From jason@bic.mni.mcgill.ca Tue Mar 1 12:02:05 2005 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Tue Mar 1 12:02:05 2005 Subject: [MINC-users] autocrop question In-Reply-To: <42236F55.3020209@bic.mni.mcgill.ca> References: <42236F55.3020209@bic.mni.mcgill.ca> Message-ID: <778C05CC-8A73-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> Greetings Pat, try autocrop -isostep 0.5 input.mnc output.mnc Cheers, Jason On Feb 28, 2005, at 11:21 AM, patrick@bic.mni.mcgill.ca wrote: > > I have a volume that has 1 mm ICBM sampling at the moment and I want > to supersample it to 0.5 mm. Now, I've already reshaped the box by > hand to > accomplish this but I thought that the following command could do the > same job more easily: > > autocrop -from /usr/local/mni/data/ICBM/icbm_template_0.50mm.mnc > 1mm_ICBM_input.mnc 0.5mm_ICBM_output.mnc > > But the output has exactly the same sampling as the input. Have I > misinterpreted or misused this command? Thanks. Cheers. > > Pat > > > -- > Patrick Bermudez > Department of Neuropsychology, Room 276 > 3801 University Street > Montreal, Quebec > Canada > H3A 2B4 > Tel: 514-398-8519 or 514-398-2579 > FAX: 514-398-1338 > URL: http://www.bic.mni.mcgill.ca/~patrick > Lab URL: http://www.zlab.mcgill.ca > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dwagne@bic.mni.mcgill.ca Tue Mar 1 12:02:51 2005 From: dwagne@bic.mni.mcgill.ca (Dylan David Wagner) Date: Tue Mar 1 12:02:51 2005 Subject: [MINC-users] Display + Cygwin In-Reply-To: References: Message-ID: <42249FEB.2070700@bic.mni.mcgill.ca> Hi, Thanks for the cygwin binary, works great on my setup. By the by, if anyone is interested I've been making a cygwin pack for easy deployment on machines for my lab. It has only the packages required to run minc (including X). It also has MINC, all the necessary libs, some of the AFNI cygwin binaries for fmri preprocessing and I fixed the perl wrappers for fmri pre-processing and tal conversion so that they work with cygwin. I've tested it on a fresh computer and it works right out of the box. I'm happy to share it, but it does weigh in at 190 megs. -- ===== Dylan David Wagner Neuropsychology and Cognitive Neuroscience Unit Montreal Neurological Institute Tel: (514) 398-4400 (x089722) Email: dylan.wagner@mail.mcgill.ca Lab website: http://www.mni.mcgill.ca/cog/jonesgotman/ From Andrew Janke Tue Mar 1 16:58:05 2005 From: Andrew Janke (Andrew Janke) Date: Tue Mar 1 16:58:05 2005 Subject: [MINC-users] Display + Cygwin In-Reply-To: References: <42249FEB.2070700@bic.mni.mcgill.ca> Message-ID: > Thanks for the cygwin binary, works great on my setup. Yay! appears that sometime you have have a win... Cygwin has proved to be somewhat of a hairy dog for pre-compiled packages. > By the by, if anyone is interested I've been making a cygwin pack > for easy deployment on machines for my lab. It has only the packages > required to run minc (including X). It also has MINC, all the necessary > libs, some of the AFNI cygwin binaries for fmri preprocessing and I > fixed the perl wrappers for fmri pre-processing and tal conversion so > that they work with cygwin. I've tested it on a fresh computer and it > works right out of the box. I'm interested if only in the approach you are using. Are you simply compiling everything on one machine and then making an installer based upon the entire contents of C:\cygwin using something like Innosetup? I ask if only because I am currently investigating the best way to provide packages for cygwin. There are perhaps three "good" approaches from what I can see. a) use dpkg (within cygwin) b) Create proper cygwin installer packages that can eb used by setup.exe if you add the proper line to the packages sources dialog c) Create .exe stand alone pointy-clicky self/extracting/installing archives. a) is the simplest (for me) to implement, b) is the most sexy IMHO as then you can handle upgrades "magically" by pointing your machine at packages.bic.mni.mcgill.ca/cygwin. c) is likely easiest for users, but one might argue that if the user can't figure out how to do a || b then MINC is going to be a problem for them Thoughts? -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From dwagne@bic.mni.mcgill.ca Wed Mar 2 12:17:07 2005 From: dwagne@bic.mni.mcgill.ca (Dylan David Wagner) Date: Wed Mar 2 12:17:07 2005 Subject: [MINC-users] Display + Cygwin In-Reply-To: References: <42249FEB.2070700@bic.mni.mcgill.ca> Message-ID: <4225F44F.20401@bic.mni.mcgill.ca> Andrew Janke wrote: > I'm interested if only in the approach you are using. > Hi, The approach is a bit mixed. There was a release of minctools all set up for cygwin posted on the Repric website late january. I believe Dr. Armony is the one who put it together. However I was unable to get it to work (different perl versions, different versions of X, etc.) I'm no unix/cygwin expert but based on the instructions I think Repric forgot to also post the install packages that were used to make the particular build of cygwin that the minc tools they posted was designed for. So I started from scratch using the repric one has a reference for where to shove the esoteric libs and how to setup the path. What I've done then is simply to download the minimum of cygwin packages necessary to run minc, then from there build cygwin and transfer the compiled minc tools into this new build along with some of the Bic perl scripts which I modified a bit to work with cygwin, as well as some path settings (had a terrible time getting minc to find all the proper perl stuff). So far I've uninstalled it and tried putting it back together from the instructions I wrote and it worked perfect. So presumably it'll work well on other computers as well. As neither myself, nor the people in my lab for which I'm putting this together, are all that unix savvy I tried to make it as easy as possible to install. Some people have emailed me asking for it, so if you or anyone else want to check it out I put up a quick and dirty webpage at http://www.bic.mni.mcgill.ca/~dwagne/ > Are you simply compiling everything on one machine and then making an > installer based upon the entire contents of C:\cygwin using something > like Innosetup? > > I ask if only because I am currently investigating the best way to > provide packages for cygwin. > > There are perhaps three "good" approaches from what I can see. > > a) use dpkg (within cygwin) > > b) Create proper cygwin installer packages that can eb used by setup.exe > if you add the proper line to the packages sources dialog > > c) Create .exe stand alone pointy-clicky self/extracting/installing archives. > > I suppose it depends on what people would be using it for. I'm putting this together specifically for fmri analysis for psychologists, with the idea that it has to be incredibly easy to install, and probably doesn't need to have it's core minc tools updated all that often as the preprocessing for fmri pipeline, I believe, doesn't change that much over time. The other reason I wanted this, both for myself and my lab, is that we can then have matlab/fmristat call cygwin to do the preprocessing from within a script or a gui (which I'm working on now) and automate the whole process. Something that can certainly be done in linux or on one of the unix machines in the bic, but, well... I like my office, and I tried dual booting linux and windows and failed miserably. To say nothing of the coolness factor of popping the lot onto a windows laptop and doing it at high altitude, for the jetset neuroimagers amongst us. But certainly A or B would be quite welcome, as I can then just make a much smaller archive of only the perl wrappers and some of the afni binaries required for fmri preprocessing. -- ===== Dylan David Wagner Neuropsychology and Cognitive Neuroscience Unit Montreal Neurological Institute Tel: (514) 398-4400 (x089722) Email: dylan.wagner@mail.mcgill.ca Lab website: http://www.mni.mcgill.ca/cog/jonesgotman/ From hpkim@ihanyang.ac.kr Thu Mar 3 17:09:05 2005 From: hpkim@ihanyang.ac.kr (Hyun-Pil Kim) Date: Thu Mar 3 17:09:05 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) Message-ID: <1109657660162368.4045@webmail> This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C51E71.5626FAA0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Recently I've been trying to use MNI tools on a Itanium2 based SGI Linux machine. (SIG Altix 350) All software and firmware are up-to-date but I don't get it work correctly. There seems to be no problems while installation, however, I don't get consistent results with those of 32bit based Fedora boxes. Anybody have an idea? Regards, Phil *------------------------------------------------* Hyun-Pil Kim, Computational Neuroimage Analysis Lab., Dept. of Biomedical Engineering, Hanyang Univ. Sungdong P.O. Box 55, Seoul, 133-605, KOREA Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 Mobile: +82-19-286-0485 E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com *------------------------------------------------* ------=_NextPart_000_001B_01C51E71.5626FAA0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Recently I’ve been trying to use MNI tools on a Itanium2 based SGI Linux machine.

