From a.janke at gmail.com Thu May 1 01:37:31 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 1 May 2008 15:37:31 +1000 Subject: [MINC-users] dcm2mnc error, seems related to slice position/orientation In-Reply-To: <160E3DD4FB702C4CB860C65186686E690202005A@MRZS152229.medizin.uni-leipzig.de> References: <115a643d0804300725r1a08c04cy65781de14404369@mail.gmail.com> <160E3DD4FB702C4CB860C65186686E6902020056@MRZS152229.medizin.uni-leipzig.de> <20080430181621.GA28243@sumost.ca> <160E3DD4FB702C4CB860C65186686E690202005A@MRZS152229.medizin.uni-leipzig.de> Message-ID: 2008/5/1 Audette, Michel : > > that would make sense. I don't know much about these data. I was expecting something 3D, as it is called DynaCT. I'll look at it with a Dicom viewer. I would certainly echo Steve's sentiments on this. If you have access to a Mac I can heartily recomend Osirix for "homogenising" problem DICOM data. ie: load into DICOM, export to a directory, convert to MINC. Pity you need a Mac to run it as it is a great bit of software. And yes dcm2mnc does require 2D/3D data. a From a.janke at gmail.com Thu May 1 03:15:15 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 1 May 2008 17:15:15 +1000 Subject: [MINC-users] nii2mnc problem In-Reply-To: References: Message-ID: > Thanks Andrew. I placed a couple of samples into > "/data/scratch/scratch1/jim/nifti". There you will find volumes for 2 > subjects: (1) subject 0002, who is reflective of most of my subjects, > and (2) subject 0008, who, following conversion using the same input > params as used for S0002, is upside-down (according to Display). I > used the following to convert: > > nii2mnc -xyz -flipz -flipx 0002-M-NC.nii Hi Jim, Well after a bit of head scratching I have an answer for you. In short, nii2mnc is doing the correct thing but for some reason, most of these volumes appear to be using various strange combinations of -ve direction cosines and then negative steps on top of this. This is where I would say the mapping between the mnc voxel to world transform and the Nifti Q-form xfm (registration) sort of breaks down. You will find that if you look at your two output mnc volumes in register that the third column (the aggregation of the two) is in fact in the correct orientation. Register always views data from the voxel perspective and just updates the world co-ordinate information to suit. If you turn "synch" on you will see what I mean. The only real "fix" for this is to mincresample them to something sensible like 100, 010, 001 as opposed to the current -100, 010, 00-1 wierdness. a From Michel.Audette at medizin.uni-leipzig.de Thu May 1 09:37:16 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 1 May 2008 15:37:16 +0200 Subject: [MINC-users] dcm2mnc error, seems related to slice position/orientation References: <115a643d0804300725r1a08c04cy65781de14404369@mail.gmail.com><160E3DD4FB702C4CB860C65186686E6902020056@MRZS152229.medizin.uni-leipzig.de><20080430181621.GA28243@sumost.ca><160E3DD4FB702C4CB860C65186686E690202005A@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902020061@MRZS152229.medizin.uni-leipzig.de> Hi Andrew, thanks for your kind message. As I answered Steve, I have to do a little digging to understand how this diverges from normal DICOM, such as trying to view it in native format. Thanks for the info on Osiris. What is the likelihood that they make source code available for Linux compilation, do you think? Best regards, Michel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke Sent: Thu 5/1/2008 7:37 AM To: MINC users mailing list Subject: Re: [MINC-users] dcm2mnc error,seems related to slice position/orientation 2008/5/1 Audette, Michel : > > that would make sense. I don't know much about these data. I was expecting something 3D, as it is called DynaCT. I'll look at it with a Dicom viewer. I would certainly echo Steve's sentiments on this. If you have access to a Mac I can heartily recomend Osirix for "homogenising" problem DICOM data. ie: load into DICOM, export to a directory, convert to MINC. Pity you need a Mac to run it as it is a great bit of software. And yes dcm2mnc does require 2D/3D data. a _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From steve at sumost.ca Thu May 1 10:16:50 2008 From: steve at sumost.ca (Steve M. Robbins) Date: Thu, 01 May 2008 09:16:50 -0500 Subject: [MINC-users] dcm2mnc error, seems related to slice position/orientation In-Reply-To: <160E3DD4FB702C4CB860C65186686E6902020061@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E6902020061@MRZS152229.medizin.uni-leipzig.de> Message-ID: <20080501141650.GC28243@sumost.ca> On Thu, May 01, 2008 at 03:37:16PM +0200, Audette, Michel wrote: > Hi Andrew, > > thanks for your kind message. As I answered Steve, I have to do a > little digging to understand how this diverges from normal DICOM, > such as trying to view it in native format. Thanks for the info on > Osiris. What is the likelihood that they make source code available > for Linux compilation, do you think? The source for Osirix is available. The "problem" is that it heavily uses mac-only libraries, so porting would require a great deal of effort. -Steve From sean at rogue-research.com Thu May 1 11:43:42 2008 From: sean at rogue-research.com (Sean McBride) Date: Thu, 1 May 2008 11:43:42 -0400 Subject: [MINC-users] For the OSX 10.5 crash test dummies. In-Reply-To: References: <20080430201119.1405142100@kingu.local> Message-ID: <20080501154342.190984568@kingu.local> On 5/1/08 9:57 AM, Andrew Janke said: >I build essentially what people ask for and for what platforms I have >access to! :) > >The only access I have to older Mac hardware is a PowerPC Tiger >machine. Will this do what you want? I have no idea how to build a >universal binary (never looked into it as I figured in 6 months there >would be no point) though... Building Universal is quite easy. Are you building MINC with CMake these days? Or configure/make? The process is different depending... -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From Michel.Audette at medizin.uni-leipzig.de Fri May 2 01:59:29 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Fri, 2 May 2008 07:59:29 +0200 Subject: [MINC-users] dcm2mnc error, seems related to slice position/orientation References: <160E3DD4FB702C4CB860C65186686E6902020061@MRZS152229.medizin.uni-leipzig.de> <20080501141650.GC28243@sumost.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E6902020067@MRZS152229.medizin.uni-leipzig.de> Hi Steve, I was thinking of making this volume available to you after all, if there is a chance that you could track down this bug. Can you send me your latest email, so that I can give you details? Btw, I heard from the Osirix people, and they said that they only supply MacOS binaries. Cheers, Michel ________________________________ From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Steve M. Robbins Sent: Thu 5/1/2008 4:16 PM To: MINC users mailing list Subject: Re: [MINC-users] dcm2mnc error, seems related to slice position/orientation On Thu, May 01, 2008 at 03:37:16PM +0200, Audette, Michel wrote: > Hi Andrew, > > thanks for your kind message. As I answered Steve, I have to do a > little digging to understand how this diverges from normal DICOM, > such as trying to view it in native format. Thanks for the info on > Osiris. What is the likelihood that they make source code available > for Linux compilation, do you think? The source for Osirix is available. The "problem" is that it heavily uses mac-only libraries, so porting would require a great deal of effort. -Steve _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Mon May 5 18:58:44 2008 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 6 May 2008 08:58:44 +1000 Subject: [MINC-users] t threshold for corrected p value of Aston's method In-Reply-To: References: Message-ID: Hi Ji, I was hoping Sylvain would answer this one as I am not that familiar with the stats associated with PET but in any case here goes... 2008/5/1 Ji Hyum KO : > As far as I understand, I should calculate the t threshold based on > Worsely et al., Human Brain Mapping, 1996. > I am really sure that it is very well-written famous paper, but I > couldn't figure out how to calculate the t-threshold in the given > conditions. Correct, to calculate this I would suggest that you use Keith Worsleys MATLAB package (called fmristat) to do this. http://www.math.mcgill.ca/keith/fmristat/ > Is there any easy way to calculate t threshold for p<0.05 (corrected)? This will depend on the number of subjects, (and thus Degrees of Freedom), the number of voxels you are considering and so forth. > And, is it going to be the same even if I consider the whole brain rather > than just striatum, e.g., fallypride study? It will be different, but again this will depend on the method you use to calculate the t-value. Certainly it will change if you calculate pooled variance across you data (or mask). Again though I would suggest that you spend some time getting acquainted with the fmristat package. Keith has a number of examples on his webpages that should help you get going. a -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From nikelski at bic.mni.mcgill.ca Mon May 5 22:50:51 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Mon, 5 May 2008 22:50:51 -0400 Subject: [MINC-users] t threshold for corrected p value of Aston's method In-Reply-To: References: Message-ID: Hi all, Reading this e-mail reminded me that I could use some advise on a related issue. Pls forgive me if its a wee bit tangential to the subject line. Specifically, given that Keith's fmristat (for PET) assumes that the input volumes have already been spatially normalized, do we have any tools to help with