> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Mon Jul 25 17:09:56 2011 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 25 Jul 2011 17:09:56 -0400 Subject: [MINC-users] compiling minc tools for ubuntu 11.04 Message-ID: <4E2DDBA4.8040309@gmail.com> Hello Everybody, after building minc tools for Ubuntu 11.04 ,I came across a problem with compiling N3 caused by "bad" template definitions in ebtks, see patch: http://www.bic.mni.mcgill.ca/~vfonov/software/ebtks-1.6.4-VF.patch.gz which fixes the error. Also, to build Display ( 1.5.0) you have to run following commands: aclocal -I m4 autoheader libtoolize --automake automake --add-missing --copy autoconf and then usual ./configure ...;make;make install alternatively - apply patch: http://www.bic.mni.mcgill.ca/~vfonov/software/Display-1.5.0-VF.patch.gz -- Best regards, Vladimir S. FONOV ~ vladimir fonov gmail com From redoute at cermep.fr Tue Jul 26 05:45:35 2011 From: redoute at cermep.fr (=?ISO-8859-1?Q?J=E9r=F4me_Redout=E9?=) Date: Tue, 26 Jul 2011 11:45:35 +0200 Subject: [MINC-users] Segfault in dcm2mnc on PET data from the Siemens mCT Message-ID: <4E2E8CBF.7060007@cermep.fr> Dear all, We have the same issue regarding dcm2mnc conversion for PET images coming from Siemens mCT scanner. We tried the following command: dcmodify -e "(0029,1010)" *.dcm before to run dcm2minc, but it didn't fix the segfault crash. Any ideas on what we are doing wrong? Thanks for your help Jerome > We have been using dcm2mnc for many years to convert our Siemens PET > images to Minc. dcm2mnc is now failing with segfault after a scanner > upgrade to Siemens newest PET scanner, the mCT PET/CT with TOF. This > is the case both for minc 2.0 and 2.1. > > We have tried to localize the error - dcm2mnc is failing on a private > tag (0029,1010) not present in older Siemens implementations (VR is OB > accordint to Siemens Conformance statement) and we get the following: > > > Using dcm2mnc on the new Siemens PET images results in a segmentation > fault occuring at > line 487 in acr_io.c: > > 485 ptr1 = (char *) input_value; > 485 ptr2 = (char *) mach_value; > 486 for (i=0; i 487 ptr2[i] = ptr1[i]; > 488 } > > The problem occurs in the acr_parse_siemens_proto2 call after having obtained > a non-null element in dicom_to_minc.c, line 886: > > 886 element = acr_find_group_element(group_list, SPI_Protocol2); > 887 if (element != NULL) { > 888 group_list = parse_siemens_proto2(group_list, element); > 889 } > > acr_find_group_element(group_list, SPI_Protocol2) finds the > (group,element) pair > corresponding to SPI_Protocol2 (0029,1010) (see spi_element_defs.h). It returns > an Acr_element if it exists and NULL if it does not. > > > The segmentation fault occurs in the call to > > acr_get_long(ACR_LITTLE_ENDIAN, 1, byte_ptr + byte_pos,&len); > > in dicom_to_minc.c:803 during the second iteration of the loop. > The update in line 813 > > 813 byte_pos += ((len + 3) / 4) * 4; > > causes byte_pos to become very large (overflow?), which may be the > source of the segfault. > > > A quick fix is to delete the tag (0029,1010) using standard dicom > tools or f.eks Osirix, Uncommenting of the parse_siemens_proto code > will also work. > Any suggestens is welcome, I will be happy to test and can also > provide testdata to anyone interested into looking into this. > > Best regards, > Flemming > > -- > Flemming Littrup Andersen, Ph.D > Rigshospitalet Copenhagen, Dep. PET-3982 > Phone: +45 3545-8143 > Mobile: +45 2615-7368 -- ================================================================== J?r?me Redout? Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 CERMEP - Imagerie du vivant Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire 59 Bd Pinel 69677 Bron - FRANCE tel : 33 (0)4 72 68 86 13 (bureau) tel : 33 (0)4 72 68 86 00 (standard) fax : 33 (0)4 72 68 86 10 ================================================================== From fling at pet.rh.dk Tue Jul 26 06:20:00 2011 From: fling at pet.rh.dk (Flemming Littrup Andersen) Date: Tue, 26 Jul 2011 12:20:00 +0200 Subject: [MINC-users] Segfault in dcm2mnc on PET data from the Siemens mCT In-Reply-To: <4E2E8CBF.7060007@cermep.fr> References: <4E2E8CBF.7060007@cermep.fr> Message-ID: Hi Jerome, This is stange - dcmodify -e "(0029,1010)" *.dcm works perfectly for our mCT files. Maybe you could try just dcmodify -ep *.dcm to remove all the Siemens private tags before convertion. Best, Flemming 2011/7/26 J?r?me Redout? : > Dear all, > We have the same issue regarding dcm2mnc conversion for PET images coming > from Siemens mCT scanner. > We tried the following command: > > dcmodify -e "(0029,1010)" *.dcm > > before to run dcm2minc, but it didn't fix the segfault crash. > Any ideas on what we are doing wrong? > Thanks for your help > Jerome > > > >> We have been using dcm2mnc for many years to convert our Siemens PET >> images to Minc. dcm2mnc is now failing with segfault after a scanner >> upgrade to Siemens newest PET scanner, the mCT PET/CT with TOF. This >> is the case both for minc 2.0 and 2.1. >> >> We have tried to localize the error - dcm2mnc is failing on a private >> tag (0029,1010) not present in older Siemens implementations (VR is OB >> accordint to Siemens Conformance statement) and we get the following: >> >> >> Using dcm2mnc on the new Siemens PET images results in a segmentation >> fault occuring at >> line 487 in acr_io.c: >> >> 485 ? ? ?ptr1 = (char *) input_value; >> 485 ? ? ?ptr2 = (char *) mach_value; >> 486 ? ? ?for (i=0; i> 487 ? ? ? ? ptr2[i] = ptr1[i]; >> 488 ? ? ?