(SIG Altix 350) All software and firmware are up-to-date but I don’t get it work correctly.

There seems to be no problems while installation, however, I don’t get consistent results with those of 32bit based Fedora boxes. Anybody have an idea?

 

Regards,

Phil

*------------------------------------------------*
Hyun-Pil Kim,
Computational Neuroimage Analysis Lab.,
Dept. of Biomedical Engineering, Hanyang Univ.
Sungdong P.O. Box 55, Seoul, 133-605, KOREA
Tel: +82-2-2290-0697; FAX: +82-2-2296-5943
Mobile: +82-19-286-0485
E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com
*------------------------------------------------*

 

------=_NextPart_000_001B_01C51E71.5626FAA0-- From yangjo@upstate.edu Thu Mar 3 17:20:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Thu Mar 3 17:20:04 2005 Subject: [MINC-users] V and W coordinates in mni register Message-ID: Hi, Would someone tell me what coodindates are the two coordinates, V and W, shown at the bottom of "register"? Is one of them Talairach coodindates? Thanks. Nam. From bert@bic.mni.mcgill.ca Thu Mar 3 17:28:04 2005 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Mar 3 17:28:04 2005 Subject: [MINC-users] V and W coordinates in mni register In-Reply-To: Message-ID: Hi Nam, The V coordinate is the "voxel" coordinate. It corresponds to the physical array indices within the 3D MINC volume. The W coordinate is the "world" coordinate. Every MINC file contains a transform from voxel to world coordinates. Unless the file has been explicitly registered and resampled to Talairach space, the world coordinate system is probably derived from the scanner's patient position information, and therefore may be somewhat arbitrary. -bert On Thu, 3 Mar 2005, Joongnam Yang wrote: > Hi, > > Would someone tell me what coodindates are the two coordinates, V and W, > shown at the bottom of "register"? > Is one of them Talairach coodindates? > > Thanks. > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From mhough@fmrib.ox.ac.uk Fri Mar 4 04:52:05 2005 From: mhough@fmrib.ox.ac.uk (Morgan Hough) Date: Fri Mar 4 04:52:05 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) In-Reply-To: <1109657660162368.4045@webmail> References: <1109657660162368.4045@webmail> Message-ID: <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> Phil, You might be the first person to try this as I think MNI only supports IRIX/MIPS builds for SGIs (I could be wrong). I assume you are downloading the source and using the autoconf build process which you say is working without any errors. Can you say anything more about the differences you have been seeing versus Linux/x86? Which tools have you been building? Do you use the Intel compiler or GCC? Is that a 2.4 or 2.6 kernel (I have heard they backported 2.6 features to 2.4 for some of their system configurations)? We are thinking about getting one of these systems and I am interested to hear more about the issues you are having. Cheers, -Morgan -- Morgan Hough DPhil student FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 On Tue, 2005-03-01 at 06:14, Hyun-Pil Kim wrote: > > > Recently I’ve been trying to use MNI tools on a Itanium2 based SGI > Linux machine. > > (SIG Altix 350) All software and firmware are up-to-date but I don’t > get it work correctly. > > There seems to be no problems while installation, however, I don’t get > consistent results with those of 32bit based Fedora boxes. Anybody > have an idea? > > > > Regards, > > Phil > > *------------------------------------------------* > Hyun-Pil Kim, > Computational Neuroimage Analysis Lab., > Dept. of Biomedical Engineering, Hanyang Univ. > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > Mobile: +82-19-286-0485 > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > *------------------------------------------------* > > > From jason@bic.mni.mcgill.ca Fri Mar 4 10:18:04 2005 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Fri Mar 4 10:18:04 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) In-Reply-To: <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> References: <1109657660162368.4045@webmail> <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> Message-ID: <6D970CC5-8CC0-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> Greetings, On Mar 4, 2005, at 1:48 AM, Morgan Hough wrote: > You might be the first person to try this as I think MNI only supports > IRIX/MIPS builds for SGIs (I could be wrong). that's the only build we've tried - but that doesn't mean that MINC and friends should not build and run on Itanium chips. So please let us know what went wrong (and if you have patches, even better), and we'll try our best to help out. Cheers, Jason From bert@bic.mni.mcgill.ca Fri Mar 4 10:27:04 2005 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri Mar 4 10:27:04 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) In-Reply-To: <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> Message-ID: Hi, We strictly have SGI IRIX systems here (so far)... We'd be happy to help in any way possible to get our tools working on the SGI Itaniums. Let me know what kinds of problems you're seeing. -bert On Fri, 4 Mar 2005, Morgan Hough wrote: > Phil, > > You might be the first person to try this as I think MNI only supports > IRIX/MIPS builds for SGIs (I could be wrong). I assume you are > downloading the source and using the autoconf build process which you > say is working without any errors. Can you say anything more about the > differences you have been seeing versus Linux/x86? Which tools have you > been building? Do you use the Intel compiler or GCC? Is that a 2.4 or > 2.6 kernel (I have heard they backported 2.6 features to 2.4 for some of > their system configurations)? > > We are thinking about getting one of these systems and I am interested > to hear more about the issues you are having. > > Cheers, > > -Morgan > > -- > Morgan Hough DPhil student > FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough > tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 > > On Tue, 2005-03-01 at 