this task, short of doing the minctracc (or mritoself, mritotal) calls manually? In the days of 'dot' (ah, the good old days), Greg Ward's scripts (do_mritopet, do_mritotal, do_pettopet) were nicely able to generate the required xfms -- however, while still available on Yorick, they do not appear to be migrating to the Linux systems. I suppose that one could use fmr_preprocess to do PET motion correction (with some fiddling), however, the version of this script that I have seen is buggy (at least the version that I found has bugs), and it does not appear to be quality controlled (i.e. no official release). So in sum, the questions are (1) are the old PET preprocessing tools (Greg's stuff) unsupported and therefore not being migrated off of Yorick, (2) and what are other BIC PET researchers using to do motion correction, cross-modality alignment, and stereotactic transformation? Ideas and suggestions? Thanks, -Jim On Mon, May 5, 2008 at 6:58 PM, Andrew Janke wrote: > Hi Ji, > > I was hoping Sylvain would answer this one as I am not that familiar > with the stats associated with PET but in any case here goes... > > > 2008/5/1 Ji Hyum KO : > > As far as I understand, I should calculate the t threshold based on > > Worsely et al., Human Brain Mapping, 1996. > > I am really sure that it is very well-written famous paper, but I > > couldn't figure out how to calculate the t-threshold in the given > > conditions. > > Correct, to calculate this I would suggest that you use Keith Worsleys > MATLAB package (called fmristat) to do this. > > http://www.math.mcgill.ca/keith/fmristat/ > > > Is there any easy way to calculate t threshold for p<0.05 (corrected)? > > This will depend on the number of subjects, (and thus Degrees of > Freedom), the number of voxels you are considering and so forth. > > > And, is it going to be the same even if I consider the whole brain rather > > than just striatum, e.g., fallypride study? > > It will be different, but again this will depend on the method you use > to calculate the t-value. Certainly it will change if you calculate > pooled variance across you data (or mask). > > Again though I would suggest that you spend some time getting > acquainted with the fmristat package. Keith has a number of examples > on his webpages that should help you get going. > > > a > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From sylvain at bic.mni.mcgill.ca Tue May 6 09:00:55 2008 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 6 May 2008 09:00:55 -0400 (EDT) Subject: [MINC-users] t threshold for corrected p value of Aston's method In-Reply-To: References: Message-ID: Hello, Greg Ward's scripts will work under linux with some fiddling - they are written in perl after all but they also make system calls to a wide variety of tools! I have used them under linux but they will require more work before making them available for mass comsumption. The bulk of the work resides in rewriting the code used for the creation of verification images since the current versions use an Irix image toolbox based on Irix's ImageVision Library. Also the code using batch needs revamping! So use do_mritotal -noverify -resample all -background ... and verify the images in the mrital_rsl directory. Better yet, do the following: qbatch do_mritotal -noverify -resample all qbatch is available on all linux systems and I hopefully fixed all the bugs ... but do_mritotal is NOT yet available - I suppose a version could be made available with a few options disabled to prevent havoc. I'll see what I can do in the next couple of weeks. do_mritopet needs to be revamped and I don't use do_pettopet anymore as mritopet is more robust - hence the reason why do_mritopet needs revamping. Yorick's days are counted and it will be retired in 2008 so I suspect I will be tempted at some point to do the work, same goes for dot ... but time is a luxury I don't have anymore since I'm a fulltime sys admin. As for PET motion correction, another option might be available, ie using Anthonin Reilhac's Dynamic PET motion correction method. It would have to be adapted for static PET images by pooling together a 12-(static)-scan study for example and then considering individual scan as time frames. I gave that a try last year but the results weren't very good and I failed to find time to get back to it. Anthonin seemed confident that it could work so there's still some hope. BUT concerning Ji Hyum KO's data - it is Dynamic PET, so Anthonin's method should be preferred ! Under BIC linux systems, you will find /usr/local/bin/do_PET_frame_realignment to do the job. As for Keith's fmristat (for PET), I never got around to using/testing it. It uses a different approach to estimate the variance - Keith calls it a "local form of pooling" and he posted something on the bic-users mailing list many years ago ... here it is: > Well I must admit PET scanners have changed in the last 10 years > and the assumption of equal sd probably needs to be checked. In the mean > time, fmristat's multistat program does (almost) everything that DOT's > statistical analysis does, but better. Instead of pooling the sd, it > smoothes it, i.e. > a sort of local pooling. We usually choose the amount of smoothing so > that the resulting df is large, say 100. If you set the FWHM of the > smoother very large (say 100mm), you get the pooled sd (almost); if you > set it to 0 you get the voxel sd. > I would suggest you look into this - the help of multistat (look under > INPUT_FILES_SDEFFECT) tells you how to run it for PET data - essentially > all you do is leave the input sd files blank - > > Keith Worsley > Department of Mathematics and Statistics, McGill University > 805 ouest, rue Sherbrooke, Montreal, Quebec, Canada H3A 2K6 > tel: (514) 398-3842, fax: (514) 398-3899 > e-mail: keith.worsley at mcgill.ca, web: http://www.math.mcgill.ca/keith HTH, S On Mon, 5 May 2008, EJ Nikelski wrote: > Hi all, > > Reading this e-mail reminded me that I could use some advise on a > related issue. Pls forgive me if its a wee bit tangential to the > subject line. > > Specifically, given that Keith's fmristat (for PET) assumes that > the input volumes have already been spatially normalized, do we have > any tools to help with this task, short of doing the minctracc (or > mritoself, mritotal) calls manually? In the days of 'dot' (ah, the > good old days), Greg Ward's scripts (do_mritopet, do_mritotal, > do_pettopet) were nicely able to generate the required xfms -- > however, while still available on Yorick, they do not appear to be > migrating to the Linux systems. I suppose that one could use > fmr_preprocess to do PET motion correction (with some fiddling), > however, the version of this script that I have seen is buggy (at > least the version that I found has bugs), and it does not appear to be > quality controlled (i.e. no official release). > > So in sum, the questions are (1) are the old PET preprocessing > tools (Greg's stuff) unsupported and therefore not > being migrated off of Yorick, (2) and what are other BIC PET > researchers using to do motion correction, cross-modality alignment, > and stereotactic transformation? Ideas and suggestions? > > Thanks, > > > -Jim > > > > On Mon, May 5, 2008 at 6:58 PM, Andrew Janke wrote: >> Hi Ji, >> >> I was hoping Sylvain would answer this one as I am not that familiar >> with the stats associated with PET but in any case here goes... >> >> >> 2008/5/1 Ji Hyum KO : >> > As far as I understand, I should calculate the t threshold based on >> > Worsely et al., Human Brain Mapping, 1996. >> > I am really sure that it is very well-written famous paper, but I >> > couldn't figure out how to calculate the t-threshold in the given >> > conditions. >> >> Correct, to calculate this I would suggest that you use Keith Worsleys >> MATLAB package (called fmristat) to do this. >> >> http://www.math.mcgill.ca/keith/fmristat/ >> >> > Is there any easy way to calculate t threshold for p<0.05 (corrected)? >> >> This will depend on the number of subjects, (and thus Degrees of >> Freedom), the number of voxels you are considering and so forth. >> >> > And, is it going to be the same even if I consider the whole brain rather >> > than just striatum, e.g., fallypride study? >> >> It will be different, but again this will depend on the method you use >> to calculate the t-value. Certainly it will change if you calculate >> pooled variance across you data (or mask). >> >> Again though I would suggest that you spend some time getting >> acquainted with the fmristat package. Keith has a number of examples >> on his webpages that should help you get going. >> >> >> a >> >> -- >> Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) >> Canberra->Australia +61 (402) 700 883 >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > ================================= > Jim Nikelski, Ph.D. > Postdoctoral Research Fellow > Bloomfield Centre for Research in Aging > Lady Davis Institute for Medical Research > Sir Mortimer B. Davis - Jewish General Hospital > McGill University > Tel: (514) 340-8222 x 2298 > Fax: (514) 340-8295 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://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 kojinet at bic.mni.mcgill.ca Tue May 6 09:07:29 2008 From: kojinet at bic.mni.mcgill.ca (Ji Hyum KO) Date: Tue, 6 May 2008 09:07:29 -0400 Subject: [MINC-users] t threshold for corrected p value of Aston's method In-Reply-To: References: Message-ID: Thank you so much! This is exactly what I wanted, a reference that I dig in. Thanks, Ji Hyun On Tue, 6 May 2008, Sylvain Milot wrote: > > Hello, > > Greg Ward's scripts will work under linux with some fiddling - they are > written in perl after