} >> >> The problem occurs in the acr_parse_siemens_proto2 call after having >> obtained >> a non-null element in dicom_to_minc.c, line 886: >> >> 886 ? ?element = acr_find_group_element(group_list, SPI_Protocol2); >> 887 ? ?if (element != NULL) { >> 888 ? ? ? ?group_list = parse_siemens_proto2(group_list, element); >> 889 ? ?} >> >> acr_find_group_element(group_list, SPI_Protocol2) finds the >> (group,element) pair >> corresponding to SPI_Protocol2 (0029,1010) (see spi_element_defs.h). It >> returns >> an Acr_element if it exists and NULL if it does not. >> >> >> The segmentation fault occurs in the call to >> >> ? acr_get_long(ACR_LITTLE_ENDIAN, 1, byte_ptr + byte_pos,&len); >> >> in dicom_to_minc.c:803 during the second iteration of the loop. >> The update in line 813 >> >> 813 ? ? byte_pos += ((len + 3) / 4) * 4; >> >> causes byte_pos to become very large (overflow?), which may be the >> source of the segfault. >> >> >> A quick fix is to delete the tag (0029,1010) using standard dicom >> tools or f.eks Osirix, Uncommenting of the parse_siemens_proto code >> will also work. >> Any suggestens is welcome, I will be happy to test and can also >> provide testdata to anyone interested into looking into this. >> >> Best regards, >> Flemming >> >> -- >> Flemming Littrup Andersen, Ph.D >> Rigshospitalet Copenhagen, Dep. PET-3982 >> Phone: +45 3545-8143 >> Mobile: +45 2615-7368 > > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire > 59 Bd Pinel > 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 13 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > -- Flemming Littrup Andersen, Ph.D Rigshospitalet Copenhagen, Dep. PET-3982 Phone: +45 3545-8143 Mobile: +45 2615-7368 From jfochoaster at gmail.com Tue Jul 26 08:33:51 2011 From: jfochoaster at gmail.com (John Fredy) Date: Tue, 26 Jul 2011 07:33:51 -0500 Subject: [MINC-users] basic tutorials Message-ID: Hello all, I am new in this list, I have a great interest in the minc tools but I see little amount of information in the web. Someone can suggest me some tutorials to begin? To the date I can transform a dicom series to minc format and apply the insect algorithm for white matter gray matter segmentation How I can use the ANIMAL algorithm?, Is possible obtain cortical thickness? Thanks in advance From pierre.bellec at criugm.qc.ca Thu Jul 28 22:57:13 2011 From: pierre.bellec at criugm.qc.ca (Pierre Bellec) Date: Thu, 28 Jul 2011 22:57:13 -0400 Subject: [MINC-users] compiling the minc suite Message-ID: Dear MINC users, I just finished compiling all of the MINC tools using the big make file writen by Vladimir and it worked like a charm. A million thanks for that ! I still ran into a couple of minor issues to get NIAK to work, and I thought I would report them for potential future improvements : 1. mincmorph does not build with the "minc-full" option of make. I am not sure whether this is intentional or not, because it is possible to build mincmorph latter using a dedicated "make mincmorph" command. 2. Two packages are missing that are used in the NIAK T1 preprocessing pipeline : inormalize and classify. Again, I don't know if that was meant to be that way, but it would be useful for me to have them in the installation script. 3. There was a couple of dependencies on packages that were missing in the documentation (autoconf and byacc). I added them in the wiki : sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev \ fftw-dev libgsl0-dev libgetopt-tabular-perl libxext-dev glutg3-dev libsoqt3-dev \ libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 \ libsimage-dev libpcre++-dev autoconf perl-byacc However I did not apply these changes in the documentation of the makefile itself. I hope this helps. Best regards, Pierre Bellec, PhD Chercheur adjoint D?partement d'informatique et de recherche op?rationnelle Centre de recherche de l'institut de G?riatrie de Montr?al 4565, Chemin Queen-Mary Montr?al (Qu?bec) H3W 1W5 Universit? de Montr?al http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec (001)(514) 340 3540 #3367 From jcupitt at gmail.com Fri Jul 29 11:42:32 2011 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Fri, 29 Jul 2011 16:42:32 +0100 Subject: [MINC-users] upet2mnc with CT images Message-ID: Hi all, I'm using upet2mnc to read PET scans with success, but I can't read the accompanying CT image. Looking at