From thomas_mitchell2 at merck.com Mon Oct 3 10:48:32 2005 From: thomas_mitchell2 at merck.com (Mitchell, Thomas William (WP)) Date: Mon, 3 Oct 2005 10:48:32 -0400 Subject: [MINC-users] Display OS X Message-ID: <5986DC4529536A418C8C581C726F589D5237C3@usctmx1105.merck.com> Dear List, I am using the Linux version of Display at work and I want to also use the OS X version at home. I am unable to load successfully the OS X version. As I am a user, and not an experienced OS person, any help is appreciated. Such as: 1) downloading the Display OS X software 2) other software that I have to have on the Apple Macintosh to get Display to work. 3) other that I need to know. Thanks for any help. Tom ------------------------------------------------------- Thomas W. Mitchell, V.M.D., Ph.D. Merck & Co., Inc. Merck Research Laboratories Laboratory Animal Resources WP44-201 West Point, PA 19486 (215) 652-3249 (Office) (267) 446-4660 (cellular) (215) 652-3241 (fax) mailto:thomas_mitchell2 at merck.com ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------ From a.janke at gmail.com Mon Oct 3 10:57:25 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 3 Oct 2005 10:57:25 -0400 Subject: [MINC-users] Display OS X In-Reply-To: <5986DC4529536A418C8C581C726F589D5237C3@usctmx1105.merck.com> References: <5986DC4529536A418C8C581C726F589D5237C3@usctmx1105.merck.com> Message-ID: Hi Thomas, Try the pre-built packages here: packages.bic.mni.mcgill.ca/osx They should be nice pretty point and click installers. Andrew On 03/10/05, Mitchell, Thomas William (WP) wrote: > Dear List, > > I am using the Linux version of Display at work and I want to also use > the OS X version at home. I am unable to load successfully the OS X version. > As I am a user, and not an experienced OS person, any help is appreciated. > Such as: > > 1) downloading the Display OS X software > 2) other software that I have to have on the Apple Macintosh to get > Display to work. > 3) other that I need to know. > > Thanks for any help. > > > Tom > > ------------------------------------------------------- > Thomas W. Mitchell, V.M.D., Ph.D. > Merck & Co., Inc. > Merck Research Laboratories > Laboratory Animal Resources > WP44-201 > West Point, PA 19486 > > (215) 652-3249 (Office) > (267) 446-4660 (cellular) > (215) 652-3241 (fax) > mailto:thomas_mitchell2 at merck.com > > > ------------------------------------------------------------------------------ > Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. > ------------------------------------------------------------------------------ > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From acveilleux at mrs.mni.mcgill.ca Mon Oct 3 11:31:34 2005 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Mon, 3 Oct 2005 11:31:34 -0400 Subject: [MINC-users] Display OS X In-Reply-To: ; from a.janke@gmail.com on Mon, Oct 03, 2005 at 10:57:25AM -0400 References: <5986DC4529536A418C8C581C726F589D5237C3@usctmx1105.merck.com> Message-ID: <20051003113134.A10565@mrs.mni.mcgill.ca> On Mon, Oct 03, 2005 at 10:57:25AM -0400, Andrew Janke wrote: > > Try the pre-built packages here: > > packages.bic.mni.mcgill.ca/osx > > They should be nice pretty point and click installers. The only thing I might add to this is you may want to install the X11 package from Apple, it's an optional install on your Mac OS X CDs or DVDs. I'm not sure if the pre-built packages need it, but many other tools you may want later will for sure. Alex From a.janke at gmail.com Mon Oct 3 11:35:20 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 3 Oct 2005 11:35:20 -0400 Subject: [MINC-users] Display OS X In-Reply-To: <20051003113134.A10565@mrs.mni.mcgill.ca> References: <5986DC4529536A418C8C581C726F589D5237C3@usctmx1105.merck.com> <20051003113134.A10565@mrs.mni.mcgill.ca> Message-ID: Correct. the packages there do depend on it (but don't check for it that I know of). You'll also have to fiddle with your PATH variable. a On 03/10/05, Alexandre CARMEL-VEILLEUX wrote: > On Mon, Oct 03, 2005 at 10:57:25AM -0400, Andrew Janke wrote: > > > > Try the pre-built packages here: > > > > packages.bic.mni.mcgill.ca/osx > > > > They should be nice pretty point and click installers. > > The only thing I might add to this is you may want to install the > X11 package from Apple, it's an optional install on your Mac OS X CDs > or DVDs. I'm not sure if the pre-built packages need it, but many other > tools you may want later will for sure. > > Alex > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From LeslieqG at ccpc.net Tue Oct 4 05:12:24 2005 From: LeslieqG at ccpc.net (Nathaniel Munoz) Date: Tue, 4 Oct 2005 05:12:24 -0400 Subject: [MINC-users] Registration confirmation Message-ID: <0b50f093e0f9$417a4810$17efb5ef@qrms> Everything inside the attach From a.janke at gmail.com Tue Oct 4 23:22:03 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 4 Oct 2005 23:22:03 -0400 Subject: [MINC-users] negative zstep causes trouble In-Reply-To: <1128038314.433c7faa10753@webmail.mcgill.ca> References: <1128038314.433c7faa10753@webmail.mcgill.ca> Message-ID: Hi Marc, Looks like an "amusing" bug you have found... Out of interest, what does mincstats return on this file as the CoM? As for +dimension not working, have a read of the man page for mincreshape, there is some functionality left in mincreshape that treats slice dimensions differently to image dimensions. I think this should now be deprecated myself, but then that is just me. The safest thing to do would be to reshape your data to have all positive steps as such: (note that this will not in any way cause flips of the volume) mincreshape +direction \ -dimsize zspace=-1 \ -dimsize zspace=-1 \ -dimsize zspace=-1 \ Do this before any other processing. the -1's indicate to flip the dimensions specified irrespective of their position in the file. Still the minctracc bug should be fixed! Can I have a copy of the file you are using? And which version of minctracc are you using? Andrew On 29/09/05, Marc Schoenwiesner wrote: > Hi, > > I am struggling with the conversion/analysis of fMRI data from outside > BIC, but have located the problem more or less. Maybe someone knows about this. > > Problem: fmr_preprocess crashes with a dynamic minc file. > The trouble maker is the positive zstep: > >> > file: run1.mncimage: signed__ short 0 to 4095 > image dimensions: time zspace yspace xspace dimension name > length step start > -------------- ------ ---- ----- > time 71 9 0 > zspace 19 4 -3.29857 > yspace 64 -3.12497 95.4729 > xspace 64 -3.12497 97.9577 > >> > > fmr_preprocess crashed when resampling the volume, because $nelem_z (resampling > steps in z direction) gets negative. I copied fmr_preprocess and added an abs() > to the 238 to make the calculation robust against positive zsteps: > $nelem_z = abs (int ((($z_sp - 1) * $z_step ) / $resampling_step)); > > This step works now. The next hang is when minctracc is called. I found that > this is because the center of gravity of the volume seems to be either > incorrectly calculated by volume_cog, or minctracc cannot handle centroids in > certain quadrants. > > center with zstep=4 0.912580 -4.248807 35.571903 (minctracc crashes) > center with zstep=-4 -0.077238 -9.411657 -41.277493 (works fine) > > I can work around this problem by setting zstep to -4: > % minc_modify_header -dinsert zspace:step=4 run1.mnc > then run fmr_preprocess and setting it back, but this is ugly and I might mess > up my file orientations (this is a left-brain right-brain thing, so I really > don't want to risk anything of that sort. By the way, mincreshape +/-zdirection > doesn't seem to do anything at all with this file.) > > volume_cog and mictracc are binary, so I am stuck here. > I'd be very grateful if anyone could clarify the centroid issue! I am new to the > BIC and MINC (had my first look at the software this week) and don't seem to be > able to get this straightened out myself. > > Cheers > Marc > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From Paul.Rasser at newcastle.edu.au Tue Oct 4 23:25:31 2005 From: Paul.Rasser at newcastle.edu.au (Paul Rasser) Date: Wed, 05 Oct 2005 13:25:31 +1000 Subject: [MINC-users] Display .obj under OS X Message-ID: Dear All, I am using OS X and have been experiencing a problem with Display. When an obj is loaded into Display and the window resized, Display crashes under OS X 10.3.9 through to 10.4.2 (Display works fine under 10.3.3). I have been using the binary OS X distribution 1.1 and thought this might be the problem, however I've recently recompiled Display and prerequisites under 10.4.2 and the problem still persists. Any suggestions would be appreciated. With thanks, Paul. From a.janke at gmail.com Tue Oct 4 23:49:22 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 4 Oct 2005 23:49:22 -0400 Subject: [MINC-users] Display .obj under OS X In-Reply-To: References: Message-ID: Hi Paul, I must admit that whilst I have recompiled Display under Tiger I haven't tested it all that much. But I do remember that a few things changed with GLUT/OpenGL. This would sound very much like a glut problem to me. Are you compiling against the apple GLUT or a darwinports/fink glut? I suspect the former if you are using the --with-apple-.... configure switch. a On 04/10/05, Paul Rasser wrote: > Dear All, > > I am using OS X and have been experiencing a problem with Display. > > When an obj is loaded into Display and the window resized, Display crashes under OS X 10.3.9 through to 10.4.2 (Display works fine under 10.3.3). > > I have been using the binary OS X distribution 1.1 and thought this might be the problem, however I've recently recompiled Display and prerequisites under 10.4.2 and the problem still persists. Any suggestions would be appreciated. > > With thanks, > > Paul. > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From marc.schoenwiesner at mcgill.ca Wed Oct 5 15:17:10 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Wed, 5 Oct 2005 15:17:10 -0400 Subject: [MINC-users] negative zstep causes trouble In-Reply-To: References: <1128038314.433c7faa10753@webmail.mcgill.ca> Message-ID: <1128539830.434426b65e6e2@webmail.mcgill.ca> Hi Andrew, your suggestion worked well (I reshaped the data to have all negative steps, though, since positive steps don't work with fmr_preprocess [$nelem gets negative...]). Dimentions are now (works with minctracc): zspace 19 -4 68.7014 yspace 64 -3.12497 95.4729 xspace 64 -3.12497 97.9577 before (crashes minctracc): zspace 19 4 -3.29857 yspace 64 -3.12497 95.4729 xspace 64 -3.12497 97.9577 So