06:14, Hyun-Pil Kim wrote: > > > > > > Recently I’ve been trying to use MNI tools on a Itanium2 based SGI > > Linux machine. > > > > (SIG Altix 350) All software and firmware are up-to-date but I don’t > > get it work correctly. > > > > There seems to be no problems while installation, however, I don’t get > > consistent results with those of 32bit based Fedora boxes. Anybody > > have an idea? > > > > > > > > Regards, > > > > Phil > > > > *------------------------------------------------* > > Hyun-Pil Kim, > > Computational Neuroimage Analysis Lab., > > Dept. of Biomedical Engineering, Hanyang Univ. > > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > > Mobile: +82-19-286-0485 > > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > > *------------------------------------------------* > > > > > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From Jean-Francois.Malouin@bic.mni.mcgill.ca Fri Mar 4 12:43:04 2005 From: Jean-Francois.Malouin@bic.mni.mcgill.ca (Jean-Francois Malouin) Date: Fri Mar 4 12:43:04 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) In-Reply-To: <6D970CC5-8CC0-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> References: <1109657660162368.4045@webmail> <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> <6D970CC5-8CC0-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <20050304174203.GA1860292@shadow.bic.mni.mcgill.ca> Namaste, You will soon have the chance to try this build on a Itanium2 platform as we have 2 systems on their way to the BIC: an Altix 350 16P and a Prism 4P and 2 graphics pipe, both Intel Itanium2. jf * Jason Lerch [20050304 10:21]: > Greetings, > > On Mar 4, 2005, at 1:48 AM, Morgan Hough wrote: > > >You might be the first person to try this as I think MNI only supports > >IRIX/MIPS builds for SGIs (I could be wrong). > > that's the only build we've tried - but that doesn't mean that MINC and > friends should not build and run on Itanium chips. So please let us > know what went wrong (and if you have patches, even better), and we'll > try our best to help out. > > Cheers, > > Jason > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- <° >< From yangjo@upstate.edu Mon Mar 7 16:23:03 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Mon Mar 7 16:23:03 2005 Subject: [MINC-users] putting an *.mnc into the talairach space Message-ID: Hi All, I have amri.mnc in native space. I want to turn it into one in talairach space. Would someone let me know how to do it? Nam. From bert@bic.mni.mcgill.ca Mon Mar 7 16:34:04 2005 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Mon Mar 7 16:34:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: Message-ID: Hi Nam, Take a look at the mni_autoreg package: http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg -bert On Mon, 7 Mar 2005, Joongnam Yang wrote: > Hi All, > > I have amri.mnc in native space. > I want to turn it into one in talairach space. > Would someone let me know how to do it? > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From yangjo@upstate.edu Mon Mar 7 19:03:05 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Mon Mar 7 19:03:05 2005 Subject: [MINC-users] putting an *.mnc into the talairach space Message-ID: Thanks for the info. if I do, mritotal amri.mnc amri_tal.xfm, it gives me the talairach transform file, but it does not actually change the input volume "amri.mnc". Is there a way of transforming the input mnc volume into another mnc file using the transform file? Nam. >>> Robert VINCENT 03/07/05 4:33 PM >>> Hi Nam, Take a look at the mni_autoreg package: http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg -bert On Mon, 7 Mar 2005, Joongnam Yang wrote: > Hi All, > > I have amri.mnc in native space. > I want to turn it into one in talairach space. > Would someone let me know how to do it? > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From hpkim@bme.hanyang.ac.kr Mon Mar 7 19:34:04 2005 From: hpkim@bme.hanyang.ac.kr (???) Date: Mon Mar 7 19:34:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: Message-ID: <200503080033.j280XnxO2091373@shadow.bic.mni.mcgill.ca> You should actually 'resample' the original volume with the transform matrix using mincresample program. http://wiki.bic.mni.mcgill.ca/index.php/MincresampleManPage Regards, Phil. *------------------------------------------------* Hyun-Pil Kim, Computational Neuroimage Analysis Lab., Dept. of Biomedical Engineering, Hanyang Univ. Sungdong P.O. Box 55, Seoul, 133-605, KOREA Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 Mobile: +82-19-286-0485 E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com *------------------------------------------------* |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Joongnam Yang |Sent: Tuesday, March 08, 2005 9:02 AM |To: bert@bic.mni.mcgill.ca |Cc: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] putting an *.mnc into the talairach space | |Thanks for the info. |if I do, |mritotal amri.mnc amri_tal.xfm, |it gives me the talairach transform file, but it does not actually |change the input volume "amri.mnc". | |Is there a way of transforming the input mnc volume into another mnc |file using the transform file? | |Nam. | |>>> Robert VINCENT 03/07/05 4:33 PM >>> |Hi Nam, | |Take a look at the mni_autoreg package: | |http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg | | -bert | |On Mon, 7 Mar 2005, Joongnam Yang wrote: | |> Hi All, |> |> I have amri.mnc in native space. |> I want to turn it into one in talairach space. |> Would someone let me know how to do it? |> |> Nam. |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From hpkim@bme.hanyang.ac.kr Mon Mar 7 19:36:04 2005 From: hpkim@bme.hanyang.ac.kr (???) Date: Mon Mar 7 19:36:04 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits LinuxMachine (IA64) In-Reply-To: <1109929727.10973.46.camel@dhania.fmrib.ox.ac.uk> Message-ID: <200503080035.j280Z2xO2068055@shadow.bic.mni.mcgill.ca> Dear Morgan, I am trying to build almost every tool from MNI (public or private). And I found that there are numerous problems out there for