all but they also make system calls to a wide > variety of tools! I have used them under linux but they will > require more work before making them available for mass comsumption. The > bulk of the work resides in rewriting the code used for the creation of > verification images since the current versions use an Irix image toolbox > based on Irix's ImageVision Library. Also the code using batch needs > revamping! > > So use do_mritotal -noverify -resample all -background ... and verify the > images in the mrital_rsl directory. > > Better yet, do the following: > > qbatch do_mritotal -noverify -resample all > > qbatch is available on all linux systems and I hopefully fixed all > the bugs ... but do_mritotal is NOT yet available - I suppose a version > could be made available with a few options disabled to prevent havoc. I'll > see what I can do in the next couple of weeks. > > do_mritopet needs to be revamped and I don't use do_pettopet anymore as > mritopet is more robust - hence the reason why do_mritopet needs > revamping. > > Yorick's days are counted and it will be retired in 2008 so I suspect I > will be tempted at some point to do the work, same goes for dot ... but > time is a luxury I don't have anymore since I'm a fulltime sys admin. > > As for PET motion correction, another option might be available, ie using > Anthonin Reilhac's Dynamic PET motion correction method. It would have to > be adapted for static PET images by pooling together a 12-(static)-scan > study for example and then considering individual scan as time frames. I > gave that a try last year but the results weren't very good and I failed > to find time to get back to it. Anthonin seemed confident that it could > work so there's still some hope. > > BUT concerning Ji Hyum KO's data - it is Dynamic PET, so Anthonin's method > should be preferred ! Under BIC linux systems, you will find > /usr/local/bin/do_PET_frame_realignment to do the job. > > As for Keith's fmristat (for PET), I never got around to using/testing it. > It uses a different approach to estimate the variance - Keith calls it a > "local form of pooling" and he posted something on the bic-users mailing > list many years ago ... here it is: > > > Well I must admit PET scanners have changed in the last 10 years > > and the assumption of equal sd probably needs to be checked. In the mean > > time, fmristat's multistat program does (almost) everything that DOT's > > statistical analysis does, but better. Instead of pooling the sd, it > > smoothes it, i.e. > > a sort of local pooling. We usually choose the amount of smoothing so > > that the resulting df is large, say 100. If you set the FWHM of the > > smoother very large (say 100mm), you get the pooled sd (almost); if you > > set it to 0 you get the voxel sd. > > I would suggest you look into this - the help of multistat (look under > > INPUT_FILES_SDEFFECT) tells you how to run it for PET data - essentially > > all you do is leave the input sd files blank - > > > > Keith Worsley > > Department of Mathematics and Statistics, McGill University > > 805 ouest, rue Sherbrooke, Montreal, Quebec, Canada H3A 2K6 > > tel: (514) 398-3842, fax: (514) 398-3899 > > e-mail: keith.worsley at mcgill.ca, web: http://www.math.mcgill.ca/keith > > HTH, > > S > > On Mon, 5 May 2008, EJ Nikelski wrote: > > > Hi all, > > > > Reading this e-mail reminded me that I could use some advise on a > > related issue. Pls forgive me if its a wee bit tangential to the > > subject line. > > > > Specifically, given that Keith's fmristat (for PET) assumes that > > the input volumes have already been spatially normalized, do we have > > any tools to help with this task, short of doing the minctracc (or > > mritoself, mritotal) calls manually? In the days of 'dot' (ah, the > > good old days), Greg Ward's scripts (do_mritopet, do_mritotal, > > do_pettopet) were nicely able to generate the required xfms -- > > however, while still available on Yorick, they do not appear to be > > migrating to the Linux systems. I suppose that one could use > > fmr_preprocess to do PET motion correction (with some fiddling), > > however, the version of this script that I have seen is buggy (at > > least the version that I found has bugs), and it does not appear to be > > quality controlled (i.e. no official release). > > > > So in sum, the questions are (1) are the old PET preprocessing > > tools (Greg's stuff) unsupported and therefore not > > being migrated off of Yorick, (2) and what are other BIC PET > > researchers using to do motion correction, cross-modality alignment, > > and stereotactic transformation? Ideas and suggestions? > > > > Thanks, > > > > > > -Jim > > > > > > > > On Mon, May 5, 2008 at 6:58 PM, Andrew Janke wrote: > >> Hi Ji, > >> > >> I was hoping Sylvain would answer this one as I am not that familiar > >> with the stats associated with PET but in any case here goes... > >> > >> > >> 2008/5/1 Ji Hyum KO : > >> > As far as I understand, I should calculate the t threshold based on > >> > Worsely et al., Human Brain Mapping, 1996. > >> > I am really sure that it is very well-written famous paper, but I > >> > couldn't figure out how to calculate the t-threshold in the given > >> > conditions. > >> > >> Correct, to calculate this I would suggest that you use Keith Worsleys > >> MATLAB package (called fmristat) to do this. > >> > >> http://www.math.mcgill.ca/keith/fmristat/ > >> > >> > Is there any easy way to calculate t threshold for p<0.05 (corrected)? > >> > >> This will depend on the number of subjects, (and thus Degrees of > >> Freedom), the number of voxels you are considering and so forth. > >> > >> > And, is it going to be the same even if I consider the whole brain rather > >> > than just striatum, e.g., fallypride study? > >> > >> It will be different, but again this will depend on the method you use > >> to calculate the t-value. Certainly it will change if you calculate > >> pooled variance across you data (or mask). > >> > >> Again though I would suggest that you spend some time getting > >> acquainted with the fmristat package. Keith has a number of examples > >> on his webpages that should help you get going. > >> > >> > >> a > >> > >> -- > >> Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > >> Canberra->Australia +61 (402) 700 883 > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > > > > > > > > -- > > ================================= > > Jim Nikelski, Ph.D. > > Postdoctoral Research Fellow > > Bloomfield Centre for Research in Aging > > Lady Davis Institute for Medical Research > > Sir Mortimer B. Davis - Jewish General Hospital > > McGill University > > Tel: (514) 340-8222 x 2298 > > Fax: (514) 340-8295 > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://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 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jween at klaru-baycrest.on.ca Tue May 13 16:27:47 2008 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Tue, 13 May 2008 16:27:47 -0400 Subject: [MINC-users] newbee segmentation question Message-ID: Hi First time on list, sorry if I've missed similar threads before, but nothing popped up with any search. I'm hoping someone has a hint! Issue: I'm trying to get stroke lesion segmentations into standard space to finally plug into VLSM (Bates et al) to correlate with behavioral measures. Problem is, I have non-standardized (clinical) scans to work with. Here's my procedure: 1) Convert DICOMs into mnc format using UCLA debabeler. Seems to work. 2) Generate a transform (target.xfm) from target scan to standard scan using Register. Looks good enough. 3) Segment lesion in target brain using threshold fill in Display and "save labels as mnc" (lbl.mnc). Looks good. 4) Resample labels into standard space using: mincresample -like standardbrain.mnc -transform target.xfm lbl.mnc lbl_stnd.mnc Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in Display and the segmentation is WAY off, not even close. Would anyone know what I'm doing wrong? Cheers Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimmel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. From sorench at gmail.com Tue May 13 18:45:28 2008 From: sorench at gmail.com (Soren Christensen) Date: Wed, 14 May 2008 00:45:28 +0200 Subject: [MINC-users] newbee segmentation question In-Reply-To: References: Message-ID: Hi Jon, Just as a first quick check did you see if the transform you got from register is inverted realtive to what you think it is (ie. definition of target and source volume). You could add in -invert_xfm in step 4 for a quick check. Cheers Soren On Tue, May 13, 2008 at 10:27 PM, Jon Erik Ween wrote: > Hi > > First time on list, sorry if I've missed similar threads before, but > nothing popped up with any search. I'm hoping someone has a hint! > > Issue: I'm trying to get stroke lesion segmentations into standard > space to finally plug into VLSM (Bates et al) to correlate with > behavioral measures. Problem is, I have non-standardized (clinical) > scans to work with. Here's my procedure: > > 1) Convert DICOMs into mnc format using UCLA debabeler. Seems to work. > 2) Generate a transform (target.xfm) from target scan to standard > scan using Register. Looks good enough. > 3) Segment lesion in target brain using threshold fill in Display and > "save labels as mnc" (lbl.mnc). Looks good. > 4) Resample labels into standard space using: > mincresample -like standardbrain.mnc -transform target.xfm > lbl.mnc lbl_stnd.mnc > Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in > Display and the segmentation is WAY off, not even close. > > Would anyone know what I'm doing wrong? > > Cheers > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimmel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From louis.collins at mcgill.ca Tue May 13 18:50:44 2008 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 13 May 2008 18:50:44 -0400 Subject: [MINC-users] newbee segmentation question In-Reply-To: References: Message-ID: <17B62F7F-84BC-4336-9BB4-4D530B7507A0@mcgill.ca> Jon, how did you do the registration with register. The register program computes the transform from volume 2 (the middle column) to volume 1 (the first column). If you loaded the subject's dataset into column one, and the target brain in volume 2, ie: register subject_mri.mnc target mri.mnc then your transform saved is backwards from what you want. If this is the problem, then the following should solve it: mincresample -like standardbrain.mnc -invert_transformation - transform target.xfm lbl.mnc lbl_stnd.mnc -Louis On May 13, 2008, at 4:27 PM, Jon Erik Ween wrote: > Hi > > First time on list, sorry if I've missed similar threads before, but > nothing popped up with any search. I'm hoping someone has a hint! > > Issue: I'm trying to get stroke lesion segmentations into standard > space to finally plug into VLSM (Bates et al) to correlate with > behavioral measures. Problem is, I have non-standardized (clinical) > scans to work with. Here's my procedure: > > 1) Convert DICOMs into mnc format using UCLA debabeler. Seems to work. > 2) Generate a transform (target.xfm) from target scan to standard > scan using Register. Looks good enough. > 3) Segment lesion in target brain using threshold fill in Display and > "save labels as mnc" (lbl.mnc). Looks good. > 4) Resample labels into standard space using: > mincresample -like standardbrain.mnc -transform target.xfm > lbl.mnc lbl_stnd.mnc > Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in > Display and the segmentation is WAY off, not even close. > > Would anyone know what I'm doing wrong? > > Cheers > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimmel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From claude at bic.mni.mcgill.ca Tue May 13 22:41:32 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 13 May 2008 22:41:32 -0400 (EDT) Subject: [MINC-users] newbee segmentation question Message-ID: <200805140241.m4E2fWEF6149158@yorick.bic.mni.mcgill.ca> Hi, > 4) Resample labels into standard space using: > mincresample -like standardbrain.mnc -transform target.xfm > lbl.mnc lbl_stnd.mnc > Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in > Display and the segmentation is WAY off, not even close. In addition to the suggestion to invert the transformation, I would suggest to add the options -nearest_neighbour -byte if you are resampling integer labels. -keep_real_range may also be required. Otherwise, a label like 10 may be resampled as 10.2. Claude From se at hst.aau.dk Wed May 14 02:59:38 2008 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Wed, 14 May 2008 08:59:38 +0200 Subject: [MINC-users] newbee segmentation question In-Reply-To: References: Message-ID: <482A8DDA.30502@hst.aau.dk> Hi Jon, > 3) Segment lesion in target brain using threshold fill in Display and > "save labels as mnc" (lbl.mnc). Looks good. Usually I switch "Crop save labels" off when saving, but I'm not entirely sure it'll make a difference in your case. Simon From jween at klaru-baycrest.on.ca Wed May 14 09:25:32 2008 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 14 May 2008 09:25:32 -0400 Subject: [MINC-users] newbee segmentation question In-Reply-To: <200805140241.m4E2fWEF6149158@yorick.bic.mni.mcgill.ca> References: <200805140241.m4E2fWEF6149158@yorick.bic.mni.mcgill.ca> Message-ID: <1E28060B-D61D-49D1-BC47-A8B6006B4B5C@klaru-baycrest.on.ca> Thanks to S?ren, Luis Claude and Simon for suggestions. I had indeed registered the volumes the wrong way. Inverting the transform solved the problem and handling integer labels cleaned the results up further. Cheers Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimmel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 13-May-08, at 10:41 PM, Claude LEPAGE wrote: > Hi, > >> 4) Resample labels into standard space using: >> mincresample -like standardbrain.mnc -transform target.xfm >> lbl.mnc lbl_stnd.mnc >> Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in >> Display and the segmentation is WAY off, not even close. > > In addition to the suggestion to invert the transformation, > I would suggest to add the options -nearest_neighbour -byte > if you are resampling integer labels. -keep_real_range may > also be required. Otherwise, a label like 10 may be resampled > as 10.2. > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From nikelski at bic.mni.mcgill.ca Sat May 17 11:57:08 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Sat, 17 May 2008 11:57:08 -0400 Subject: [MINC-users] minc-2.0.15 build error Message-ID: Hi All, For reasons that I would rather not get into, I found myself rebuilding minc2 on my Intel mac (os x 10.5). Although I'm certain that this worked previously, I now get an error during "make check" -- specifically: Testing icv_dim1 Testing icv_fillvalue PASS: run_test2.sh PASS: xfmconcat_01.sh PASS: xfmconcat_02.sh Assertion failed: (extent != 0), function px_get, file posixio.c, line 412. /bin/sh: line 1: 66090 Abort trap ${dir}$tst FAIL: mincapi ================================== 1 of 5 tests failed Please report to a.janke at gmail.com ================================== I've done some snooping, and the problem is related to this bit of code in mincapi.c ... /* Try to open the file for write - should fail. */ fd2 = miopen(ip->name, NC_WRITE); if (fd2 >= 0) { FUNC_ERROR("miopen"); } The call to miopen does indeed fail, but instead of returning, it fails on the assertion in posixio.c. Andrew, given that you've dutifully attached your name to the error message, I suppose that you get first kick at the can. What do you think? BTW - I'm building minc2 with hdf5-1.6.7 and netcdf-3.6.2. Cheers, -Jim From lasse at hst.aau.dk Mon May 19 17:11:59 2008 From: lasse at hst.aau.dk (=?ISO-8859-1?Q?Lasse_Riis_=D8stergaard?=) Date: Mon, 19 May 2008 23:11:59 +0200 Subject: [MINC-users] ray_trace issue! Message-ID: <4831ED1F.50806@hst.aau.dk> Hi Any ray_trace experts here? I am using ray_trace to render images of surface cross sections on top of volume cross sections. I have been following the steps in David's tutorial (Example 14). This works very fine if the z-axis in world and voxel space are parallel. If this is not the case their seem to be an issue with the texture mapping as the gray levels are not interpolated correct! Here is what I do: 1. make_slice volume.mnc slice.obj z w 5 2 2 2. plane_polygon_intersect surface.obj lines.obj z 5 3. ray_trace -output image.rgb -nolight -line_width 1 lines.obj -gray 0 300 volume.mnc 0 1 slice.obj -size 1024 1024 -bg white -crop -top -sup 3 ray_trace maps the grey levels of a slice along the z-axis in voxel space - not in world space! By inspection I have found that the rendered slice exactly corresponds to z=78 (voxel space) wich cuts through z-coordinates 0.9-6.8 in world space. Am I doing anything wrong? cheers Lasse From lasse at hst.aau.dk Mon May 19 17:56:28 2008 From: lasse at hst.aau.dk (=?ISO-8859-1?Q?Lasse_Riis_=D8stergaard?=) Date: Mon, 19 May 2008 23:56:28 +0200 Subject: [MINC-users] ray_trace issue! In-Reply-To: <4831ED1F.50806@hst.aau.dk> References: <4831ED1F.50806@hst.aau.dk> Message-ID: <4831F78C.5050107@hst.aau.dk> Hi again I now see that the issue is related to make_slice and not ray_trace! In the example I provided make_slice creates this: Q 0.3 0.3 0.4 10 1 2 2 F F 0 1 1 1 1 98.8034 140.093 0.842139 98.8034 -59.1943 6.75685 -100.572 140.093 0.842139 -100.572 -59.1943 6.75685 0 0 1 0 0 1 0 0 1 0 0 1 I had expected a constant z-value of 5. Does make_slice find the closest slice in voxel space? Lasse Lasse Riis ?stergaard wrote: > Hi > > Any ray_trace experts here? > > I am using ray_trace to render images of surface cross sections on top > of volume cross sections. I have been following the steps in David's > tutorial (Example 14). This works very fine if the z-axis in world and > voxel space are parallel. If this is not the case their seem to be an > issue with the texture mapping as the gray levels are not interpolated > correct! > > Here is what I do: > > 1. make_slice volume.mnc slice.obj z w 5 2 2 > 2. plane_polygon_intersect surface.obj lines.obj z 5 > 3. ray_trace -output image.rgb -nolight -line_width 1 lines.obj -gray 0 > 300 volume.mnc 0 1 slice.obj -size 1024 1024 -bg white -crop -top -sup 3 > > ray_trace maps the grey levels of a slice along the z-axis in voxel > space - not in world space! > > By inspection I have found that the rendered slice exactly corresponds > to z=78 (voxel space) wich cuts through z-coordinates 0.9-6.8 in world > space. > > Am I doing anything wrong? > > cheers > Lasse > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vikingy at gmail.com Tue May 20 23:15:16 2008 From: vikingy at gmail.com (bin lv) Date: Tue, 20 May 2008 23:15:16 -0400 Subject: [MINC-users] problem while install the Minc on ubuntu Message-ID: <93e2f0200805202015r78cf8af9va8cf2532eb020e6e@mail.gmail.com> Hi, I want to install the Minc tools on my ubuntu system (8.04 hardy).Following the instruction on: ( http://wiki.bic.mni.mcgill.ca/index.php/InstallingBicSoftware and http://wiki.bic.mni.mcgill.ca/index.php/MincDebian ), I met the problem: The following packages have unmet dependencies: mni-autoreg: Depends: netcdf but it is not installable register: Depends: netcdf but it is not installable ......... It seems that I didn't install the packages netcdf, while in fact I have installed this packages, and I can find these in my system: libnetcdf++3, libnetcdf3. netcdf-bin, netcdfg-dev. I'm confused that why the package dependencies problem still occur. Does anyone can point out what's wrong with me? Thanks in advance! bin lv From a.janke at gmail.com Tue May 20 23:21:05 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 21 May 2008 13:21:05 +1000 Subject: [MINC-users] problem while install the Minc on ubuntu In-Reply-To: <93e2f0200805202015r78cf8af9va8cf2532eb020e6e@mail.gmail.com> References: <93e2f0200805202015r78cf8af9va8cf2532eb020e6e@mail.gmail.com> Message-ID: Hi, Seems that that page is somewhat out of date (I never even knew it existed). Use this line for /etc/apt/sources.list deb http://packages.bic.mni.mcgill.ca/ubuntu-hardy/ ./ And all should be good. Also if you want "full" MINC functionality (to build code and other things) then this list of packages will also prove handy: sudo apt-get install netcdfg-dev libhdf5-serial-dev libnetpbm9-dev fftw-dev libgsl0-dev libgetopt-tabular-perl \ libmni-perllib-perl libxext-dev glutg3-dev libsoqt-dev libxmu-dev libxi-dev a On Wed, May 21, 2008 at 1:15 PM, bin lv wrote: > Hi, > > I want to install the Minc tools on my ubuntu system (8.04 > hardy).Following the instruction on: ( > http://wiki.bic.mni.mcgill.ca/index.php/InstallingBicSoftware and > http://wiki.bic.mni.mcgill.ca/index.php/MincDebian ), I met the problem: > > The following packages have unmet dependencies: > mni-autoreg: Depends: netcdf but it is not installable > register: Depends: netcdf but it is not installable > ......... > > It seems that I didn't install the packages netcdf, while in fact I have > installed this packages, and I can find these in my system: libnetcdf++3, > libnetcdf3. netcdf-bin, netcdfg-dev. I'm confused that why the package > dependencies problem still occur. > > Does anyone can point out what's wrong with me? Thanks in advance! > > bin lv > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From vikingy at gmail.com Wed May 21 00:42:18 2008 From: vikingy at gmail.com (bin lv) Date: Wed, 21 May 2008 00:42:18 -0400 Subject: [MINC-users] problem while install the Minc on ubuntu In-Reply-To: References: <93e2f0200805202015r78cf8af9va8cf2532eb020e6e@mail.gmail.com> Message-ID: <93e2f0200805202142x746d87dbld61e8ac9f48bf776@mail.gmail.com> Thanks for your reply. I tried it as you suggested,but still i get the same problem. My system is 64 bit, is this a cause? 2008/5/20 Andrew Janke : > Hi, > > Seems that that page is somewhat out of date (I never even knew it > existed). Use this line for /etc/apt/sources.list > > deb http://packages.bic.mni.mcgill.ca/ubuntu-hardy/ ./ > > And all should be good. Also if you want "full" MINC functionality (to > build code and other things) then this list of packages will also > prove handy: > > sudo apt-get install netcdfg-dev libhdf5-serial-dev libnetpbm9-dev > fftw-dev libgsl0-dev libgetopt-tabular-perl \ > libmni-perllib-perl libxext-dev glutg3-dev libsoqt-dev > libxmu-dev libxi-dev > > a > > > On Wed, May 21, 2008 at 1:15 PM, bin lv wrote: > > Hi, > > > > I want to install the Minc tools on my ubuntu system (8.04 > > hardy).Following the instruction on: ( > > http://wiki.bic.mni.mcgill.ca/index.php/InstallingBicSoftware and > > http://wiki.bic.mni.mcgill.ca/index.php/MincDebian ), I met the problem: > > > > The following packages have unmet dependencies: > > mni-autoreg: Depends: netcdf but it is not installable > > register: Depends: netcdf but it is not installable > > ......... > > > > It seems that I didn't install the packages netcdf, while in fact I > have > > installed this packages, and I can find these in my system: libnetcdf++3, > > libnetcdf3. netcdf-bin, netcdfg-dev. I'm confused that why the package > > dependencies problem still occur. > > > > Does anyone can point out what's wrong with me? Thanks in advance! > > > > bin lv > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Wed May 21 00:54:25 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 21 May 2008 14:54:25 +1000 Subject: [MINC-users] problem while install the Minc on ubuntu In-Reply-To: <93e2f0200805202142x746d87dbld61e8ac9f48bf776@mail.gmail.com> References: <93e2f0200805202015r78cf8af9va8cf2532eb020e6e@mail.gmail.com> <93e2f0200805202142x746d87dbld61e8ac9f48bf776@mail.gmail.com> Message-ID: On Wed, May 21, 2008 at 2:42 PM, bin lv wrote: > Thanks for your reply. > > I tried it as you suggested,but still i get the same problem. My system is > 64 bit, is this a cause? Nope, the fault is mine... Vlad just alerted me to the same problem. I had tested these packages on an upgraded system (from gutsy) in which netcdf is a virtual package to netcdfg-dev and libnetcdf3 so the problem did not manifest. I have just rebuilt all the packages and am uploading them now. Try again in 1/2 hour once they upload from Oz to Canada and things should be good. I have simply removed the netcdf dependency for now. a From ayman.oweida at mail.mcgill.ca Wed May 21 01:01:29 2008 From: ayman.oweida at mail.mcgill.ca (Ayman Oweida) Date: Wed, 21 May 2008 01:01:29 -0400 Subject: [MINC-users] Selecting a single slice from a mnc volume Message-ID: <87016016B286AD429079D616EA89E51E688F1A@EXCHANGE2VS4.campus.mcgill.ca> This is probably a trivial problem, yet I'm struggling to figure it out. How can I select a single slice from a 120 slice minc volume? I then want to import this slice into R using RMINC (minc.get.volumes) so I guess I would have to first extract the slice using a minc-related operation, save it and then import it into R. Any suggestions on what the minc-operation would be? Thanks, Ayman From jason at bic.mni.mcgill.ca Wed May 21 07:19:55 2008 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 21 May 2008 07:19:55 -0400 Subject: [MINC-users] Selecting a single slice from a mnc volume In-Reply-To: <87016016B286AD429079D616EA89E51E688F1A@EXCHANGE2VS4.campus.mcgill.ca> References: <87016016B286AD429079D616EA89E51E688F1A@EXCHANGE2VS4.campus.mcgill.ca> Message-ID: <29C7444C-9003-4E1C-B96D-C187F33F7246@bic.mni.mcgill.ca> Hello Ayman, that depends somewhat on the version of RMINC you are using - but you can get a slice directly inside R as well. Use the minc.get.hyperslab function (or, in the newest version, mincGetHyperslab). Otherwise, working outside of R, the mincextract program can do this type of stuff. Cheers, Jason On 21-May-08, at 1:01 AM, Ayman Oweida wrote: > > This is probably a trivial problem, yet I'm struggling to figure it > out. How can I select a single slice from a 120 slice minc volume? > I then want to import this slice into R using RMINC > (minc.get.volumes) so I guess I would have to first extract the > slice using a minc-related operation, save it and then import it > into R. Any suggestions on what the minc-operation would be? > > Thanks, > Ayman > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From alex at bic.mni.mcgill.ca Wed May 21 09:03:28 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Wed, 21 May 2008 09:03:28 -0400 Subject: [MINC-users] Selecting a single slice from a mnc volume In-Reply-To: <29C7444C-9003-4E1C-B96D-C187F33F7246@bic.mni.mcgill.ca> References: <87016016B286AD429079D616EA89E51E688F1A@EXCHANGE2VS4.campus.mcgill.ca> <29C7444C-9003-4E1C-B96D-C187F33F7246@bic.mni.mcgill.ca> Message-ID: Alternatively, mincreshape will allow you to pull an arbitrary slice (or hyperslab) ouf of a minc volume. -- A On Wed, May 21, 2008 at 7:19 AM, Jason Lerch wrote: > Hello Ayman, > > that depends somewhat on the version of RMINC you are using - but you > can get a slice directly inside R as well. Use the minc.get.hyperslab > function (or, in the newest version, mincGetHyperslab). > > Otherwise, working outside of R, the mincextract program can do this > type of stuff. > > Cheers, > > Jason > > On 21-May-08, at 1:01 AM, Ayman Oweida wrote: > >> >> This is probably a trivial problem, yet I'm struggling to figure it >> out. How can I select a single slice from a 120 slice minc volume? >> I then want to import this slice into R using RMINC >> (minc.get.volumes) so I guess I would have to first extract the >> slice using a minc-related operation, save it and then import it >> into R. Any suggestions on what the minc-operation would be? >> >> Thanks, >> Ayman >> >> _______________________________________________ >> 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 a.janke at gmail.com Thu May 22 10:14:04 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 23 May 2008 00:14:04 +1000 Subject: [MINC-users] minc-2.0.15 build error In-Reply-To: References: Message-ID: Hi Jim, I have tried to reproduce this error on another leopard machine but to no avail... 'make check' works fine. Have you made any progress on this yourself? The machine I am using has a 64bit build of hdf/netcdf that Alexandre did, are you also building 64 bit of 32 bit? a On Sun, May 18, 2008 at 1:57 AM, EJ Nikelski wrote: > > For reasons that I would rather not get into, I found myself > rebuilding minc2 on my Intel mac (os x 10.5). Although I'm certain > that this worked previously, I now get an error during "make check" -- > specifically: > > Testing icv_dim1 > Testing icv_fillvalue > PASS: run_test2.sh > PASS: xfmconcat_01.sh > PASS: xfmconcat_02.sh > Assertion failed: (extent != 0), function px_get, file posixio.c, line 412. > /bin/sh: line 1: 66090 Abort trap ${dir}$tst > FAIL: mincapi > ================================== > 1 of 5 tests failed > Please report to a.janke at gmail.com > ================================== > > I've done some snooping, and the problem is related to this bit of > code in mincapi.c ... > > /* Try to open the file for write - should fail. > */ > fd2 = miopen(ip->name, NC_WRITE); > if (fd2 >= 0) { > FUNC_ERROR("miopen"); > } > > The call to miopen does indeed fail, but instead of returning, it > fails on the assertion in posixio.c. Andrew, given that you've > dutifully attached your name to the error message, I suppose that you > get first kick at the can. What do you think? BTW - I'm building > minc2 with hdf5-1.6.7 and netcdf-3.6.2. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From nikelski at bic.mni.mcgill.ca Thu May 22 11:26:41 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Thu, 22 May 2008 11:26:41 -0400 Subject: [MINC-users] minc-2.0.15 build error In-Reply-To: References: Message-ID: Hi Andrew (and List), I've built using 32-bit on Leopard (other than the larger flat addressing space, I'm at a loss with regard to why 64-bit should be any faster). In addition, I'm also using netcdf-3.6.2 and hdf5-1.6.5. The use of hdf5-1.6.5 was required to solve some EMMA/minc2-related problems (hdf5-1.6.5 is the version that Matlab R2007a ships with, and using a different version causes nasty problems). At any rate, other than the failure of the minc2 make test, everything is working well (even EMMA writing minc2 volumes), so I'm hoping that this failure is limited to the test. Sadly, I have little time to throw at this ... however, if you have a suggestion WRT putting some debug code somewhere, I will happily recompile and re-test. -Jim On Thu, May 22, 2008 at 10:14 AM, Andrew Janke wrote: > Hi Jim, > > I have tried to reproduce this error on another leopard machine but to > no avail... 'make check' works fine. > > Have you made any progress on this yourself? The machine I am using > has a 64bit build of hdf/netcdf that Alexandre did, are you also > building 64 bit of 32 bit? > > > a > > On Sun, May 18, 2008 at 1:57 AM, EJ Nikelski wrote: >> >> For reasons that I would rather not get into, I found myself >> rebuilding minc2 on my Intel mac (os x 10.5). Although I'm certain >> that this worked previously, I now get an error during "make check" -- >> specifically: >> >> Testing icv_dim1 >> Testing icv_fillvalue >> PASS: run_test2.sh >> PASS: xfmconcat_01.sh >> PASS: xfmconcat_02.sh >> Assertion failed: (extent != 0), function px_get, file posixio.c, line 412. >> /bin/sh: line 1: 66090 Abort trap ${dir}$tst >> FAIL: mincapi >> ================================== >> 1 of 5 tests failed >> Please report to a.janke at gmail.com >> ================================== >> >> I've done some snooping, and the problem is related to this bit of >> code in mincapi.c ... >> >> /* Try to open the file for write - should fail. >> */ >> fd2 = miopen(ip->name, NC_WRITE); >> if (fd2 >= 0) { >> FUNC_ERROR("miopen"); >> } >> >> The call to miopen does indeed fail, but instead of returning, it >> fails on the assertion in posixio.c. Andrew, given that you've >> dutifully attached your name to the error message, I suppose that you >> get first kick at the can. What do you think? BTW - I'm building >> minc2 with hdf5-1.6.7 and netcdf-3.6.2. > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From acveilleux at mrs.mni.mcgill.ca Thu May 22 13:44:53 2008 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 22 May 2008 13:44:53 -0400 Subject: [MINC-users] minc-2.0.15 build error In-Reply-To: References: Message-ID: <20080522174453.GK7617@mrs.mni.mcgill.ca> For what it's worth: PASS: testminctools.sh =================== All 17 tests passed =================== make[2]: Nothing to be done for `check-am'. mrspc [/localscratch/compile/minc-2.0.15] mincmath -version program: 2.0.15 libminc: 2.0.15 netcdf : "3.6.2" of Apr 1 2008 14:09:41 $ HDF5 : 1.6.7 mrspc [/localscratch/compile/minc-2.0.15] file /usr/local/bic/bin/mincmath /usr/local/bic/bin/mincmath: Mach-O 64-bit executable x86_64 mrspc [/localscratch/compile/minc-2.0.15] And now the useful suggestion: Does the user running make check have write permissions over the directories? Alex On Fri, May 23, 2008 at 12:14:04AM +1000, Andrew Janke wrote: > Date: Fri, 23 May 2008 00:14:04 +1000 > From: Andrew Janke > Subject: Re: [MINC-users] minc-2.0.15 build error > To: MINC users mailing list > > Hi Jim, > > I have tried to reproduce this error on another leopard machine but to > no avail... 'make check' works fine. > > Have you made any progress on this yourself? The machine I am using > has a 64bit build of hdf/netcdf that Alexandre did, are you also > building 64 bit of 32 bit? > > > a > > On Sun, May 18, 2008 at 1:57 AM, EJ Nikelski wrote: > > > > For reasons that I would rather not get into, I found myself > > rebuilding minc2 on my Intel mac (os x 10.5). Although I'm certain > > that this worked previously, I now get an error during "make check" -- > > specifically: > > > > Testing icv_dim1 > > Testing icv_fillvalue > > PASS: run_test2.sh > > PASS: xfmconcat_01.sh > > PASS: xfmconcat_02.sh > > Assertion failed: (extent != 0), function px_get, file posixio.c, line 412. > > /bin/sh: line 1: 66090 Abort trap ${dir}$tst > > FAIL: mincapi > > ================================== > > 1 of 5 tests failed > > Please report to a.janke at gmail.com > > ================================== > > > > I've done some snooping, and the problem is related to this bit of > > code in mincapi.c ... > > > > /* Try to open the file for write - should fail. > > */ > > fd2 = miopen(ip->name, NC_WRITE); > > if (fd2 >= 0) { > > FUNC_ERROR("miopen"); > > } > > > > The call to miopen does indeed fail, but instead of returning, it > > fails on the assertion in posixio.c. Andrew, given that you've > > dutifully attached your name to the error message, I suppose that you > > get first kick at the can. What do you think? BTW - I'm building > > minc2 with hdf5-1.6.7 and netcdf-3.6.2. > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From nikelski at bic.mni.mcgill.ca Thu May 22 16:08:22 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Thu, 22 May 2008 16:08:22 -0400 Subject: [MINC-users] minc-2.0.15 build error In-Reply-To: <20080522174453.GK7617@mrs.mni.mcgill.ca> References: <20080522174453.GK7617@mrs.mni.mcgill.ca> Message-ID: Hi Alex, I suppose I owe you a cup of coffee! Now, but really, why should I need to 'sudo' my 'make check'? I *do* have write permissions to all of my build subdirs ... so I'm confused ... but happy that the 'make check' completes. Thanks again, -Jim On Thu, May 22, 2008 at 1:44 PM, Alexandre CARMEL-VEILLEUX wrote: > For what it's worth: > > PASS: testminctools.sh > =================== > All 17 tests passed > =================== > make[2]: Nothing to be done for `check-am'. > mrspc [/localscratch/compile/minc-2.0.15] mincmath -version > program: 2.0.15 > libminc: 2.0.15 > netcdf : "3.6.2" of Apr 1 2008 14:09:41 $ > HDF5 : 1.6.7 > mrspc [/localscratch/compile/minc-2.0.15] file /usr/local/bic/bin/mincmath > /usr/local/bic/bin/mincmath: Mach-O 64-bit executable x86_64 > mrspc [/localscratch/compile/minc-2.0.15] > > And now the useful suggestion: Does the user running make check > have write permissions over the directories? > > Alex > > On Fri, May 23, 2008 at 12:14:04AM +1000, Andrew Janke wrote: >> Date: Fri, 23 May 2008 00:14:04 +1000 >> From: Andrew Janke >> Subject: Re: [MINC-users] minc-2.0.15 build error >> To: MINC users mailing list >> >> Hi Jim, >> >> I have tried to reproduce this error on another leopard machine but to >> no avail... 'make check' works fine. >> >> Have you made any progress on this yourself? The machine I am using >> has a 64bit build of hdf/netcdf that Alexandre did, are you also >> building 64 bit of 32 bit? >> >> >> a >> >> On Sun, May 18, 2008 at 1:57 AM, EJ Nikelski wrote: >> > >> > For reasons that I would rather not get into, I found myself >> > rebuilding minc2 on my Intel mac (os x 10.5). Although I'm certain >> > that this worked previously, I now get an error during "make check" -- >> > specifically: >> > >> > Testing icv_dim1 >> > Testing icv_fillvalue >> > PASS: run_test2.sh >> > PASS: xfmconcat_01.sh >> > PASS: xfmconcat_02.sh >> > Assertion failed: (extent != 0), function px_get, file posixio.c, line 412. >> > /bin/sh: line 1: 66090 Abort trap ${dir}$tst >> > FAIL: mincapi >> > ================================== >> > 1 of 5 tests failed >> > Please report to a.janke at gmail.com >> > ================================== >> > >> > I've done some snooping, and the problem is related to this bit of >> > code in mincapi.c ... >> > >> > /* Try to open the file for write - should fail. >> > */ >> > fd2 = miopen(ip->name, NC_WRITE); >> > if (fd2 >= 0) { >> > FUNC_ERROR("miopen"); >> > } >> > >> > The call to miopen does indeed fail, but instead of returning, it >> > fails on the assertion in posixio.c. Andrew, given that you've >> > dutifully attached your name to the error message, I suppose that you >> > get first kick at the can. What do you think? BTW - I'm building >> > minc2 with hdf5-1.6.7 and netcdf-3.6.2. >> >> >> >> -- >> Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) >> Canberra->Australia +61 (402) 700 883 >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://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 > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From Michel.Audette at medizin.uni-leipzig.de Wed May 28 03:45:15 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 28 May 2008 09:45:15 +0200 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register References: <48064019.6060705@bic.mni.mcgill.