it looks more like the negative zstart might be the problem? I am slowly loosing the overview here... Mincstats says the CoM (real) is 0.8057721547 -4.288294074 35.31203982 volume_cog gives about the same: 0.942109 -4.382087 35.610321 The file is at /scratch2/marcs/run1.mnc, feel free to play around with it. I am using whatever version is at /usr/local/mni/bin/minctracc Cheers, Marc Quoting Andrew Janke : > Hi Marc, > > Looks like an "amusing" bug you have found... Out of interest, what > does mincstats return on this file as the CoM? > > As for +dimension not working, have a read of the man page for > mincreshape, there is some functionality left in mincreshape that > treats slice dimensions differently to image dimensions. I think this > should now be deprecated myself, but then that is just me. > > The safest thing to do would be to reshape your data to have all > positive steps as such: (note that this will not in any way cause > flips of the volume) > > mincreshape +direction \ > -dimsize zspace=-1 \ > -dimsize zspace=-1 \ > -dimsize zspace=-1 \ > > > Do this before any other processing. > > the -1's indicate to flip the dimensions specified irrespective of > their position in the file. Still the minctracc bug should be fixed! > Can I have a copy of the file you are using? And which version of > minctracc are you using? > > > Andrew From marc.schoenwiesner at mcgill.ca Sat Oct 8 20:14:49 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Sat, 8 Oct 2005 20:14:49 -0400 Subject: [MINC-users] clamping minc files Message-ID: <1128816889.434860f932af3@webmail.mcgill.ca> Hi, mritotal fails totally on some volumes that were converted from dicom to minc. On closer inspection I found that the global voxel intensity maximum (edge of skull + artefacts) is about 4000, while the maximum inside the skull is below 1000. Would a few very bright voxels throw mritotal off? How do I get rid of them? The same seems to be true for my functional volumes - fmr_preprocess does all it's tricks, but rather than motion corrected the the output is even more misaligned than before... Any pointers are welcome. Cheers, Marc From a.janke at gmail.com Sat Oct 8 21:50:44 2005 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 8 Oct 2005 21:50:44 -0400 Subject: [MINC-users] clamping minc files In-Reply-To: <1128816889.434860f932af3@webmail.mcgill.ca> References: <1128816889.434860f932af3@webmail.mcgill.ca> Message-ID: Hi Marc, I use the attached perl script. It clamps and rescales a file within two PCT's from the histrogram. Obviously you would have to adjust the script so that it doesn't rescale your fMRI data (and only clamps) Once you have the values you want to clamp between, this is all you need do: mincmath -clamp -const2 10 3800 in.mnc out.mnc -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From marc.schoenwiesner at mcgill.ca Sun Oct 9 22:48:04 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Sun, 9 Oct 2005 22:48:04 -0400 Subject: [MINC-users] clamping minc files Message-ID: <1128912484.4349d66451801@webmail.mcgill.ca> Hi Andrew, > I use the attached perl script. It wasn't there. But anyway, I got the right clamping values for the structural scan from register. This helped - mritotal does a neat job now. (How do you get an intensity histogram of a volume?) The realignment of the functional volumes is still far from perfect. The remaining motion in z direction (x and y seem to be fine) is a good 5mm. Just to check, I registered the same data with AIR5 (compiled at a PC, with an analyze version of the data) and - that got rid of all visible movement. Does minctracc have problems with movement in z direction? Well, it's probably just me. Thanks for your help, Andrew! Cheers, Marc PS.: The fmr_preprocess help seems to have gotten mixed up a bit over the years: -blur do not blur frames -align perform motion correction this is the default, opposite is -noblur, do not perform motion correction From a.janke at gmail.com Sun Oct 9 22:57:49 2005 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 9 Oct 2005 22:57:49 -0400 Subject: [MINC-users] clamping minc files In-Reply-To: <1128912484.4349d66451801@webmail.mcgill.ca> References: <1128912484.4349d66451801@webmail.mcgill.ca> Message-ID: Hrm, I'll try inline... mincstats will make your histogram of a volume as such: mincstats -histogram out.hist file.mnc a --- #! /usr/bin/env perl # # Andrew Janke - rotor at cmr.uq.edu.au # Center for Magnetic Resonance # The University of Queensland # http://www.cmr.uq.edu.au/~rotor # # Copyright Andrew Janke, The University of Queensland. # Permission to use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and the University of Queensland make no representations about the # suitability of this software for any purpose. It is provided "as is" # without express or implied warranty. # # Fri Jun 20 17:30:06 EST 2003 - initial version use strict; use warnings "all"; use Getopt::Tabular; use File::Basename; my($Help, $Usage, $me, @opt_table, %opt); my(@args, $infile, $outfile); $me = basename($0); %opt = ('verbose' => 0, 'quiet', => 0, 'clobber' => 0, 'cutoff' => 0.01, 'lowwer' => undef, 'upper' => undef, 'clamp' => 1, 'out_floor' => 0, 'out_ceil' => 100, ); $Help = < wrote: > Hi Andrew, > > > I use the attached perl script. > It wasn't there. But anyway, I got the right clamping values for the structural > scan from register. This helped - mritotal does a neat job now. (How do you get > an intensity histogram of a volume?) > > The realignment of the functional volumes is still far from perfect. The > remaining motion in z direction (x and y seem to be fine) is a good 5mm. Just > to check, I registered the same data with AIR5 (compiled at a PC, with an > analyze version of the data) and - that got rid of all visible movement. Does > minctracc have problems with movement in z direction? Well, it's probably just > me. > > Thanks for your help, Andrew! > > Cheers, > Marc > > PS.: The fmr_preprocess help seems to have gotten mixed up a bit over the years: > -blur do not blur frames > -align perform motion correction this is the default, opposite is > -noblur, do not perform motion correction > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From dwagne at bic.mni.mcgill.ca Mon Oct 10 15:00:34 2005 From: dwagne at bic.mni.mcgill.ca (Dylan David Wagner) Date: Mon, 10 Oct 2005 15:00:34 -0400 Subject: [MINC-users] Slice time correction and justification for aquiring co-planar In-Reply-To: References: Message-ID: <434ABA52.4000704@bic.mni.mcgill.ca> Dear Minc Users, I've since moved to another center where they have different scanning protocols and I'm trying to understand why they do what they do and by extension why we did what we did! Firstly: For event related fMRI data analysis using SPM, it's neccessary to perform slice timing correction (to correct for the fact that slices have been aquired at different times over the TR). How does fMRISTAT get away with not doing this? I found this in something Keith wrote that seems to explain, but I'm afraid I'm not very clear on what it means!!! "Finally, the regressors for the linear model are formed by subsampling the convolved stimuli at the slice acquisition times." I'm assuming this means it corrects for slice timing issues without having to interpolate a new dataset. Second: it's the norm here to collect a coplanar volume in addition to functional and anatomical images. The functional data are then registered to this coplanar volume which is itself registered to the anatomical. Apparently you get a better fit with this intermediary step than if you directly registered functional to anatomical. Is there some advantage of MINC or our registration packages which allows us to skip this step? Raw volumes seem to register great as they come off the scanner. Thanks, __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From joel-bruss at uiowa.edu Mon Oct 10 18:16:00 2005 From: joel-bruss at uiowa.edu (joel-bruss@uiowa.edu) Date: Mon, 10 Oct 2005 17:16:00 -0500 Subject: [MINC-users] N3 Message-ID: <1128982560.434ae820b26f4@webmail2.its.uiowa.edu> Currently I have data from a GE 1.5T, and Siemens 1.5 and 3T (Avanto and Trio) scanners. I am looking for a way to bias-correct these images so that they can be used with Gray/White segmentation and other volumetrics. My data is in 16-bit Analyze format and I have a minc converter (ana2mnc). When I run nu_correct, with default parameters (-V1.0) as well as specifying a mask of the brain image, I get very awful results. In my 124-slice volume, there are regions where the image is totally washed out (5-10 slice runs) and others where the brain looks nice but the bias-correction happened outside of the skull. When specifying for temp files to be saved as well as a tempdir, after converting the bias field, it looks like a perfectly uniform smoothing kernel (ovular/egg shape) which is definitely not what the bias appears as (more polar, specifically in the frontal lobe). I've tried downloading the test data but am unsure of how to even work with it. I've read Sled et al's IEEE paper but don't find it that useful in configuring nu_correct. Also, I set the max iteration for 150 but it runs through 3 iterations (in about 2 minutes) and says that it is done. Is this really possible? Is there a help file, other than the README, or tutorial out there? Any suggestions on how to configure nu_correct? Should I use a different Minc converter? Is it OK to use 16-bit images or do they need to be 8-bit? Any help would be useful right now. Thanks for your time -Joel From jason at bic.mni.mcgill.ca Tue Oct 11 09:20:25 2005 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 11 Oct 2005 09:20:25 -0400 Subject: [MINC-users] N3 In-Reply-To: <1128982560.434ae820b26f4@webmail2.its.uiowa.edu> References: <1128982560.434ae820b26f4@webmail2.its.uiowa.edu> Message-ID: <434BBC19.90208@bic.mni.mcgill.ca> Make sure that the intensity histogram of your volumes is adequate for N3 - which means that it should not lie between 0 and 1. If the actual values don't matter to you, try multiplying the volume with a large enough constant, then run N3. Hope this helps, Jason joel-bruss at uiowa.edu wrote: >Currently I have data from a GE 1.5T, and Siemens 1.5 and 3T (Avanto and Trio) >scanners. I am looking for a way to bias-correct these images so that they can >be used with Gray/White segmentation and other volumetrics. My data is in >16-bit Analyze format and I have a minc converter (ana2mnc). When I run >nu_correct, with default parameters (-V1.0) as