compiling, installing, and running MNI Software and needed libraries on GNU/Linux/x86/x86_64 combinations. I hope that people have more interest in Intel/GNU/Linux boxes. :) ######################################### F.Y.I. from my personal correspondence: We had to patch: N3 -> extracttag.c . "-mintags", ARGV_LONG, (char *) NULL, (char *) &min_tags, . . "-maxtags", ARGV_LONG, . Also, the following should be patched minc 1.3 -> image_conversion.c line 680~ /* Check for image dimension properties */ if ((icv_property>=MI_ICV_DIM_START) && (icv_propertyderv_dim_start[idim]; } else if ((icv_property>=MI_ICV_DIM_STEP) && (icv_propertyderv_dim_step[idim]; } else if ((icv_property>=MI_ICV_DIM_SIZE) && (icv_propertyuser_dim_size[idim]; } ...... CGAL 2.4 package for mni_surfreg. However I needed additional patch again to work around a problem. That seems to be compatibility problems between IRIS(n32? n64?) and GCC/G++. I had to link following object for building shared library to work around 'hidden symbols not found in libCGAL.so error'. This might not be safe. static void init(){} static void fini(){} static void preinit(){} typedef void (*fp)(); fp __init_array_start[]={init}; fp __init_array_end[]={init}; fp __fini_array_start[]={fini}; fp __fini_array_end[]={fini}; fp __preinit_array_start[]={preinit}; fp __preinit_array_end[]={preinit}; ############################################ And some of the software working on x86_32 machine does not work properly on an IA64 machine. Regards, Phil. |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Morgan Hough |Sent: Friday, March 04, 2005 6:49 PM |To: Hyun-Pil Kim |Cc: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] Running MNI software on SGI Intel 64bits |LinuxMachine (IA64) | |Phil, | |You might be the first person to try this as I think MNI only supports |IRIX/MIPS builds for SGIs (I could be wrong). I assume you are |downloading the source and using the autoconf build process which you |say is working without any errors. Can you say anything more about the |differences you have been seeing versus Linux/x86? Which tools have you |been building? Do you use the Intel compiler or GCC? Is that a 2.4 or |2.6 kernel (I have heard they backported 2.6 features to 2.4 for some |of their system configurations)? | |We are thinking about getting one of these systems and I am interested |to hear more about the issues you are having. | |Cheers, | |-Morgan | |-- |Morgan Hough DPhil student |FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK |mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 |222545 fax +44 (0) 1865 222717 | |On Tue, 2005-03-01 at 06:14, Hyun-Pil Kim wrote: |> |> |> Recently I've been trying to use MNI tools on a Itanium2 based SGI |> Linux machine. |> |> (SIG Altix 350) All software and firmware are up-to-date but I don't |> get it work correctly. |> |> There seems to be no problems while installation, however, I don't |> get consistent results with those of 32bit based Fedora boxes. |> Anybody have an idea? |> |> |> |> Regards, |> |> Phil |> |> *------------------------------------------------* |> Hyun-Pil Kim, |> Computational Neuroimage Analysis Lab., Dept. of Biomedical |> Engineering, Hanyang Univ. |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> Mobile: +82-19-286-0485 |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> *------------------------------------------------* |> |> |> | | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From yangjo@upstate.edu Tue Mar 8 11:45:03 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Tue Mar 8 11:45:03 2005 Subject: [MINC-users] putting an *.mnc into the talairach space Message-ID: Thanks Phil. I actually thought about using 'resample', but when I use it, what do I use for the '-like' option? to resample amri.mnc into amri_tal.mnc, I would do, mincresample -like XXXX amri.mnc -transf amri_tal.xfm amri_tal.mnc in the above commands what should be XXXX? Nam. >>> "???" 03/07/05 7:32 PM >>> You should actually 'resample' the original volume with the transform matrix using mincresample program. http://wiki.bic.mni.mcgill.ca/index.php/MincresampleManPage Regards, Phil. *------------------------------------------------* Hyun-Pil Kim, Computational Neuroimage Analysis Lab., Dept. of Biomedical Engineering, Hanyang Univ. Sungdong P.O. Box 55, Seoul, 133-605, KOREA Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 Mobile: +82-19-286-0485 E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com *------------------------------------------------* |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Joongnam Yang |Sent: Tuesday, March 08, 2005 9:02 AM |To: bert@bic.mni.mcgill.ca |Cc: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] putting an *.mnc into the talairach space | |Thanks for the info. |if I do, |mritotal amri.mnc amri_tal.xfm, |it gives me the talairach transform file, but it does not actually |change the input volume "amri.mnc". | |Is there a way of transforming the input mnc volume into another mnc |file using the transform file? | |Nam. | |>>> Robert VINCENT 03/07/05 4:33 PM >>> |Hi Nam, | |Take a look at the mni_autoreg package: | |http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg | | -bert | |On Mon, 7 Mar 2005, Joongnam Yang wrote: | |> Hi All, |> |> I have amri.mnc in native space. |> I want to turn it into one in talairach space. |> Would someone let me know how to do it? |> |> Nam. |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From pgravel@bic.mni.mcgill.ca Tue Mar 8 11:55:04 2005 From: pgravel@bic.mni.mcgill.ca (Paul GRAVEL) Date: Tue Mar 8 11:55:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: Message-ID: Hi All, Just wondering, when using mritotal, the xfm file obtained is the transformation from native space to the mni305 space, is that correct? Aren't there some differences between the talairach space and the mni305 space? Thanks in advance. Regards, Paul From vsingh@bic.mni.mcgill.ca Tue Mar 8 12:03:04 2005 From: vsingh@bic.mni.mcgill.ca (Vivek SINGH) Date: Tue Mar 8 