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> Hi all, I've obtained a transformation from register from homologous point pairs, and the rotation part of the result looks orthonormal, but I want to make sure that this isn't a coincidence. I cannot see the Transform Type that register assumes, because when I do, I see: freeglut (no_program_name): Unable to create direct context rendering for window 'Transform Type Selection' This may hurt performance. (is there an easy fix to this?) Can anyone indicate what is the default transformation for homologous point pairs on register? Rigid or Procrustes, or something else altogether? Cheers, Michel From louis.collins at mcgill.ca Wed May 28 08:53:44 2008 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Wed, 28 May 2008 08:53:44 -0400 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register In-Reply-To: <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> References: <48064019.6060705@bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> Message-ID: <5C105199-4EA2-43B1-A526-1AAAEF54378F@mcgill.ca> Michel, The default register transformation type is 6 parameter (3 trans, 3 rots) rigid body. If you need to see the actual transformation parameters, use xfm2param yourfile.xfm -Louis On May 28, 2008, at 3:45 AM, Audette, Michel wrote: > Hi all, > > I've obtained a transformation from register from homologous point > pairs, and the rotation part of the result looks orthonormal, but I > want to make sure that this isn't a coincidence. > > I cannot see the Transform Type that register assumes, because when > I do, I see: > > freeglut (no_program_name): Unable to create direct context > rendering for window 'Transform Type Selection' > This may hurt performance. > (is there an easy fix to this?) > > Can anyone indicate what is the default transformation for > homologous point pairs on register? Rigid or Procrustes, or > something else altogether? > > Cheers, > > Michel > _______________________________________________ > 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 Wed May 28 09:08:41 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 28 May 2008 15:08:41 +0200 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register References: <48064019.6060705@bic.mni.mcgill.ca><160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> <5C105199-4EA2-43B1-A526-1AAAEF54378F@mcgill.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E690202018C@MRZS152229.medizin.uni-leipzig.de> Hi Louis, not sure if you got my last reply. Thanks for that. Both 6 and 7 seem to call procrustes(), so I suppose that procrustes() knows whether it's dealing with 6 or 7. Glad that I checked. Cheers, Michel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of D. Louis Collins Sent: Wed 5/28/2008 2:53 PM To: MINC users mailing list Subject: Re: [MINC-users] freeglut error on transform type in register,and default tranform type on register Michel, The default register transformation type is 6 parameter (3 trans, 3 rots) rigid body. If you need to see the actual transformation parameters, use xfm2param yourfile.xfm -Louis On May 28, 2008, at 3:45 AM, Audette, Michel wrote: > Hi all, > > I've obtained a transformation from register from homologous point > pairs, and the rotation part of the result looks orthonormal, but I > want to make sure that this isn't a coincidence. > > I cannot see the Transform Type that register assumes, because when > I do, I see: > > freeglut (no_program_name): Unable to create direct context > rendering for window 'Transform Type Selection' > This may hurt performance. > (is there an easy fix to this?) > > Can anyone indicate what is the default transformation for > homologous point pairs on register? Rigid or Procrustes, or > something else altogether? > > Cheers, > > Michel > _______________________________________________ > 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 louis.collins at mcgill.ca Wed May 28 10:11:04 2008 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Wed, 28 May 2008 10:11:04 -0400 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register In-Reply-To: <160E3DD4FB702C4CB860C65186686E690202018C@MRZS152229.medizin.uni-leipzig.de> References: <48064019.6060705@bic.mni.mcgill.ca><160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> <5C105199-4EA2-43B1-A526-1AAAEF54378F@mcgill.ca> <160E3DD4FB702C4CB860C65186686E690202018C@MRZS152229.medizin.uni-leipzig.de> Message-ID: procrustes returns the translations, rotations and scaling required for the two transforms. register simply ignores the scaling value returned (ie, sets it to 1.0) when doing a rigid body transform. -L On May 28, 2008, at 9:08 AM, Audette, Michel wrote: > Hi Louis, > > not sure if you got my last reply. Thanks for that. > > Both 6 and 7 seem to call procrustes(), so I suppose that > procrustes() knows whether it's dealing with 6 or 7. > > Glad that I checked. > > Cheers, > > Michel > > > -----Original Message----- > From: minc-users-bounces at bic.mni.mcgill.ca on behalf of D. Louis > Collins > Sent: Wed 5/28/2008 2:53 PM > To: MINC users mailing list > Subject: Re: [MINC-users] freeglut error on transform type in > register,and default tranform type on register > > Michel, > > The default register transformation type is 6 parameter (3 trans, 3 > rots) rigid body. > > If you need to see the actual transformation parameters, use xfm2param > yourfile.xfm > > -Louis > > On May 28, 2008, at 3:45 AM, Audette, Michel wrote: > >> Hi all, >> >> I've obtained a transformation from register from homologous point >> pairs, and the rotation part of the result looks orthonormal, but I >> want to make sure that this isn't a coincidence. >> >> I cannot see the Transform Type that register assumes, because when >> I do, I see: >> >> freeglut (no_program_name): Unable to create direct context >> rendering for window 'Transform Type Selection' >> This may hurt performance. >> (is there an easy fix to this?) >> >> Can anyone indicate what is the default transformation for >> homologous point pairs on register? Rigid or Procrustes, or >> something else altogether? >> >> Cheers, >> >> Michel >> _______________________________________________ >> 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 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Thu May 29 06:22:52 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 29 May 2008 20:22:52 +1000 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register In-Reply-To: <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> References: <48064019.6060705@bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> Message-ID: > I've obtained a transformation from register from homologous point pairs, and the rotation part of the result looks orthonormal, but I want to make sure that this isn't a coincidence. > > I cannot see the Transform Type that register assumes, because when I do, I see: > > freeglut (no_program_name): Unable to create direct context rendering for window 'Transform Type Selection' > This may hurt performance. > (is there an easy fix to this?) Hi Michel, I have often seen this bug and have always presumed it to be somewhat harmless... Seems that I am (now) wrong, I get no text on any of the dialog boxes and I presume this is what you are referring to. Register and Display relied on a lot of (at times) undocumented "features" of glut given how embryonic the library was when register was written. I suspect this will be an evil bug to track down but I will see what I can do. -- Andrew Janke (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 May 29 06:49:30 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 29 May 2008 12:49:30 +0200 Subject: [MINC-users] errors going from DICOM startxyz to MINC startxyz In-Reply-To: References: <48064019.6060705@bic.mni.mcgill.ca><160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902424F64@MRZS152229.medizin.uni-leipzig.de> Hi folks, I'm frantically trying to meet a conference paper deadline, and have it a snag. I have some expert validation data for anatomical boundaries, which come in stl format, and these have been produced with a software called Mimics from Dicom. Looking at these stls, the vertex coordinates do not coincide with the reasonable world coordinates in the minc file that I'm getting after doing dicom3_to_minc, and resampling with positive xyz. The start x,y,z of the minc volume also bears little resemblance to image position patient (0020-0037) visible under Image Position Patient. Can anyone suggest a way of reconciling Dicom with minc start x,y,z, to begin with? Cheers, 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 Michel.Audette at medizin.uni-leipzig.de Thu May 29 06:56:49 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 29 May 2008 12:56:49 +0200 Subject: [MINC-users] freeglut error on transform type in register, and default tranform type on register In-Reply-To: References: <48064019.6060705@bic.mni.mcgill.ca><160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902424F66@MRZS152229.medizin.uni-leipzig.de> Hi Andrew, thanks for the kind reply. It's not critical to me, now that I know the nature of the registration. Cheers, 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: May 29, 2008 12:23 PM To: MINC users mailing list Subject: Re: [MINC-users] freeglut error on transform type in register,and default tranform type on register > I've obtained a transformation from register from homologous point pairs, and the rotation part of the result looks orthonormal, but I want to make sure that this isn't a coincidence. > > I cannot see the Transform Type that register assumes, because when I do, I see: > > freeglut (no_program_name): Unable to create direct context rendering for window 'Transform Type Selection' > This may hurt performance. > (is there an easy fix to this?) Hi Michel, I have often seen this bug and have always presumed it to be somewhat harmless... Seems that I am (now) wrong, I get no text on any of the dialog boxes and I presume this is what you are referring to. Register and Display relied on a lot of (at times) undocumented "features" of glut given how embryonic the library was when register was written. I suspect this will be an evil bug to track down but I will see what I can do. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Thu May 29 07:10:43 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 29 May 2008 21:10:43 +1000 Subject: [MINC-users] errors going from DICOM startxyz to MINC startxyz In-Reply-To: <160E3DD4FB702C4CB860C65186686E6902424F64@MRZS152229.medizin.uni-leipzig.de> References: <48064019.6060705@bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902424F64@MRZS152229.medizin.uni-leipzig.de> Message-ID: Michel, At a first hack I would use dcm2mnc instead of dicom3_to_minc the code in there is far more up to date. a On Thu, May 29, 2008 at 8:49 PM, Audette, Michel wrote: > Hi folks, > > I'm frantically trying to meet a conference paper deadline, and have it a snag. > > I have some expert validation data for anatomical boundaries, which come in stl format, and these have been produced with a software called Mimics from Dicom. Looking at these stls, the vertex coordinates do not coincide with the reasonable world coordinates in the minc file that I'm getting after doing dicom3_to_minc, and resampling with positive xyz. The start x,y,z of the minc volume also bears little resemblance to image position patient (0020-0037) visible under Image Position Patient. > > Can anyone suggest a way of reconciling Dicom with minc start x,y,z, to begin with? > > Cheers, > > 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 (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 May 29 07:30:51 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 29 May 2008 13:30:51 +0200 Subject: [MINC-users] errors going from DICOM startxyz to MINC startxyz References: <48064019.6060705@bic.mni.mcgill.ca><160E3DD4FB702C4CB860C65186686E6902020187@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902424F64@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902020196@MRZS152229.medizin.uni-leipzig.de> Hi, I had a problem just now with dcm2mnc and this dicom volume, but I think that this was because the volume was on a vfat partition. I'm moving things around and retrying. Michel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke Sent: Thu 5/29/2008 1:10 PM To: MINC users mailing list Subject: Re: [MINC-users] errors going from DICOM startxyz to MINC startxyz Michel, At a first hack I would use dcm2mnc instead of dicom3_to_minc the code in there is far more up to date. a On Thu, May 29, 2008 at 8:49 PM, Audette, Michel wrote: > Hi folks, > > I'm frantically trying to meet a conference paper deadline, and have it a snag. > > I have some expert validation data for anatomical boundaries, which come in stl format, and these have been produced with a software called Mimics from Dicom. Looking at these stls, the vertex coordinates do not coincide with the reasonable world coordinates in the minc file that I'm getting after doing dicom3_to_minc, and resampling with positive xyz. The start x,y,z of the minc volume also bears little resemblance to image position patient (0020-0037) visible under Image Position Patient. > > Can anyone suggest a way of reconciling Dicom with minc start x,y,z, to begin with? > > Cheers, > > 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 (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 sean at rogue-research.com Thu May 29 12:48:04 2008 From: sean at rogue-research.com (Sean McBride) Date: Thu, 29 May 2008 12:48:04 -0400 Subject: [MINC-users] For the OSX 10.5 crash test dummies. In-Reply-To: References: <20080430201119.1405142100@kingu.local> Message-ID: <20080529164804.528493279@kingu.local> On 5/1/08 9:57 AM, Andrew Janke said: >> Are there installers anywhere for a Universal Binary version of minc? >> Or at least for 32bit PowerPC? I've looked on > packages.bic.mni.mcgill.ca> but everything seems to be Intel-only or >> several years old. > >I build essentially what people ask for and for what platforms I have >access to! :) > >The only access I have to older Mac hardware is a PowerPC Tiger >machine. Will this do what you want? I have no idea how to build a >universal binary (never looked into it as I figured in 6 months there >would be no point) though... Sorry for my delayed reply. Let's say you want to build a 4-way universal MINC that works on 10.4 and 10.5. You do the following: For CMake: Very easy. Just set the following settings: CMAKE_OSX_ARCHITECTURES i386;x86_64;ppc;ppc64 CMAKE_OSX_SYSROOT /Developer/SDKs/MacOSX10.4u.sdk CMAKE_CXX_FLAGS -mmacosx-version-min=10.4 CMAKE_C_FLAGS -mmacosx-version-min=10.4 For configure/make: You basically just need to add "-mmacosx-version-min=10.4 -isysroot / Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc -arch ppc64 -arch x86_64" to CFLAGS and CXXFLAGS. See also: -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From nikelski at bic.mni.mcgill.ca Thu May 29 16:09:30 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Thu, 29 May 2008 16:09:30 -0400 Subject: [MINC-users] mincresample and minctracc question Message-ID: Hi All, I'm trying to align a PET volume to it's anatomy, and am running into some problems (and could use some help). I just have a couple of questions ... (1) do I need to resample my anatomical volume to match that of the functional volume prior to calling minctracc? (2) when I try to resample the native MRI to the functional, I usually get an empty volume out. I suspect that this is related to the difference in z-start values, but am unsure how to proceed. The 2 input volumes look like this ... ** MRI ** file: lestat_t1_native.mnc image: signed__ short 0 to 4095 image dimensions: xspace zspace yspace dimension name length step start -------------- ------ ---- ----- xspace 176 1 -85.4759 zspace 256 -1 113.831 yspace 224 -1 144.386 ** PET ** file: pibXmean.mnc image: unsigned byte 0 to 255 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 63 -2.425 -452.7 yspace 128 2.05941 -130.772 xspace 128 2.05941 -130.772 The mincresample command and the resulting volume looks this ... >>mincresample -verbose -clobber -like pibXmean.mnc lestat_t1_native.mnc lestat_t1_native_rsl.mnc ** resampled empty T1 volume -- file: lestat_t1_native_rsl.mnc image: signed__ short 0 to 4095 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 63 -2.425 -452.7 yspace 128 2.05941 -130.772 xspace 128 2.05941 -130.772 (3) does minctracc want both volumes to share the same data type (e.g. byte) or does this not matter? (4) should I blur the native T1 prior to fitting? ... or does minctrac deal with this? Thanks, -Jim From jason at bic.mni.mcgill.ca Thu May 29 16:39:36 2008 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 29 May 2008 16:39:36 -0400 Subject: [MINC-users] mincresample and minctracc question In-Reply-To: References: Message-ID: <483F1488.5070304@bic.mni.mcgill.ca> Hi Jim, > (1) do I need to resample my anatomical volume to match that of the > functional volume prior to calling minctracc? > Nope. > (2) when I try to resample the native MRI to the functional, I usually > get an empty volume out. I suspect that this is related to the > difference in z-start values, but am unsure how to proceed. The 2 > input volumes look like this ... > That mincresample call won't work due to the difference in starts and steps between the two images - you'll need to compute the transform first and then resample. > > (3) does minctracc want both volumes to share the same data type (e.g. > byte) or does this not matter? > This does not matter - though if you need to do mutual information registration, then it will reshape them to unsigned byte automatically. > (4) should I blur the native T1 prior to fitting? ... or does minctrac > deal with this? > Probably - especially with those differences in initial position you'll probably want to use a multiscale algorithm anyway; i.e. first transform with quite blurred data, second transform with less blurring, etc. Hope this helps, Jason > > Thanks, > > > -Jim > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vikingy at gmail.com Fri May 30 04:20:54 2008 From: vikingy at gmail.com (vikingy) Date: Fri, 30 May 2008 16:20:54 +0800 Subject: [MINC-users] replace the parcellation template in ANIMAL Message-ID: <200805301620513906297@gmail.com> Hi all, In SPM community, peopel usually use the ALL template (90 anatomical volumes) to parcellate the brain structure, in fact the ALL template is also derived from the MNI template. While in MINC, the ANIMAL template has 90 areas, I'm not sure about their difference, coulud I use the ALL template to label the brain structure in the process of ANIMAL? (in stx_segment?) Many thanks!~ bin lv 2008-05-30 vikingy From vikingy at gmail.com Fri May 30 05:36:15 2008 From: vikingy at gmail.com (bin lv) Date: Fri, 30 May 2008 17:36:15 +0800 Subject: [MINC-users] replace the parcellation template in ANIMAL In-Reply-To: <200805301620513906297@gmail.com> References: <200805301620513906297@gmail.com> Message-ID: <93e2f0200805300236laf23d65k2ad48ef11f54000d@mail.gmail.com> sorry, a mistake on above letter, the ANIMAL template has 96 areas according to http://www.bic.mni.mcgill.ca/~noor/brain_volume.html 2008/5/30 vikingy : > Hi all, > > In SPM community, peopel usually use the ALL template (90 anatomical > volumes) to parcellate the brain structure, in fact the ALL template is also > derived from the MNI template. While in MINC, the ANIMAL template has 90 > areas, I'm not sure about their difference, coulud I use the ALL template > to label the brain structure in the process of ANIMAL? (in stx_segment?) > > Many thanks!~ > > bin lv > > 2008-05-30 > ------------------------------ > vikingy >