well as specifying a mask of the >brain image, I get very awful results. In my 124-slice volume, there are >regions where the image is totally washed out (5-10 slice runs) and others where >the brain looks nice but the bias-correction happened outside of the skull. >When specifying for temp files to be saved as well as a tempdir, after >converting the bias field, it looks like a perfectly uniform smoothing kernel >(ovular/egg shape) which is definitely not what the bias appears as (more polar, >specifically in the frontal lobe). I've tried downloading the test data but am >unsure of how to even work with it. I've read Sled et al's IEEE paper but don't >find it that useful in configuring nu_correct. Also, I set the max iteration >for 150 but it runs through 3 iterations (in about 2 minutes) and says that it >is done. Is this really possible? > >Is there a help file, other than the README, or tutorial out there? Any >suggestions on how to configure nu_correct? Should I use a different Minc >converter? Is it OK to use 16-bit images or do they need to be 8-bit? Any help >would be useful right now. > >Thanks for your time > >-Joel > > > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From mhough at fmrib.ox.ac.uk Tue Oct 11 12:11:18 2005 From: mhough at fmrib.ox.ac.uk (Morgan Hough) Date: Tue, 11 Oct 2005 17:11:18 +0100 Subject: [MINC-users] scripting mniweb Message-ID: <1129047078.3220.7.camel@dhania.fmrib.ox.ac.uk> I was wondering if anyone knows a way to script mniweb output. How can I request datasets with varying parameters? Thanks in advance. Cheers, -Morgan -- Morgan G. Hough, DPhil Candidate University of Oxford, Centre for Functional MRI of the Brain (FMRIB) John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom Tel: +44 (0) 1865 222545 / Fax: +44 (0) 1865 222717 e-mail: mhough at fmrib.ox.ac.uk / URL: http://www.fmrib.ox.ac.uk/~mhough From marc.schoenwiesner at mcgill.ca Mon Oct 17 11:54:48 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Mon, 17 Oct 2005 11:54:48 -0400 Subject: [MINC-users] registering the 'old' way Message-ID: <1129564488.4353c948365dc@webmail.mcgill.ca> Hi, which anatomical locations should one tag when registering by hand with MNI register? Cheers, Marc From sylvain at bic.mni.mcgill.ca Mon Oct 17 14:44:23 2005 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon, 17 Oct 2005 14:44:23 -0400 Subject: [MINC-users] registering the 'old' way In-Reply-To: <1129564488.4353c948365dc@webmail.mcgill.ca> Message-ID: Hello Marc, You could look over Louis Collins phd thesis as he mentions various landmark points to choose from (section 3) although you won't need as much to get good results. Typically one needs around 12 to 15 point pairs. A short recipe would be to identify the AC-PC line and then select point pairs which determine brain extent in x,y,z. See here for an example: (in register select transform type = full affine 12 parameter) register /usr/local/mni/models/norm_avg_305_mri.mnc \ /data/aces/aces1/sylvain/clinical/Bokos/mri/bokos_panorea_18703000_007007_mri.mnc \ /data/aces/aces1/sylvain/clinical/Bokos/bokos_panorea_mrital.tag I then create a .xfm file with tagtoxfm -lsq12 bokos_panorea_mrital.{tag,xfm} and feed this back to mritotal with mritotal -transformation bokos_panorea_mrital.xfm ... and if that doesn't do the trick which sometimes occur when I deal with GD enhanced mri volumes, I keep the transformed (to xfm) tag file. Typically when I know I'm going to feed it back to mritotal, I select roughly 8 point pairs covering the entire cerebrum and if mritotal still fails, I add point pairs to bring the total to 12-15 point pairs. HTH, Sylvain On Mon, 17 Oct 2005, Marc Schoenwiesner wrote: > Hi, > > which anatomical locations should one tag when registering by hand with MNI > register? > > Cheers, > Marc > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From sylvain at bic.mni.mcgill.ca Mon Oct 17 15:16:40 2005 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon, 17 Oct 2005 15:16:40 -0400 Subject: [MINC-users] registering the 'old' way In-Reply-To: Message-ID: I shouldn't have made this data *public* ... look here instead for an example: register /usr/local/mni/models/norm_avg_305_mri.mnc \ /data/analysis1/sylvain/register/mri/anonymous_test_mri.mnc \ /data/analysis1/sylvain/register/anonymous_test_mrital.tag Sylvain On Mon, 17 Oct 2005, Sylvain MILOT wrote: > > Hello Marc, > > You could look over Louis Collins phd thesis as he mentions various landmark > points to choose from (section 3) although you won't need as much to get > good results. Typically one needs around 12 to 15 point pairs. A short recipe > would be to identify the AC-PC line and then select point pairs which determine > brain extent in x,y,z. > > See here for an example: (in register select transform type = full affine 12 parameter) > > register /usr/local/mni/models/norm_avg_305_mri.mnc \ > /data/aces/aces1/sylvain/clinical/Bokos/mri/bokos_panorea_18703000_007007_mri.mnc \ > /data/aces/aces1/sylvain/clinical/Bokos/bokos_panorea_mrital.tag > > I then create a .xfm file with > > tagtoxfm -lsq12 bokos_panorea_mrital.{tag,xfm} > > and feed this back to mritotal with > > mritotal -transformation bokos_panorea_mrital.xfm ... > > and if that doesn't do the trick which sometimes occur when I deal with GD enhanced mri volumes, > I keep the transformed (to xfm) tag file. Typically when I know I'm going to feed it back to > mritotal, I select roughly 8 point pairs covering the entire cerebrum and if mritotal still fails, > I add point pairs to bring the total to 12-15 point pairs. > > HTH, > > Sylvain > > > > On Mon, 17 Oct 2005, Marc Schoenwiesner wrote: > > > Hi, > > > > which anatomical locations should one tag when registering by hand with MNI > > register? > > > > Cheers, > > Marc > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > Webster 2B, Room 208 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From U951678 at STUDMED.AU.DK Tue Oct 18 20:29:11 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Wed, 19 Oct 2005 02:29:11 +0200 Subject: [MINC-users] mnc2nii and mnc2ana Message-ID: Hi, I am having trouble using mnc2nii and mnc2ana. I run: mnc2nii se1.mnc se.nii nii2mnc se.nii se1n.mnc and mincinfo gives: file: se1.mnc image: signed__ short 0 to 1462 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 19 7 -47.3 yspace 256 -0.859375 101.87 xspace 256 -0.859375 109.57 file: se1n.mnc image: signed__ float 0 to 1026 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 19 7 -66.5 yspace 256 0.859375 -110 xspace 256 0.859375 -110 I was wondering if someone has an explanation. The version is: mnc2nii -version program: 1.4 libminc: 1.4 netcdf : 3.6.0-p1 of Jun 10 2005 16:14:06 $ When doing the same back and forth procedure with mnc2ana descrepancies in step and start also arises. Spatially, mnc2nii -> nii2mnc throws the scan a bit off position while mnc2ana -> ana2mnc flips the x-axis and also change the start points numerically. If anyone has a good way of using FSL's BET with MINC i'd be interested to hear about it! Best regards Soren From bert at bic.mni.mcgill.ca Tue Oct 18 21:17:52 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Tue, 18 Oct 2005 21:17:52 -0400 Subject: [MINC-users] mnc2nii and mnc2ana In-Reply-To: Message-ID: Hi Soren, I think I understand what is happening with mnc2nii... First off, we generally have to map the MINC information into a form NIfTI and Analyze can handle. This means that we have to set step sizes to a positive value and rearrange the data appropriately. There's no real way around this. You have found a bug, however. There is a field named "spacetype" which is supposed to be set in the MINC header, and this guides the conversion to .NII format. This field is normally set to the value "native____". The problem is that when I wrote the code I do not handle the situation where the field is not set at all, and so we discard the MINC header spatial information. This is why the transform in the header is wrong I'll put a fix for this into the next version. In the meantime, I would recommend that you try setting the field in the header of the file you'd like to convert and see if that helps: minc_modify_header -sinsert zspace:spacetype="native____" sel.mnc Try the conversion again after making this adjustment. Sorry for the complication, -bert On Wed, 19 Oct 2005, S?ren Christensen wrote: > Hi, > I am having trouble using mnc2nii and mnc2ana. > I run: > mnc2nii se1.mnc se.nii > nii2mnc se.nii se1n.mnc > > and mincinfo gives: > > file: se1.mnc > image: signed__ short 0 to 1462 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 19 7 -47.3 > yspace 256 -0.859375 101.87 > xspace 256 -0.859375 109.57 > > > file: se1n.mnc > image: signed__ float 0 to 1026 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 19 7 -66.5 > yspace 256 0.859375 -110 > xspace 256 0.859375 -110 > > > I was wondering if someone has an explanation. The version is: > > mnc2nii -version > program: 1.4 > libminc: 1.4 > netcdf : 3.6.0-p1 of Jun 10 2005 16:14:06 $ > > > > When doing the same back and forth procedure with mnc2ana descrepancies in step and start also arises. Spatially, mnc2nii -> nii2mnc throws the scan a bit off position while mnc2ana -> ana2mnc flips the x-axis and also change the start points numerically. > > > > If anyone has a good way of using FSL's BET with MINC i'd be interested to hear about it! > > > > > > Best regards > Soren > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From U951678 at STUDMED.AU.DK Tue Oct 18 22:01:17 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Wed, 19 Oct 2005 04:01:17 +0200 Subject: [MINC-users] mnc2nii and mnc2ana Message-ID: Hi Bert, Cheers, with this kind of help i will never use a commercial program again.. It works perfectly. Thanks! Soren -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Robert VINCENT Sent: Wed 19-10-2005 11:17 To: MINC users mailing list Subject: Re: [MINC-users] mnc2nii and mnc2ana Hi Soren, I think I understand what is happening with mnc2nii... First off, we generally have to map the MINC information into a form NIfTI and Analyze can handle. This means that we have to set step sizes to a positive value and rearrange the data appropriately. There's no real way around this. You have found a bug, however. There is a field named "spacetype" which is supposed to be set in the MINC header, and this guides the conversion to .NII format. This field is normally set to the value "native____". The problem is that when I wrote the code I do not handle the