12:03:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: Message-ID: Hi Paul, The following website my be of interest to you: http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml Vivek On Tue, 8 Mar 2005, Paul GRAVEL wrote: > Hi All, > > Just wondering, when using mritotal, the xfm file obtained is the > transformation from native space to the mni305 space, is that correct? > > Aren't there some differences between the talairach space and the mni305 > space? > > Thanks in advance. > > Regards, > > Paul > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jason@bic.mni.mcgill.ca Tue Mar 8 12:06:04 2005 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Tue Mar 8 12:06:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: References: Message-ID: <419AB97F-8FF4-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> On Mar 8, 2005, at 11:43 AM, Joongnam Yang wrote: > Thanks Phil. > > I actually thought about using 'resample', but when I use it, what do > I use > for > the '-like' option? The sampling space you want - i.e. a MINC file with the right xyz dimensions and steps. The model you used to register towards with mritotal is often a good choice here. Jason > > to resample amri.mnc into amri_tal.mnc, I would do, > > mincresample -like XXXX amri.mnc -transf amri_tal.xfm amri_tal.mnc > > in the above commands what should be XXXX? > > Nam. > >>>> "???" 03/07/05 7:32 PM >>> > You should actually 'resample' the original volume with the transform > matrix > using mincresample program. > > http://wiki.bic.mni.mcgill.ca/index.php/MincresampleManPage > > Regards, > Phil. > > *------------------------------------------------* > Hyun-Pil Kim, > Computational Neuroimage Analysis Lab., Dept. of Biomedical > Engineering, > Hanyang Univ. > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > Mobile: +82-19-286-0485 > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > *------------------------------------------------* > > > |-----Original Message----- > |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- > |admin@bic.mni.mcgill.ca] On Behalf Of Joongnam Yang > |Sent: Tuesday, March 08, 2005 9:02 AM > |To: bert@bic.mni.mcgill.ca > |Cc: minc-users@bic.mni.mcgill.ca > |Subject: Re: [MINC-users] putting an *.mnc into the talairach space > | > |Thanks for the info. > |if I do, > |mritotal amri.mnc amri_tal.xfm, > |it gives me the talairach transform file, but it does not actually > |change the input volume "amri.mnc". > | > |Is there a way of transforming the input mnc volume into another mnc > |file using the transform file? > | > |Nam. > | > |>>> Robert VINCENT 03/07/05 4:33 PM >>> > |Hi Nam, > | > |Take a look at the mni_autoreg package: > | > |http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg > | > | -bert > | > |On Mon, 7 Mar 2005, Joongnam Yang wrote: > | > |> Hi All, > |> > |> I have amri.mnc in native space. > |> I want to turn it into one in talairach space. > |> Would someone let me know how to do it? > |> > |> Nam. > |> _______________________________________________ > |> MINC-users@bic.mni.mcgill.ca > |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > |> > | > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > | > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jason@bic.mni.mcgill.ca Tue Mar 8 12:06:14 2005 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Tue Mar 8 12:06:14 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: References: Message-ID: <1CF51604-8FF4-11D9-A50A-000A95DBBFD8@bic.mni.mcgill.ca> On Mar 8, 2005, at 11:54 AM, Paul GRAVEL wrote: > Hi All, > > Just wondering, when using mritotal, the xfm file obtained is the > transformation from native space to the mni305 space, is that correct? That is the default behaviour, but can be changed with the -model and -modeldir arguments. > > Aren't there some differences between the talairach space and the > mni305 > space? Yes. See here for some in-depth discussion of this topic: http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml Cheers, Jason P.S. Anyone else find the reply-to behaviour of this list irritating? I vote to change that it does a reply-to-list as the default behaviour ... From schwarzd@feec.vutbr.cz Wed Mar 9 02:24:03 2005 From: schwarzd@feec.vutbr.cz (schwarzd) Date: Wed Mar 9 02:24:03 2005 Subject: [MINC-users] mritotal and nu_correct Message-ID: <1110353008.422ea470c44a1@email.fit.vutbr.cz> Dear minc-users, is there any comparison of registration results (accuracy) when: 1. mritotal is performed on native mri image 2. mritotal is performed on corrected mri image with N3 algorithm (nu_correct). In my opinion, the results may be better for corrected images when thinking about cross correlation and mutual information. However, mritotal on native mri image is recommended on the web-page http://www.imaging.robarts.ca/Software/mni_software/mri_segment/ . Any suggestions, explanations, links or comments? Thank you. Daniel Schwarz From steven.robbins@videotron.ca Wed Mar 9 08:15:04 2005 From: steven.robbins@videotron.ca (Steve M. Robbins) Date: Wed Mar 9 08:15:04 2005 Subject: [MINC-users] mritotal and nu_correct In-Reply-To: <1110353008.422ea470c44a1@email.fit.vutbr.cz> References: <1110353008.422ea470c44a1@email.fit.vutbr.cz> Message-ID: <20050309131254.GA26750@nyongwa.montreal.qc.ca> On Wed, Mar 09, 2005 at 08:23:28AM +0100, schwarzd wrote: > Dear minc-users, > > is there any comparison of registration results (accuracy) when: > 1. mritotal is performed on native mri image > 2. mritotal is performed on corrected mri image with N3 algorithm (nu_correct). > > In my opinion, the results may be better for corrected images when thinking > about cross correlation and mutual information. However, mritotal on native mri > image is recommended on the web-page > http://www.imaging.robarts.ca/Software/mni_software/mri_segment/ . > > Any suggestions, explanations, links or comments? I believe that John Sled's MSc thesis (on the N3 algorithm) has some experiments of that nature. Maybe the journal paper does as well. -Steve From yangjo@upstate.edu Wed Mar 9 