upet2mnc.c it seems to assume that both calibration_factor and isotope_branching_fraction will be set for all images, but of course the CT will not have these two fields. How are people converting upet CT images to mnc? Is there some other tool I should use? Alternatively, should calibration_factor and isotope_branching_fraction default to 1.0? That would fix the problem, I think (untested). John From pbellec at bic.mni.mcgill.ca Fri Jul 29 11:51:29 2011 From: pbellec at bic.mni.mcgill.ca (Pierre Bellec) Date: Fri, 29 Jul 2011 11:51:29 -0400 Subject: [MINC-users] compiling the minc suite Message-ID: Dear MINC users, I just finished compiling all of the MINC tools using the big make file writen by Vladimir and it worked like a charm. A million thanks for that ! I still ran into a couple of minor issues to get NIAK to work, and I thought I would report them for potential future improvements : 1. mincmorph does not build with the "minc-full" option of make. I am not sure whether this is intentional or not, because it is possible to build mincmorph latter using a dedicated "make mincmorph" command. 2. Two packages are missing that are used in the NIAK T1 preprocessing pipeline : inormalize and classify. Again, I don't know if that was meant to be that way, but it would be useful for me to have them in the installation script. 3. There was a couple of dependencies on packages that were missing in the documentation (autoconf and byacc). I added them in the wiki : sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev \ fftw-dev libgsl0-dev libgetopt-tabular-perl libxext-dev glutg3-dev libsoqt3-dev \ libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 \ libsimage-dev libpcre++-dev autoconf perl-byacc However I did not apply these changes in the documentation of the makefile itself. I hope this helps. Best regards, Pierre Bellec, PhD Chercheur adjoint Centre de recherche de l'institut de G?riatrie de Montr?al D?partement d'informatique et de recherche op?rationnelle Universit? de Montr?al http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec (001)(514) 340 3540 #3367 From a.janke at gmail.com Sun Jul 31 08:52:08 2011 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 31 Jul 2011 22:52:08 +1000 Subject: [MINC-users] upet2mnc with CT images In-Reply-To: References: Message-ID: Hi John, I don't have much to do with upet data so can't really comment on this much beyond to say that what you are suggesting makes sense to me. If you are a github user you could always fork from here: https://github.com/andrewjanke/minc/tree/master/conversion/micropet and see how this change works out for you? If it goes well I dont see any reason as to why we shouldn't bring this change back into MINC itself. Thanks a On 30 July 2011 01:42, wrote: > Hi all, > > I'm using upet2mnc to read PET scans with success, but I can't read > the accompanying CT image. > > Looking at upet2mnc.c it seems to assume that both calibration_factor > and isotope_branching_fraction will be set for all images, but of > course the CT will not have these two fields. > > How are people converting upet CT images to mnc? Is there some other > tool I should use? > > Alternatively, should calibration_factor and > isotope_branching_fraction default to 1.0? That would fix the problem, > I think (untested). > > John > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Sun Jul 31 08:55:31 2011 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 31 Jul 2011 22:55:31 +1000 Subject: [MINC-users] basic tutorials In-Reply-To: References: Message-ID: Hi John, On 26 July 2011 22:33, John Fredy wrote: > Hello all, I am new in this list, I have a great interest in the minc tools > but I see little amount of information in the web. Someone can suggest me > some tutorials to begin? A few of us have put together various documentation here: http://en.wikibooks.org/wiki/MINC/Tutorials Over the years. > To the date I can transform a dicom series to minc format and apply the > insect algorithm for white matter gray matter segmentation > > How I can use the ANIMAL algorithm?, For this there is a small howto here: http://en.wikibooks.org/wiki/MINC/Tools/mni_autoreg > Is possible obtain cortical thickness? Last I checked the cortial thickness code from the BIC (Specifically Prof Alan Evans lab) has not been released. You could always email Alan directly and ask. Thanks a From jcupitt at gmail.com Sun Jul 31 12:55:45 2011 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Sun, 31 Jul 2011 17:55:45 +0100 Subject: [MINC-users] upet2mnc with CT images In-Reply-To: References: Message-ID: On Sunday, July 31, 2011, Andrew Janke wrote: > If you are a github user you could always fork from here: > > https://github.com/andrewjanke/minc/tree/master/conversion/micropet > > and see how this change works out for you? I didn't realise you were on github now, that's great. I'll fork and push a change your way if it works out. Thanks, John