situation where the field is not set at all, and so we discard the MINC header spatial information. This is why the transform in the header is wrong I'll put a fix for this into the next version. In the meantime, I would recommend that you try setting the field in the header of the file you'd like to convert and see if that helps: minc_modify_header -sinsert zspace:spacetype="native____" sel.mnc Try the conversion again after making this adjustment. Sorry for the complication, -bert On Wed, 19 Oct 2005, S?ren Christensen wrote: > Hi, > I am having trouble using mnc2nii and mnc2ana. > I run: > mnc2nii se1.mnc se.nii > nii2mnc se.nii se1n.mnc > > and mincinfo gives: > > file: se1.mnc > image: signed__ short 0 to 1462 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 19 7 -47.3 > yspace 256 -0.859375 101.87 > xspace 256 -0.859375 109.57 > > > file: se1n.mnc > image: signed__ float 0 to 1026 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 19 7 -66.5 > yspace 256 0.859375 -110 > xspace 256 0.859375 -110 > > > I was wondering if someone has an explanation. The version is: > > mnc2nii -version > program: 1.4 > libminc: 1.4 > netcdf : 3.6.0-p1 of Jun 10 2005 16:14:06 $ > > > > When doing the same back and forth procedure with mnc2ana descrepancies in step and start also arises. Spatially, mnc2nii -> nii2mnc throws the scan a bit off position while mnc2ana -> ana2mnc flips the x-axis and also change the start points numerically. > > > > If anyone has a good way of using FSL's BET with MINC i'd be interested to hear about it! > > > > > > Best regards > Soren > > > > _______________________________________________ > 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 o.winz at fz-juelich.de Thu Oct 20 07:11:38 2005 From: o.winz at fz-juelich.de (Oliver Winz) Date: Thu, 20 Oct 2005 13:11:38 +0200 Subject: [MINC-users] time and time-width dimension in dynamic image Message-ID: <43577B6A.6060808@fz-juelich.de> Hi, i have a problem with the "time" and "time-width" dimensions in a dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get the correct values about both dimensions. When i splitting the dynamic image into single frame images, e.g. for realignment, and afterwards concat the single frames together to a new dynamic, the previous information is lost. How can i easy modifiy (at best command line) the mincheader and change the values for "time" and "time-width". Thanks! Oliver -- Oliver Winz, M.Sc. Molecular Neuroimaging Group Institute of Medicine (IME) Research Centre Juelich D-52425 Juelich Germany Phone: +49 2461 61-6493 Web: http://www.fz-juelich.de/ime/mni Location: Building 15.9, Room 3010 From runa at medphys.ucl.ac.uk Thu Oct 20 18:10:35 2005 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Thu, 20 Oct 2005 23:10:35 +0100 Subject: [MINC-users] Masking brain + CSF Message-ID: <5.2.0.9.0.20051020230207.00b06830@pop3-server> Hi everybody, I have several questions regarding this package: 1. How I would know that image has been transferred correctly to *.minc format? 2. In Display menu, are the image dimension appears as width, height, and slices? 3. would anybody please let me know can I create 'brain masking +CSF' with this package, or I have to do it first to run NU_correction? 4. Also, in nu_correct, would anybody let me know the command line arguments? I don't wish these are stupid questions. Thanks in advance, Yours sincerely, Runa ******************************************************************** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From sylvain at bic.mni.mcgill.ca Fri Oct 21 13:07:00 2005 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Fri, 21 Oct 2005 13:07:00 -0400 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: <43577B6A.6060808@fz-juelich.de> Message-ID: Hello Oliver, I'm not sure this will help but here are some thoughts for a quick hack: The quickest way would be to use mincedit of course or something like the following: ncdump -v 'time,time-width' original.mnc > time.cdl mincheader realigned.mnc > realigned.cdl $MERGE time.cdl realigned.cdl > new.cdl ncgen -o new.mnc new.cdl minccopy realigned.mnc new.mnc $MERGE is the unknown and could hinder the "quick" hack! Sylvain On Thu, 20 Oct 2005, Oliver Winz wrote: > Hi, > > i have a problem with the "time" and "time-width" dimensions in a > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > the correct values about both dimensions. When i splitting the dynamic > image into single frame images, e.g. for realignment, and afterwards > concat the single frames together to a new dynamic, the previous > information is lost. How can i easy modifiy (at best command line) the > mincheader and change the values for "time" and "time-width". > > Thanks! > > Oliver > > -- > Oliver Winz, M.Sc. > Molecular Neuroimaging Group > Institute of Medicine (IME) > Research Centre Juelich > D-52425 Juelich > Germany > > Phone: +49 2461 61-6493 > Web: http://www.fz-juelich.de/ime/mni > Location: Building 15.9, Room 3010 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From jharlap at bic.mni.mcgill.ca Fri Oct 21 17:19:39 2005 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri, 21 Oct 2005 17:19:39 -0400 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: References: <43577B6A.6060808@fz-juelich.de> Message-ID: <20051021211938.GA4956077@bic.mni.mcgill.ca> alternately (without the ambiguity of $MERGE) something on the order of... if X is an attribute in a minc header... minc_modify_header -sinsert "X=`mincinfo -quiet -attvar X original.mnc`" realigned.mnc would be an inefficient but simple way to do it... cheers, j On Fri, Oct 21, 2005 at 01:07:00PM -0400, Sylvain MILOT wrote: > > Hello Oliver, > > I'm not sure this will help but here are some thoughts for a > quick hack: > > The quickest way would be to use mincedit of course or something like > the following: > > ncdump -v 'time,time-width' original.mnc > time.cdl > mincheader realigned.mnc > realigned.cdl > $MERGE time.cdl realigned.cdl > new.cdl > ncgen -o new.mnc new.cdl > minccopy realigned.mnc new.mnc > > $MERGE is the unknown and could hinder the "quick" hack! > > Sylvain > > > On Thu, 20 Oct 2005, Oliver Winz wrote: > > > Hi, > > > > i have a problem with the "time" and "time-width" dimensions in a > > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > > the correct values about both dimensions. When i splitting the dynamic > > image into single frame images, e.g. for realignment, and afterwards > > concat the single frames together to a new dynamic, the previous > > information is lost. How can i easy modifiy (at best command line) the > > mincheader and change the values for "time" and "time-width". > > > > Thanks! > > > > Oliver > > > > -- > > Oliver Winz, M.Sc. > > Molecular Neuroimaging Group > > Institute of Medicine (IME) > > Research Centre Juelich > > D-52425 Juelich > > Germany > > > > Phone: +49 2461 61-6493 > > Web: http://www.fz-juelich.de/ime/mni > > Location: Building 15.9, Room 3010 > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > Webster 2B, Room 208 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From sylvain at bic.mni.mcgill.ca Fri Oct 21 17:42:29 2005 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Fri, 21 Oct 2005 17:42:29 -0400 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: <20051021211938.GA4956077@bic.mni.mcgill.ca> Message-ID: Yes this is fine for attributes but how do you do this for variables ? time and time-width are extracted with : mincinfo -varvalue time dynamic.mnc mincinfo -varvalue time-width dynamic.mnc How do you do this with minc_modify_header ? Sylvain On Fri, 21 Oct 2005, Jonathan HARLAP wrote: > alternately (without the ambiguity of $MERGE) something on the order of... > > if X is an attribute in a minc header... > minc_modify_header -sinsert "X=`mincinfo -quiet -attvar X original.mnc`" realigned.mnc > > would be an inefficient but simple way to do it... > > cheers, > j > > On Fri, Oct 21, 2005 at 01:07:00PM -0400, Sylvain MILOT wrote: > > > > Hello Oliver, > > > > I'm not sure this will help but here are some thoughts for a > > quick hack: > > > > The quickest way would be to use mincedit of course or something like > > the following: > > > > ncdump -v 'time,time-width' original.mnc > time.cdl > > mincheader realigned.mnc > realigned.cdl > > $MERGE time.cdl realigned.cdl > new.cdl > > ncgen -o new.mnc new.cdl > > minccopy realigned.mnc new.mnc > > > > $MERGE is the unknown and could hinder the "quick" hack! > > > > Sylvain > > > > > > On Thu, 20 Oct 2005, Oliver Winz wrote: > > > > > Hi, > > > > > > i have a problem with the "time" and "time-width" dimensions in a > > > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > > > the correct values about both dimensions. When i splitting the dynamic > > > image into single frame images, e.g. for realignment, and afterwards > > > concat the single frames together to a new dynamic, the previous > > > information is lost. How can i easy modifiy (at best command line) the > > > mincheader and change the values for "time" and "time-width". > > > > > > Thanks! > > > > > > Oliver > > > > > > -- > > > Oliver Winz, M.Sc. > > > Molecular Neuroimaging Group > > > Institute of Medicine (IME) > > > Research Centre Juelich > > > D-52425 Juelich > > > Germany > > > > > > Phone: +49 2461 61-6493 > > > Web: http://www.fz-juelich.de/ime/mni > > > Location: Building 15.9, Room 3010 > > > > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > --- > > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > (trinity at bic.mni.mcgill.ca) > > Brain Imaging Centre > > Montreal Neurological Institute > > Webster 2B, Room 208 > > Montreal, Qc., Canada, H3A 2B4 > > Phone : (514) 398-4965, Fax: 398-8948 > > Mobile : (514) 712-1768 > > Office : 527 Av Des Pins O., Room 204 > > Montreal, Qc., H2W 1S4 > > > > > > > > _______________________________________________ > > 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 > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From sylvain at bic.mni.mcgill.ca Fri Oct 21 17:56:51 2005 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Fri, 21 Oct 2005 17:56:51 -0400 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: Message-ID: Hmmm, I think there might be a way to do this with mincconcat but I've never tried it, see mincconcat -help ... -coordlist: Specify the dimension coordinates (",,..."). -widthlist: Specify the dimension widths (",,..."). ... Sylvain On Fri, 21 Oct 2005, Sylvain MILOT wrote: > > Yes this is fine for attributes but how do you do this for variables ? > > time