16:44:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Wed Mar 9 16:44:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space Message-ID: Thanks, Jason, but I am not sure I understand your comments. Could you give me an example of 'mincresample' ? My purpose is to turn amri.mnc into talairach space. mritotal only gives me the transformation from mni to talairach. I tried mincresample -talairach amri.mnc amri_tal.mnc but when I looked at the amri.mnc and amri_tal.mnc, they were identical... Nam. >>> Jason Lerch 03/08/05 12:05 PM >>> On Mar 8, 2005, at 11:43 AM, Joongnam Yang wrote: > Thanks Phil. > > I actually thought about using 'resample', but when I use it, what do > I use > for > the '-like' option? The sampling space you want - i.e. a MINC file with the right xyz dimensions and steps. The model you used to register towards with mritotal is often a good choice here. Jason > > to resample amri.mnc into amri_tal.mnc, I would do, > > mincresample -like XXXX amri.mnc -transf amri_tal.xfm amri_tal.mnc > > in the above commands what should be XXXX? > > Nam. > >>>> "???" 03/07/05 7:32 PM >>> > You should actually 'resample' the original volume with the transform > matrix > using mincresample program. > > http://wiki.bic.mni.mcgill.ca/index.php/MincresampleManPage > > Regards, > Phil. > > *------------------------------------------------* > Hyun-Pil Kim, > Computational Neuroimage Analysis Lab., Dept. of Biomedical > Engineering, > Hanyang Univ. > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > Mobile: +82-19-286-0485 > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > *------------------------------------------------* > > > |-----Original Message----- > |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- > |admin@bic.mni.mcgill.ca] On Behalf Of Joongnam Yang > |Sent: Tuesday, March 08, 2005 9:02 AM > |To: bert@bic.mni.mcgill.ca > |Cc: minc-users@bic.mni.mcgill.ca > |Subject: Re: [MINC-users] putting an *.mnc into the talairach space > | > |Thanks for the info. > |if I do, > |mritotal amri.mnc amri_tal.xfm, > |it gives me the talairach transform file, but it does not actually > |change the input volume "amri.mnc". > | > |Is there a way of transforming the input mnc volume into another mnc > |file using the transform file? > | > |Nam. > | > |>>> Robert VINCENT 03/07/05 4:33 PM >>> > |Hi Nam, > | > |Take a look at the mni_autoreg package: > | > |http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg > | > | -bert > | > |On Mon, 7 Mar 2005, Joongnam Yang wrote: > | > |> Hi All, > |> > |> I have amri.mnc in native space. > |> I want to turn it into one in talairach space. > |> Would someone let me know how to do it? > |> > |> Nam. > |> _______________________________________________ > |> MINC-users@bic.mni.mcgill.ca > |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > |> > | > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > | > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jason@bic.mni.mcgill.ca Wed Mar 9 16:48:05 2005 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Wed Mar 9 16:48:05 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: References: Message-ID: On Mar 9, 2005, at 4:42 PM, Joongnam Yang wrote: > Thanks, Jason, > > but I am not sure I understand your comments. > Could you give me an example of 'mincresample' ? sure: > mritotal native.mnc to_stx.xfm > mincresample native.mnc -like model.mnc -transform to_stx.xfm stx.mnc where model.mnc is some volume with the desired sampling and already in Talairach space. > My purpose is to turn amri.mnc into talairach space. > mritotal only gives me the transformation from mni to talairach. > I tried > mincresample -talairach amri.mnc amri_tal.mnc That just changes a flag in the header, I think, so isn't particularly useful. Jason > but when I looked at the amri.mnc and amri_tal.mnc, they were > identical... > > Nam. > >>>> Jason Lerch 03/08/05 12:05 PM >>> > > On Mar 8, 2005, at 11:43 AM, Joongnam Yang wrote: > >> Thanks Phil. >> >> I actually thought about using 'resample', but when I use it, what do >> I use >> for >> the '-like' option? > > The sampling space you want - i.e. a MINC file with the right xyz > dimensions and steps. The model you used to register towards with > mritotal is often a good choice here. > > Jason > >> >> to resample amri.mnc into amri_tal.mnc, I would do, >> >> mincresample -like XXXX amri.mnc -transf amri_tal.xfm amri_tal.mnc >> >> in the above commands what should be XXXX? >> >> Nam. >> >>>>> "???" 03/07/05 7:32 PM >>> >> You should actually 'resample' the original volume with the transform >> matrix >> using mincresample program. >> >> http://wiki.bic.mni.mcgill.ca/index.php/MincresampleManPage >> >> Regards, >> Phil. >> >> *------------------------------------------------* >> Hyun-Pil Kim, >> Computational Neuroimage Analysis Lab., Dept. of Biomedical >> Engineering, >> Hanyang Univ. >> Sungdong P.O. Box 55, Seoul, 133-605, KOREA >> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 >> Mobile: +82-19-286-0485 >> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com >> *------------------------------------------------* >> >> >> |-----Original Message----- >> |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- >> |admin@bic.mni.mcgill.ca] On Behalf Of Joongnam Yang >> |Sent: Tuesday, March 08, 2005 9:02 AM >> |To: bert@bic.mni.mcgill.ca >> |Cc: minc-users@bic.mni.mcgill.ca >> |Subject: Re: [MINC-users] putting an *.mnc into the talairach space >> | >> |Thanks for the info. >> |if I do, >> |mritotal amri.mnc amri_tal.xfm, >> |it gives me the talairach transform file, but it does not actually >> |change the input volume "amri.mnc". >> | >> |Is there a way of transforming the input mnc volume into another mnc >> |file using the transform file? >> | >> |Nam. >> | >> |>>> Robert VINCENT 03/07/05 4:33 PM >>> >> |Hi Nam, >> | >> |Take a look at the mni_autoreg package: >> | >> |http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg >> | >> | -bert >> | >> |On Mon, 7 Mar 2005, Joongnam Yang wrote: >> | >> |> Hi All, >> |> >> |> I have amri.mnc