and time-width are extracted with : > > mincinfo -varvalue time dynamic.mnc > mincinfo -varvalue time-width dynamic.mnc > > How do you do this with minc_modify_header ? > > Sylvain > > > On Fri, 21 Oct 2005, Jonathan HARLAP wrote: > > > alternately (without the ambiguity of $MERGE) something on the order of... > > > > if X is an attribute in a minc header... > > minc_modify_header -sinsert "X=`mincinfo -quiet -attvar X original.mnc`" realigned.mnc > > > > would be an inefficient but simple way to do it... > > > > cheers, > > j > > > > On Fri, Oct 21, 2005 at 01:07:00PM -0400, Sylvain MILOT wrote: > > > > > > Hello Oliver, > > > > > > I'm not sure this will help but here are some thoughts for a > > > quick hack: > > > > > > The quickest way would be to use mincedit of course or something like > > > the following: > > > > > > ncdump -v 'time,time-width' original.mnc > time.cdl > > > mincheader realigned.mnc > realigned.cdl > > > $MERGE time.cdl realigned.cdl > new.cdl > > > ncgen -o new.mnc new.cdl > > > minccopy realigned.mnc new.mnc > > > > > > $MERGE is the unknown and could hinder the "quick" hack! > > > > > > Sylvain > > > > > > > > > On Thu, 20 Oct 2005, Oliver Winz wrote: > > > > > > > Hi, > > > > > > > > i have a problem with the "time" and "time-width" dimensions in a > > > > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > > > > the correct values about both dimensions. When i splitting the dynamic > > > > image into single frame images, e.g. for realignment, and afterwards > > > > concat the single frames together to a new dynamic, the previous > > > > information is lost. How can i easy modifiy (at best command line) the > > > > mincheader and change the values for "time" and "time-width". > > > > > > > > Thanks! > > > > > > > > Oliver > > > > > > > > -- > > > > Oliver Winz, M.Sc. > > > > Molecular Neuroimaging Group > > > > Institute of Medicine (IME) > > > > Research Centre Juelich > > > > D-52425 Juelich > > > > Germany > > > > > > > > Phone: +49 2461 61-6493 > > > > Web: http://www.fz-juelich.de/ime/mni > > > > Location: Building 15.9, Room 3010 > > > > > > > > _______________________________________________ > > > > MINC-users at bic.mni.mcgill.ca > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > --- > > > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > (trinity at bic.mni.mcgill.ca) > > > Brain Imaging Centre > > > Montreal Neurological Institute > > > Webster 2B, Room 208 > > > Montreal, Qc., Canada, H3A 2B4 > > > Phone : (514) 398-4965, Fax: 398-8948 > > > Mobile : (514) 712-1768 > > > Office : 527 Av Des Pins O., Room 204 > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > Webster 2B, Room 208 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From bert at bic.mni.mcgill.ca Fri Oct 21 19:46:19 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 21 Oct 2005 19:46:19 -0400 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: Message-ID: Hi, mincconcat is the easiest way to add irregular dimension information back into a set of 3D files. It is also possible to keep the time and time-width information by simply reducing the time dimension to length one: mincreshape -dimrange time=0,1 infile.mnc outfile.mnc When you concatenate these files, they should automatically recover the irregular spacing information, since each file will retain its original time start and width. -bert On Fri, 21 Oct 2005, Sylvain MILOT wrote: > > Hmmm, I think there might be a way to do this with mincconcat > > but I've never tried it, see mincconcat -help > > ... > > -coordlist: Specify the dimension coordinates (",,..."). > -widthlist: Specify the dimension widths (",,..."). > > ... > > Sylvain > > On Fri, 21 Oct 2005, Sylvain MILOT wrote: > > > > > Yes this is fine for attributes but how do you do this for variables ? > > > > time and time-width are extracted with : > > > > mincinfo -varvalue time dynamic.mnc > > mincinfo -varvalue time-width dynamic.mnc > > > > How do you do this with minc_modify_header ? > > > > Sylvain > > > > > > On Fri, 21 Oct 2005, Jonathan HARLAP wrote: > > > > > alternately (without the ambiguity of $MERGE) something on the order of... > > > > > > if X is an attribute in a minc header... > > > minc_modify_header -sinsert "X=`mincinfo -quiet -attvar X original.mnc`" realigned.mnc > > > > > > would be an inefficient but simple way to do it... > > > > > > cheers, > > > j > > > > > > On Fri, Oct 21, 2005 at 01:07:00PM -0400, Sylvain MILOT wrote: > > > > > > > > Hello Oliver, > > > > > > > > I'm not sure this will help but here are some thoughts for a > > > > quick hack: > > > > > > > > The quickest way would be to use mincedit of course or something like > > > > the following: > > > > > > > > ncdump -v 'time,time-width' original.mnc > time.cdl > > > > mincheader realigned.mnc > realigned.cdl > > > > $MERGE time.cdl realigned.cdl > new.cdl > > > > ncgen -o new.mnc new.cdl > > > > minccopy realigned.mnc new.mnc > > > > > > > > $MERGE is the unknown and could hinder the "quick" hack! > > > > > > > > Sylvain > > > > > > > > > > > > On Thu, 20 Oct 2005, Oliver Winz wrote: > > > > > > > > > Hi, > > > > > > > > > > i have a problem with the "time" and "time-width" dimensions in a > > > > > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > > > > > the correct values about both dimensions. When i splitting the dynamic > > > > > image into single frame images, e.g. for realignment, and afterwards > > > > > concat the single frames together to a new dynamic, the previous > > > > > information is lost. How can i easy modifiy (at best command line) the > > > > > mincheader and change the values for "time" and "time-width". > > > > > > > > > > Thanks! > > > > > > > > > > Oliver > > > > > > > > > > -- > > > > > Oliver Winz, M.Sc. > > > > > Molecular Neuroimaging Group > > > > > Institute of Medicine (IME) > > > > > Research Centre Juelich > > > > > D-52425 Juelich > > > > > Germany > > > > > > > > > > Phone: +49 2461 61-6493 > > > > > Web: http://www.fz-juelich.de/ime/mni > > > > > Location: Building 15.9, Room 3010 > > > > > > > > > > _______________________________________________ > > > > > MINC-users at bic.mni.mcgill.ca > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > > > > --- > > > > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > > (trinity at bic.mni.mcgill.ca) > > > > Brain Imaging Centre > > > > Montreal Neurological Institute > > > > Webster 2B, Room 208 > > > > Montreal, Qc., Canada, H3A 2B4 > > > > Phone : (514) 398-4965, Fax: 398-8948 > > > > Mobile : (514) 712-1768 > > > > Office : 527 Av Des Pins O., Room 204 > > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > --- > > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > (trinity at bic.mni.mcgill.ca) > > Brain Imaging Centre > > Montreal Neurological Institute > > Webster 2B, Room 208 > > Montreal, Qc., Canada, H3A 2B4 > > Phone : (514) 398-4965, Fax: 398-8948 > > Mobile : (514) 712-1768 > > Office : 527 Av Des Pins O., Room 204 > > Montreal, Qc., H2W 1S4 > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > Webster 2B, Room 208 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From dcb210 at psu.edu Sat Oct 22 11:41:11 2005 From: dcb210 at psu.edu (Don Bigler) Date: Sat, 22 Oct 2005 11:41:11 -0400 Subject: [MINC-users] avg icbm templates appear to be corrupt Message-ID: <435A5D97.4090104@psu.edu> I just tried to download and display the icbm_template_*.**mm.mnc templates located in ftp://ftp.bic.mni.mcgill.ca/pub/avgbrain using Display, but they all appear to be empty images. The file sizes for each one are all 4kb, which indicates to me that the files are corrupted. They should all be much larger than 4kb. Any help would be greatly appreciated. Thanks, Don Bigler -- Don Bigler The Pennsylvania State University NMR Building H066 Radiology Hershey Medical Center Hershey, PA 17033 Phone: (717)531-5858 Fax: (717)531-8486 Hershey Confidentiality Statement: This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. From bert at bic.mni.mcgill.ca Sat Oct 22 11:47:49 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Sat, 22 Oct 2005 11:47:49 -0400 Subject: [MINC-users] avg icbm templates appear to be corrupt In-Reply-To: <435A5D97.4090104@psu.edu> Message-ID: Hi Don, These files are not corrupt. They are template files that contain only a header specifying the coordinate and sample-spacing information used when resampling images into the standard ICBM coordinates. You are looking for the actual average brain images, which are available here: http://packages.bic.mni.mcgill.ca/tgz/ Look for the three "mni-models" packages in this directory. Hope this helps, -bert On Sat, 22 Oct 2005, Don Bigler wrote: > I just tried to download and display the icbm_template_*.**mm.mnc > templates located in > ftp://ftp.bic.mni.mcgill.ca/pub/avgbrain using Display, but they all > appear to be empty images. The file sizes for each one are all 4kb, > which indicates to me that the files are corrupted. They should all be > much larger than 4kb. Any help would be greatly appreciated. > Thanks, > Don Bigler > > -- > Don Bigler > The Pennsylvania State University > NMR Building > H066 Radiology > Hershey Medical Center > Hershey, PA 17033 > Phone: (717)531-5858 > Fax: (717)531-8486 > > Hershey Confidentiality Statement: > > This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From rodell at pet.auh.dk Mon Oct 24 05:06:40 2005 From: rodell at pet.auh.dk (Anders Bertil Rodell) Date: Mon, 24 Oct 2005 11:06:40 +0200 Subject: [MINC-users] time and time-width dimension in dynamic image In-Reply-To: References: Message-ID: <1130144800.26500.30.camel@vega> Hello Oliver something along the lines of this works for me mincconcat -concat_dimension time -coordlist " 0 10 25" -widthlist "10 15 20" frame1.mnc frame2.mnc frame3.mnc out4d.mnc best regards Anders > On Thu, 20 Oct 2005, Oliver Winz wrote: > > > Hi, > > > > i have a problem with the "time" and "time-width" dimensions in a > > dynamic PET image. After converting ECAT PET to MINC (ecattominc) i get > > the correct values about both dimensions. When i splitting the dynamic > > image into single frame images, e.g. for realignment, and afterwards > > concat the single frames together to a new dynamic, the previous > > information is lost. How can i easy modifiy (at best command line) the > > mincheader and change the values for "time" and "time-width". > > > > Thanks! > > > > Oliver > > > > -- > > Oliver Winz, M.Sc. > > Molecular Neuroimaging Group > > Institute of Medicine (IME) > > Research Centre Juelich > > D-52425 Juelich > > Germany > > > > Phone: +49 2461 61-6493 > > Web: http://www.fz-juelich.de/ime/mni > > Location: Building 15.9, Room 3010 > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > -- -- Anders Bertil Rodell M.Sc. C.S. PhD. Aarhus PET Centre, Aarhus University Hospital, Norrebrogade 44, 8000 Aarhus C, phone work: +45 89 49 40 97 mobile phone: +45 61 70 85 30 email: rodell at pet.auh.dk From rodell at pet.auh.dk Mon Oct 24 05:17:27 2005 From: rodell at pet.auh.dk (Anders Bertil Rodell) Date: Mon, 24 Oct 2005 11:17:27 +0200 Subject: [MINC-users] using bet with minc In-Reply-To: References: Message-ID: <1130145447.26500.42.camel@vega> Hi Soren Christensen I have succesfully used bet with MINC by switching to the right BET version based on type and sign mincinfo -attvalue image:signtype file.mnc mincinfo -vartype image file.mnc running f.ex: bet_16SI infile.mnc outfile_basename -n -m [-f 0.4] to produce a mask mincresample to mach original file mask the brain out. Take a look at /users/rodell/Scripts/do_skullstrip (back home in Aarhus) all the best Anders -- -- Anders Bertil Rodell M.Sc. C.S. PhD. Aarhus PET Centre, Aarhus University Hospital, Norrebrogade 44, 8000 Aarhus C, phone work: +45 89 49 40 97 mobile phone: +45 61 70 85 30 email: rodell at pet.auh.dk From dwagne at bic.mni.mcgill.ca Mon Oct 24 20:47:36 2005 From: dwagne at bic.mni.mcgill.ca (Dylan David Wagner) Date: Mon, 24 Oct 2005 20:47:36 -0400 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <1130145447.26500.42.camel@vega> References: <1130145447.26500.42.camel@vega> Message-ID: <435D80A8.90601@bic.mni.mcgill.ca> Hey Minc Users, To the few people out there who use it, I added a bunch of new packages and scripts to the el cheapo cygwin build I have at: http://www.bic.mni.mcgill.ca/~dwagne/dwagne.html Namely: N3, cortical surface, classify and glim image, plus the smooth_mask perl script. In other words, everything you need to do the VBM tutorial on the wiki. So far it seems to work good and you can call it from matlab (pc). You can probably install the packages yourself, but some of them required fixing before they work (I'm looking at you classify!) or simply aren't available on packages.bic (ie:cortical_surface). You'll probably want the colin 27, icbm 152 and average 305 models at packages.bic.mni.mcgill.ca, it wasn't worth including them. They're easy to install, just follow the instructions in the readme.txt Also, don't forget, to run display in cgywin you still need to startx. Best, DDW __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From a.janke at gmail.com Mon Oct 24 22:20:38 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 24 Oct 2005 22:20:38 -0400 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <435D80A8.90601@bic.mni.mcgill.ca> References: <1130145447.26500.42.camel@vega> <435D80A8.90601@bic.mni.mcgill.ca> Message-ID: Thanks Dylan If you have any changes that you'd like included in CVS for any of the packages, forward them on and I'll see what I can do. a On 24/10/05, Dylan David Wagner wrote: > > > Hey Minc Users, > > To the few people out there who use it, I added a bunch of new > packages and scripts to the el cheapo cygwin build I have at: > http://www.bic.mni.mcgill.ca/~dwagne/dwagne.html > > Namely: N3, cortical surface, classify and glim image, plus the > smooth_mask perl script. In other words, everything you need to do the > VBM tutorial on the wiki. So far it seems to work good and you can call > it from matlab (pc). You can probably install the packages yourself, but > some of them required fixing before they work (I'm looking at you > classify!) or simply aren't available on packages.bic (ie:cortical_surface). > > You'll probably want the colin 27, icbm 152 and average 305 models > at packages.bic.mni.mcgill.ca, it wasn't worth including them. They're > easy to install, just follow the instructions in the readme.txt > > Also, don't forget, to run display in cgywin you still need to > startx. > > Best, > DDW > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From schwarz at cba.muni.cz Tue Oct 25 04:50:13 2005 From: schwarz at cba.muni.cz (Daniel Schwarz) Date: Tue, 25 Oct 2005 10:50:13 +0200 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <435D80A8.90601@bic.mni.mcgill.ca> Message-ID: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> Hi, I have a problem with mnc2ana on cygwin - the link mnc2ana.lnk does not work there. Any ideas how to make it work? Thanks. Daniel Schwarz -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Dylan David Wagner Sent: Tuesday, October 25, 2005 2:48 AM To: MINC users mailing list Subject: [MINC-users] Minc tools and scripts for cygwin Hey Minc Users, To the few people out there who use it, I added a bunch of new packages and scripts to the el cheapo cygwin build I have at: http://www.bic.mni.mcgill.ca/~dwagne/dwagne.html Namely: N3, cortical surface, classify and glim image, plus the smooth_mask perl script. In other words, everything you need to do the VBM tutorial on the wiki. So far it seems to work good and you can call it from matlab (pc). You can probably install the packages yourself, but some of them required fixing before they work (I'm looking at you classify!) or simply aren't available on packages.bic (ie:cortical_surface). You'll probably want the colin 27, icbm 152 and average 305 models at packages.bic.mni.mcgill.ca, it wasn't worth including them. They're easy to install, just follow the instructions in the readme.txt Also, don't forget, to run display in cgywin you still need to startx. Best, DDW __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From se at hst.aau.dk Tue Oct 25 06:29:37 2005 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Tue, 25 Oct 2005 12:29:37 +0200 Subject: [MINC-users] Setting the intensity range in header Message-ID: <435E0911.8090407@hst.aau.dk> Hi, I have a minor problem with the intensity range in some minc volumes. Fx in a volume the intensities range from 1 to 223, however in the header the range is given as: image:valid_range = 255., 404125398. ; image-max = 404125398, ...repeated #slices times... ; image-min = 255, ...repeated #slices times... ; This means that I cannot view the volumes in Display or register. Adjusting the "valid_range", "image-max" and "image-min" variables with mincedit solves the problem. However, this is tedious work (the range is different for each volume). Is there a way to automagically set the correct intensity range in the header? Simon -- Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) From dwagne at bic.mni.mcgill.ca Tue Oct 25 09:12:42 2005 From: dwagne at bic.mni.mcgill.ca (Dylan David Wagner) Date: Tue, 25 Oct 2005 09:12:42 -0400 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> References: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> Message-ID: <435E2F4A.9020609@bic.mni.mcgill.ca> Hi Daniel, Yeah, I just noticed that, I never use ana2mnc so I never actually ran make_links or tested to see if it works. Here's the fix: remove all the .lnk files that make_links made (ie: mnc2ana.lnk ana_show.lnk spm2mnc.lnk spm2xfm.lnk spm_show.lnk). And then make them manually one at a time (ie: ln -s /usr/local/mni/bin/ana2mnc mnc2ana). I just did this and it works. I have no idea why the make_links script makes what seems to be windows style links (ie: .lnk) rather than true unix ones. Especially since the make_links script contains the same line of code I just told you to run. Must be a cygwin issue with running sh scripts. Anyhow, I'll include them for the next update. Daniel Schwarz wrote: > Hi, > > I have a problem with mnc2ana on cygwin - the link mnc2ana.lnk does not work > there. Any ideas how to make it work? > Thanks. > > Daniel Schwarz > > -----Original Message----- > From: minc-users-bounces at bic.mni.mcgill.ca > [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Dylan David > Wagner > Sent: Tuesday, October 25, 2005 2:48 AM > To: MINC users mailing list > Subject: [MINC-users] Minc tools and scripts for cygwin > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From dwagne at bic.mni.mcgill.ca Tue Oct 25 09:37:47 2005 From: dwagne at bic.mni.mcgill.ca (Dylan David Wagner) Date: Tue, 25 Oct 2005 09:37:47 -0400 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> References: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> Message-ID: <435E352B.1020409@bic.mni.mcgill.ca> Hey, sorry bout the mincusers barrage this morning. It's been brought to my attention that I uhh... Accidentally uploaded the update from March 2005 to the minc for cygwin build rather than the most recent one. I've uploaded a zip of only the folder you need to copy into cygwin to get it to work. The actual cygwin install package will have to wait until I get home as I don't have it on my laptop. If you already have cygwin installed, or a previous build of the one I put together, then all you need is this new folder anyway. If anyone is looking to do a fresh install, I'll put up the proper cygwin packages this evening. Sorry bout the mess. Goto http://www.bic.mni.mcgill/~dwagne/dwagne.htm and follow the new instructions. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From a.janke at gmail.com Tue Oct 25 09:44:03 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 25 Oct 2005 09:44:03 -0400 Subject: [MINC-users] Minc tools and scripts for cygwin In-Reply-To: <435E2F4A.9020609@bic.mni.mcgill.ca> References: <200510250850.j9P8ob1k005041@tirith.ics.muni.cz> <435E2F4A.9020609@bic.mni.mcgill.ca> Message-ID: Hi Dylan and Daniel, In this case you'd be much better to remove mnc2ana and ana2mnc in favour of nii2mnc and mnc2nii. The latter are the NifTi-1 converters that are now included as part of the base minc distro as of about MINC 1.4. Essentially, ana2mnc is deprecated and I don't plan on doing any more work on ana2mnc in the future. a On 25/10/05, Dylan David Wagner wrote: > Hi Daniel, > > Yeah, I just noticed that, I never use ana2mnc so I never actually > ran make_links or tested to see if it works. Here's the fix: remove all > the .lnk files that make_links made (ie: mnc2ana.lnk ana_show.lnk > spm2mnc.lnk spm2xfm.lnk spm_show.lnk). And then make them manually one > at a time (ie: ln -s /usr/local/mni/bin/ana2mnc mnc2ana). I just did > this and it works. > > I have no idea why the make_links script makes what seems to be windows > style links (ie: .lnk) rather than true unix ones. Especially since the > make_links script contains the same line of code I just told you to run. > Must be a cygwin issue with running sh scripts. > > Anyhow, I'll include them for the next update. > > > > > Daniel Schwarz wrote: > > Hi, > > > > I have a problem with mnc2ana on cygwin - the link mnc2ana.lnk does not work > > there. Any ideas how to make it work? > > Thanks. > > > > Daniel Schwarz > > > > -----Original Message----- > > From: minc-users-bounces at bic.mni.mcgill.ca > > [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Dylan David > > Wagner > > Sent: Tuesday, October 25, 2005 2:48 AM > > To: MINC users mailing list > > Subject: [MINC-users] Minc tools and scripts for cygwin > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From runa at medphys.ucl.ac.uk Tue Oct 25 09:51:22 2005 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Tue, 25 Oct 2005 14:51:22 +0100 Subject: [MINC-users] NU_CORRECT In-Reply-To: References: <435D80A8.90601@bic.mni.mcgill.ca> <1130145447.26500.42.camel@vega> <435D80A8.90601@bic.mni.mcgill.ca> Message-ID: <5.2.0.9.0.20051025144953.037e5408@pop3-server> hi, I have several questions regarding this package: 1. How I would know that image has been transferred correctly to *.minc format? 2. In Display menu, are the image dimension appears as width, height, and slices? 3. would anybody please let me know can I create 'brain masking +CSF' with this package, or I have to do it first to run NU_correction? 4. Also, in nu_correct, would you please let me know the command line arguments? Thanks in advance, Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0250 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From jason at bic.mni.mcgill.ca Tue Oct 25 09:55:11 2005 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 25 Oct 2005 09:55:11 -0400 Subject: [MINC-users] NU_CORRECT In-Reply-To: <5.2.0.9.0.20051025144953.037e5408@pop3-server> References: <435D80A8.90601@bic.mni.mcgill.ca> <1130145447.26500.42.camel@vega> <435D80A8.90601@bic.mni.mcgill.ca> <5.2.0.9.0.20051025144953.037e5408@pop3-server> Message-ID: <435E393F.4050703@bic.mni.mcgill.ca> Runa Parveen wrote: > hi, > > I have several questions regarding this package: > 1. How I would know that image has been transferred correctly to *.minc format? > The easiest way is to open it in one of the tools that can view MINC files, such as register or Display. > 2. In Display menu, are the image dimension appears as width, height, and > slices? > Image dimensions tend to be xspace, yspace, and zspace. > 3. would anybody please let me know can I create 'brain masking +CSF' with > this package, or I have to do it first to run NU_correction? > I'm not quite sure what you mean, but this page might have the answers: http://wiki.bic.mni.mcgill.ca/index.php/VoxelBasedMorphometry > 4. Also, in nu_correct, would you please let me know the command line > arguments? > See the same page above. Cheers, Jason > Thanks in advance, > > > Yours sincerely, > > Runa > > ******************************************************************** > > * Runa Parveen ** > * PhD Student ** > * Medical Imaging Group ** > * Dept. of Medical Physics & Bioengineering ** > * University College London ** > * 2nd Floor, New Malet Place Engineering Building ** > * Gower Street, off Torrington Place ** > * London WC1E 6JA ** > * > UK > ** > * Tel. +44 (0) 20 7679 0250 (Dept.) > +44 (0) 7984 084 959 (mob.) ** > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > * e-mail: runa at medphys.ucl.ac.uk ** > ********************************************************************* > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Tue Oct 25 11:33:57 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 25 Oct 2005 11:33:57 -0400 Subject: [MINC-users] scripting mniweb In-Reply-To: <1129047078.3220.7.camel@dhania.fmrib.ox.ac.uk> References: <1129047078.3220.7.camel@dhania.fmrib.ox.ac.uk> Message-ID: I don't think anyone has answered this yet... So here goes: there is an email address on the brainweb page that will allow you to "order" a custom simulation. If you send me/that email exactly what you'd like I should be able to organise it. Andrew On 11/10/05, Morgan Hough wrote: > I was wondering if anyone knows a way to script mniweb output. How can I > request datasets with varying parameters? Thanks in advance. > > Cheers, > > -Morgan > > -- > Morgan G. Hough, DPhil Candidate > University of Oxford, Centre for Functional MRI of the Brain (FMRIB) > John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom > Tel: +44 (0) 1865 222545 / Fax: +44 (0) 1865 222717 > e-mail: mhough at fmrib.ox.ac.uk / URL: http://www.fmrib.ox.ac.uk/~mhough > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Wed Oct 26 09:05:45 2005 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 26 Oct 2005 09:05:45 -0400 Subject: [MINC-users] Setting the intensity range in header In-Reply-To: <435E0911.8090407@hst.aau.dk> References: <435E0911.8090407@hst.aau.dk> Message-ID: Hi Simon, One of the best ways I have found to fix "strange" range problems with a MINC file is to pass it through something like mincmath. This in effect makes a new volume in which the range has been scanned and set. ie: mincmath -mult -const 1 in.mnc out.mnc Either that or if you have range problems from outliers use the script mincnorm that I have posted in the past. Sent me an email if you'd like it. a On 25/10/05, Simon Fristed Eskildsen wrote: > Hi, > > I have a minor problem with the intensity range in some minc volumes. Fx > in a volume the intensities range from 1 to 223, however in the header > the range is given as: > image:valid_range = 255., 404125398. ; > image-max = 404125398, ...repeated #slices times... ; > image-min = 255, ...repeated #slices times... ; > This means that I cannot view the volumes in Display or register. > Adjusting the "valid_range", "image-max" and "image-min" variables with > mincedit solves the problem. However, this is tedious work (the range > is different for each volume). Is there a way to automagically set the > correct intensity range in the header? > > Simon > > -- > Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student > Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From alex at bic.mni.mcgill.ca Wed Oct 26 12:18:58 2005 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Wed, 26 Oct 2005 12:18:58 -0400 Subject: [MINC-users] dicom/minc/analyze conversions Message-ID: <20051026161858.GA3310@bic.mni.mcgill.ca> Hi all, I have a bit of a conundrum: I received a set of MRI data in DICOM format, with accompanying hand-drawn labels in ANALYZE format. When I convert both to MINC, of course the labels don't match the source images, as the world coordinate space has gotten probably lost somewhere along the way at the site that provided me with the data. I have requested that they send me the MRI data also in ANALYZE format, and I am crossing my fingers that when I convert both sets of data to MINC, things will line up. Although I suspect that will work in practice, I was wondering if anybody has other suggestions on how to deal with this? Thanks, -- A From a.janke at gmail.com Wed Oct 26 12:43:39 2005 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 26 Oct 2005 12:43:39 -0400 Subject: [MINC-users] dicom/minc/analyze conversions In-Reply-To: <20051026161858.GA3310@bic.mni.mcgill.ca> References: <20051026161858.GA3310@bic.mni.mcgill.ca> Message-ID: here is how I would attack it... 1: remove direction cosines from MINC anatomical files (ANALYZE doesn't store them) --or-- add direction cosines from anatomical files to labels 2: reorder MINC files to have standard dimension ordering 3: Be sure to use nii2mnc over ana2mnc a On 26/10/05, Alex ZIJDENBOS wrote: > Hi all, > > I have a bit of a conundrum: I received a set of MRI data in DICOM > format, with accompanying hand-drawn labels in ANALYZE format. When I > convert both to MINC, of course the labels don't match the source > images, as the world coordinate space has gotten probably lost > somewhere along the way at the site that provided me with the data. > > I have requested that they send me the MRI data also in ANALYZE > format, and I am crossing my fingers that when I convert both sets of > data to MINC, things will line up. Although I suspect that will work > in practice, I was wondering if anybody has other suggestions on how > to deal with this? > > Thanks, > > -- A > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From alex at bic.mni.mcgill.ca Wed Oct 26 13:53:00 2005 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Wed, 26 Oct 2005 13:53:00 -0400 Subject: [MINC-users] dicom/minc/analyze conversions In-Reply-To: References: <20051026161858.GA3310@bic.mni.mcgill.ca> Message-ID: <20051026175259.GA3503@bic.mni.mcgill.ca> Tanks - for removing/adding dir cosines, are you suggesting the brute force approach, i.e., (minc)editing the header? -- A On Wed, Oct 26, 2005 at 12:43:39PM -0400, Andrew Janke wrote: > here is how I would attack it... > > 1: remove direction cosines from MINC anatomical files > (ANALYZE doesn't store them) > --or-- > add direction cosines from anatomical files to labels > > 2: reorder MINC files to have standard dimension ordering > > 3: Be sure to use nii2mnc over ana2mnc > > > a > > On 26/10/05, Alex ZIJDENBOS wrote: > > Hi all, > > > > I have a bit of a conundrum: I received a set of MRI data in DICOM > > format, with accompanying hand-drawn labels in ANALYZE format. When I > > convert both to MINC, of course the labels don't match the source > > images, as the world coordinate space has gotten probably lost > > somewhere along the way at the site that provided me with the data. > > > > I have requested that they send me the MRI data also in ANALYZE > > format, and I am crossing my fingers that when I convert both sets of > > data to MINC, things will line up. Although I suspect that will work > > in practice, I was wondering if anybody has other suggestions on how > > to deal with this? > > > > Thanks, > > > > -- A > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Wed Oct 26 16:03:10 2005 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 26 Oct 2005 16:03:10 -0400 Subject: [MINC-users] dicom/minc/analyze conversions In-Reply-To: <20051026175259.GA3503@bic.mni.mcgill.ca> References: <20051026161858.GA3310@bic.mni.mcgill.ca> <20051026175259.GA3503@bic.mni.mcgill.ca> Message-ID: minc_modify_header will do the job. minc_modify_header -dinsert xspace:direction_cosines=1,0,0 foo.mnc minc_modify_header -dinsert yspace:direction_cosines=0,1,0 foo.mnc minc_modify_header -dinsert zspace:direction_cosines=0,0,1 foo.mnc a On 26/10/05, Alex ZIJDENBOS wrote: > Tanks - for removing/adding dir