in native space. >> |> I want to turn it into one in talairach space. >> |> Would someone let me know how to do it? >> |> >> |> Nam. >> |> _______________________________________________ >> |> MINC-users@bic.mni.mcgill.ca >> |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> |> >> | >> |_______________________________________________ >> |MINC-users@bic.mni.mcgill.ca >> |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> | >> |_______________________________________________ >> |MINC-users@bic.mni.mcgill.ca >> |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> >> _______________________________________________ >> MINC-users@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From yangjo@upstate.edu Wed Mar 9 18:05:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Wed Mar 9 18:05:04 2005 Subject: [MINC-users] putting an *.mnc into the talairach space Message-ID: Thanks, Jason. > where model.mnc is some volume with the desired sampling and already in > Talairach space. Is there any place where I can find a good (or standard) volume already in Talairach space, so that I can download it? Nam. From Andrew Janke Wed Mar 9 23:05:03 2005 From: Andrew Janke (Andrew Janke) Date: Wed Mar 9 23:05:03 2005 Subject: [MINC-users] putting an *.mnc into the talairach space In-Reply-To: References: Message-ID: On Wed, 09 Mar 2005 18:04:08 -0500, Joongnam Yang wrote: > Thanks, Jason. > > > where model.mnc is some volume with the desired sampling and already in > > Talairach space. > > Is there any place where I can find a good (or standard) volume already in > Talairach space, so that I can download it? You want mni_autoreg_model. It is a companion package to mni_autoreg and contains the average305 model. -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From Andrew Janke Thu Mar 10 10:26:04 2005 From: Andrew Janke (Andrew Janke) Date: Thu Mar 10 10:26:04 2005 Subject: Fwd: [MINC-users] Display + Cygwin In-Reply-To: References: <423061AC.6050009@drcmr.dk> Message-ID: ---------- Forwarded message ---------- From: Andrew Janke Date: Fri, 11 Mar 2005 01:24:25 +1000 Subject: Re: [MINC-users] Display + Cygwin To: wimb@drcmr.dk On Thu, 10 Mar 2005 16:03:08 +0100, William Baaré wrote: > > I just used your binary... it works fine, however, when I want to > overwrite an earlier saved label volume I get the following error. > > ################################### > > $ cygdisplay s069.mnc > Inputting s069.mnc. > Objects input. > Enter filename to save: aap.mnc > File exists, do you wish to overwrite (y or n): y > /bin/cp: cannot create regular file > `aap.mnc.Thu_Mar_10_15:52:18_2005_.bkp': Inv > alid argument > Error copying file aap.mnc to aap.mnc.Thu_Mar_10_15:52:18_2005_.bkp: > System message: No such file or directory > Error making backup file for: aap.mnc Hrm, I guessing this is to do with the ':' in the filename. The windows filesystem canna handle this from memory. It treats the colon as a file separator in a list IIRC. So I guess this is a bug. The backup filename should really use a '-' as the date seaparator to be more portable. The question is has anyone out there written scripts that depend on Display backup filenames being written in this fashion? -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Thu Mar 10 17:30:05 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Thu Mar 10 17:30:05 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits Linux Machine (IA64) In-Reply-To: <20050304174203.GA1860292@shadow.bic.mni.mcgill.ca> Message-ID: <1110005307635258.13967@webmail> Dear JF, I'm glad to see that you are going to try using the same SGI 350 machine with us. I hope to hear more about it when you start setting it up. I look forward to hearing more about it soon. Cheers, Phil. |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Jean-Francois Malouin |Sent: Saturday, March 05, 2005 2:42 AM |To: Jason Lerch |Cc: Morgan Hough; minc-users@bic.mni.mcgill.ca; Hyun-Pil Kim |Subject: Re: [MINC-users] Running MNI software on SGI Intel 64bits Linux |Machine (IA64) | |Namaste, | |You will soon have the chance to try this build on a Itanium2 platform |as we have 2 systems on their way to the BIC: an Altix 350 16P and a |Prism 4P and 2 graphics pipe, both Intel Itanium2. | |jf | |* Jason Lerch [20050304 10:21]: |> Greetings, |> |> On Mar 4, 2005, at 1:48 AM, Morgan Hough wrote: |> |> >You might be the first person to try this as I think MNI only supports |> >IRIX/MIPS builds for SGIs (I could be wrong). |> |> that's the only build we've tried - but that doesn't mean that MINC and |> friends should not build and run on Itanium chips. So please let us |> know what went wrong (and if you have patches, even better), and we'll |> try our best to help out. |> |> Cheers, |> |> Jason |> |> |> |> |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users | |-- |<° >< |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Thu Mar 10 17:30:52 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Thu Mar 10 17:30:52 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? Message-ID: <1110281812181263.19332@webmail> This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C5241E.51E35940 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Is there any working version of dicom to minc converter for Phillips dcm files? The most recent version of dicom3_to_minc utility didn't work for me. After some googling, I found phil_to_minc but somehow the link is not present. http://www.cmr.uq.edu.au/~rotor/minc/ Thanks, Phil. *------------------------------------------------* Hyun-Pil Kim, Computational Neuroimage Analysis Lab., Dept. of Biomedical Engineering, Hanyang Univ. Sungdong P.O. Box 55, Seoul, 133-605, KOREA Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 Mobile: +82-19-286-0485 E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com *------------------------------------------------* ------=_NextPart_000_0006_01C5241E.51E35940 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Is there any working version of dicom to minc converter for Phillips dcm files?