cosines, are you suggesting the brute > force approach, i.e., (minc)editing the header? > > -- A > > On Wed, Oct 26, 2005 at 12:43:39PM -0400, Andrew Janke wrote: > > here is how I would attack it... > > > > 1: remove direction cosines from MINC anatomical files > > (ANALYZE doesn't store them) > > --or-- > > add direction cosines from anatomical files to labels > > > > 2: reorder MINC files to have standard dimension ordering > > > > 3: Be sure to use nii2mnc over ana2mnc > > > > > > a > > > > On 26/10/05, Alex ZIJDENBOS wrote: > > > Hi all, > > > > > > I have a bit of a conundrum: I received a set of MRI data in DICOM > > > format, with accompanying hand-drawn labels in ANALYZE format. When I > > > convert both to MINC, of course the labels don't match the source > > > images, as the world coordinate space has gotten probably lost > > > somewhere along the way at the site that provided me with the data. > > > > > > I have requested that they send me the MRI data also in ANALYZE > > > format, and I am crossing my fingers that when I convert both sets of > > > data to MINC, things will line up. Although I suspect that will work > > > in practice, I was wondering if anybody has other suggestions on how > > > to deal with this? > > > > > > Thanks, > > > > > > -- A > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > > Canada->Montreal Cell: +1 (514) 924 2012 > > > > _______________________________________________ > > 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 > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From jammam2 at yahoo.com Thu Oct 27 03:17:19 2005 From: jammam2 at yahoo.com (Jamila Ahdidan) Date: Thu, 27 Oct 2005 00:17:19 -0700 (PDT) Subject: [MINC-users] mincmath and vector field (deformation maps) In-Reply-To: Message-ID: <20051027071720.56673.qmail@web60812.mail.yahoo.com> Dear all, I'm currently working on deformation maps, and I would like to know how I can perform some operations on them (like divide, multiply, add, substract). When I use the usual mincmath, then it doesn't see that it's a vector field and it only returns one value per voxel. Do you know how I can get around this, I need it in order to normalise the deformation with the time elapsed between 2 scans. Many regards, Jamila --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. From U951678 at STUDMED.AU.DK Thu Oct 27 22:10:01 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Fri, 28 Oct 2005 04:10:01 +0200 Subject: [MINC-users] Display colormapping Message-ID: Hi, Is there a good reason why Display does not re-quantify the display colormap when the min-max levels are changed? There are of course ways around it (clamping or changing the header), but it seems like a missing feature? Best regards Soren From ftni02 at ist.auc.dk Sat Oct 29 15:21:54 2005 From: ftni02 at ist.auc.dk (Flemming Nielsen) Date: Sat, 29 Oct 2005 21:21:54 +0200 Subject: [MINC-users] MatLab - EMMA Message-ID: <4363CBD2.7020507@ist.auc.dk> Hi I have a little problem, when I want to view a hole MINV-volume in MatLab. I use getimages to read the intire volume, but I can not come up wite a good solution how to visualize the entire volume. Some ideas Mvh Flemming Nielsen Student Aalborg Universitet. From U951678 at STUDMED.AU.DK Sat Oct 29 18:35:29 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Sun, 30 Oct 2005 00:35:29 +0200 Subject: [MINC-users] MatLab - EMMA Message-ID: Hi Flemming, What do you mean by viewing a volume - viewing it in a montage? Usually you can just use getimages to fetch the data and then use reshape to reconstruct the image into the original dimensions. See http://www.bic.mni.mcgill.ca/software/emma/demos/emma1.html. If you paste in your code it'd be easier to see where the problem is. Best regards Soren ________________________________ Fra: minc-users-bounces at bic.mni.mcgill.ca p? vegne af Flemming Nielsen Sendt: s? 30-10-2005 06:21 Til: 'MINC users mailing list' Emne: [MINC-users] MatLab - EMMA Hi I have a little problem, when I want to view a hole MINV-volume in MatLab. I use getimages to read the intire volume, but I can not come up wite a good solution how to visualize the entire volume. Some ideas Mvh Flemming Nielsen Student Aalborg Universitet. _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jharlap at bic.mni.mcgill.ca Sun Oct 30 05:56:32 2005 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Sun, 30 Oct 2005 05:56:32 -0500 Subject: [MINC-users] MatLab - EMMA In-Reply-To: References: Message-ID: <20051030105632.GA244852@bic.mni.mcgill.ca> While slightly off-topic, it sounds like you're just trying to visualise a MINC volume - in which case you can also consider using one of the visualisation tools that read MINC, such as Display or register which are available from http://packages.bic.mni.mcgill.ca/ Cheers, Jon On Sun, Oct 30, 2005 at 12:35:29AM +0200, S?ren Christensen wrote: > Hi Flemming, > What do you mean by viewing a volume - viewing it in a montage? > Usually you can just use getimages to fetch the data and then use reshape to reconstruct the image into the original dimensions. See http://www.bic.mni.mcgill.ca/software/emma/demos/emma1.html. > If you paste in your code it'd be easier to see where the problem is. > > Best regards > Soren > ________________________________ > > Fra: minc-users-bounces at bic.mni.mcgill.ca p? vegne af Flemming Nielsen > Sendt: s? 30-10-2005 06:21 > Til: 'MINC users mailing list' > Emne: [MINC-users] MatLab - EMMA > > > > Hi > I have a little problem, when I want to view a hole MINV-volume in MatLab. > I use getimages to read the intire volume, but I can not come up wite a > good solution how to visualize the entire volume. > Some ideas > Mvh > Flemming Nielsen > Student > Aalborg Universitet. > > _______________________________________________ > 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 jammam2 at yahoo.com Mon Oct 31 02:31:24 2005 From: jammam2 at yahoo.com (Jamila Ahdidan) Date: Sun, 30 Oct 2005 23:31:24 -0800 (PST) Subject: [MINC-users] operations on grid maps (deformation maps) Message-ID: <20051031073124.5968.qmail@web60815.mail.yahoo.com> Hi all, Since nobody answered my previous mail, I send the question again. I noticed that mincmath doesn't work on grid maps, it doesn't interpret that it's a vector field. How can I get around this problem and perform some calculation function on grid maps? Thanks! Jamila --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. From schwarz at cba.muni.cz Mon Oct 31 03:06:14 2005 From: schwarz at cba.muni.cz (Daniel Schwarz) Date: Mon, 31 Oct 2005 09:06:14 +0100 Subject: [MINC-users] discussion? Message-ID: <200510310806.j9V86NpK005025@tirith.ics.muni.cz> Dear minc-users, I am not sure if the following problem, I would like to introduce here, is not a little bit off-topic for this mail-list. However, I will try it. I will appreciate any kind of feedback. In my PhD research and the related thesis I have designed two deformable registration algorithms, suggesting to use them in the area of computational neuroanatomy, i.e. DBM, VBM (with emphasising DBM a little more). On the other hand, I am aware of the question about the use of non-linear geometrical transforms in medical applications. I mean the theoretical unwanted case, when some kind of unsuitable spatial deformation model is able to perfectly warp two brains, by accident rotated by 90 or 180 degrees......or when a spatial deformation model creates new gyral/sulcal patterns etc... I am going to defend my thesis in several days and I am awaiting a discussion of this kind there... My idea is to try the discussion with anyone interested before the day of defence. I think that someone from the min-users community might be interested - if not, I am sorry to bother you all. Thanks in advance. Daniel P.S. Any links to references discussing that topic are also strongly welcomed. From rtho03 at miba.auc.dk Mon Oct 31 07:32:02 2005 From: rtho03 at miba.auc.dk (rtho03@miba.auc.dk) Date: Mon, 31 Oct 2005 13:32:02 +0100 Subject: [MINC-users] exact midsagittal slice Message-ID: <1130761922.43660ec2b0630@www.hst.aau.dk> Does anyone have an idea how to rotate a mincvolume in order to make an exact midsagittal slice based on three landmarks selected from the volume, when the three landmarks are not in the same slice? We have tried several approaches but always seem to come up with the problem that the new slice is not exactly midsagittal. Best regards Ria Hoegh, student ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From a.janke at gmail.com Mon Oct 31 07:37:09 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 31 Oct 2005 07:37:09 -0500 Subject: [MINC-users] exact midsagittal slice In-Reply-To: <1130761922.43660ec2b0630@www.hst.aau.dk> References: <1130761922.43660ec2b0630@www.hst.aau.dk> Message-ID: Hi Ria, I suspect you have manually identified three points in both hemispheres? If so you will have to do some sort of SVD fit of the points. I wrote a quick script a while ago that does this without the points. (flips the volume, registers it to itself then applys half the reslting transform). It seems to do a pretty good job most of the time. Remember though that no brain is truly symmetric so your mileage will vary. I have attached it. Andrew On 31/10/05, rtho03 at miba.auc.dk wrote: > Does anyone have an idea how to rotate a mincvolume in order to make an exact > midsagittal slice based on three landmarks selected from the volume, when the > three landmarks are not in the same slice? > We have tried several approaches but always seem to come up with the problem > that the new slice is not exactly midsagittal. > > Best regards > Ria Hoegh, student > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Oct 31 08:22:37 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 31 Oct 2005 08:22:37 -0500 Subject: [MINC-users] Display colormapping In-Reply-To: References: Message-ID: On 27/10/05, S?ren Christensen wrote: > Hi, > Is there a good reason why Display does not re-quantify the display colormap when the min-max levels are changed? There is no good reason beyond the fact that the dat is rescaled to byte when it is read in. (memory wasn't cheap when Display was written). > There are of course ways around it (clamping or changing the header), but it seems like a missing feature? By adding it you would have to re-read the entire volume each time you pressed the button. (with a new range). Perhaps a better solution would be to hack Display to read in data as double/float and then the colourmapping would be a lot easier. a