The most recent version of dicom3_to_minc utility didn’t work for me.

After some googling, I found phil_to_minc but somehow the link is not present.

http://www.cmr.uq.edu.au/~rotor/minc/

 

Thanks,

Phil.

*------------------------------------------------*
Hyun-Pil Kim,
Computational Neuroimage Analysis Lab.,
Dept. of Biomedical Engineering, Hanyang Univ.
Sungdong P.O. Box 55, Seoul, 133-605, KOREA
Tel: +82-2-2290-0697; FAX: +82-2-2296-5943
Mobile: +82-19-286-0485
E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com
*------------------------------------------------*

 

------=_NextPart_000_0006_01C5241E.51E35940-- From minc-users@bic.mni.mcgill.ca Thu Mar 10 17:38:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Mar 10 17:38:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <1110281812181263.19332@webmail> Message-ID: Hi, I'm working on a new version of Peter Neelin and Rick Hoge's "dcm2mnc" utility that may work for Philips files. I would be happy to have you test it when I'm ready to release a test version (probably in the next few days). You are running on IRIX, yes? -bert On Tue, 8 Mar 2005, Hyun-Pil Kim wrote: > Is there any working version of dicom to minc converter for Phillips dcm > files? > > The most recent version of dicom3_to_minc utility didn't work for me. > > After some googling, I found phil_to_minc but somehow the link is not > present. > > http://www.cmr.uq.edu.au/~rotor/minc/ > > > > Thanks, > > Phil. > > *------------------------------------------------* > Hyun-Pil Kim, > Computational Neuroimage Analysis Lab., > Dept. of Biomedical Engineering, Hanyang Univ. > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > Mobile: +82-19-286-0485 > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > *------------------------------------------------* > > > > From minc-users@bic.mni.mcgill.ca Thu Mar 10 20:38:03 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Thu Mar 10 20:38:03 2005 Subject: [MINC-users] Running MNI software on SGI Intel 64bits LinuxMachine (IA64) In-Reply-To: Message-ID: <1110505016259122.18114@webmail> Dear bert, It was the last year that we tried using minc tools on Redhat/x86 based machines. The installation process (from netcdf to mni_autoreg) seemed OK but the resampled image after mritotal looked strange, totally wrong. Do you know Jun Sic Kim from Hanyang Univ, Seoul, Korea? He and someone at the MNI fixed this problem (image_conversion.c) as far as I know (not 100% sure). We had to make those changes to the original minc-1.3 package to make it work on Redhat/Fedora/x86/GCC machine. Also, I'm not sure that there are other fixed parts so I attach the fixed package we are using now. Another problem (?): EBTKS cannot be compiled with GCC version 3.4.x I think gcc was changed to meet ISO C++ standard more strictly. There was no problem with gcc version 3.3.x. I suspect this may happen with other mni software on IRIX with the architecture/compiler combinations that I used. I hope this is worth reading. Please let me know if I am missing something. Thanks, Phil. -------------------- make all-am make[1]: Entering directory `/DISTRIBUTION/MNI_SOFTWARE/EBTKS-1.3' if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT version.lo -MD -MP -MF ".deps/version.Tpo" \ -c -o version.lo `test -f 'version.cc' || echo './'`version.cc; \ then mv ".deps/version.Tpo" ".deps/version.Plo"; \ else rm -f ".deps/version.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT g++ -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT version.lo -MD -MP g++ -MF .deps/version.Tpo -c version.cc -o version.o echo timestamp > version.lo if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT FileIO.lo -MD -MP -MF ".deps/FileIO.Tpo" \ -c -o FileIO.lo `test -f 'src/FileIO.cc' || echo './'`src/FileIO.cc; \ then mv ".deps/FileIO.Tpo" ".deps/FileIO.Plo"; \ else rm -f ".deps/FileIO.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT g++ -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT FileIO.lo -MD -MP g++ -MF .deps/FileIO.Tpo -c src/FileIO.cc -o FileIO.o In file included from ./include/trivials.h:42, from ./templates/SimpleArray.h:23, from ./include/MString.h:24, from ./include/Path.h:23, from ./include/FileIO.h:26, from src/FileIO.cc:21: ./templates/miscTemplateFunc.h: In function `Histogram& add(Histogram&, const SimpleArray&)': ./templates/miscTemplateFunc.h:102: error: invalid use of undefined type `struct Histogram' ./templates/miscTemplateFunc.h:28: error: forward declaration of `struct Histogram' In file included from ./include/MString.h:24, from ./include/Path.h:23, from ./include/FileIO.h:26, from src/FileIO.cc:21: ./templates/SimpleArray.h: In member function `unsigned int SimpleArray::occurrencesOf(Type) const': ./templates/SimpleArray.h:100: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h:100: error: (Each undeclared identifier is reported only once for each function it appears in.) ./templates/SimpleArray.h: In member function `int SimpleArray::indexOf(Type, int) const': ./templates/SimpleArray.h:106: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsort(int (*)(const void*, const void*))': ./templates/SimpleArray.h:130: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:130: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsortAscending()': ./templates/SimpleArray.h:132: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:132: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsortDescending()': ./templates/SimpleArray.h:134: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:134: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `double SimpleArray::mean() const': ./templates/SimpleArray.h:144: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `SimpleArray SimpleArray::operator-() const': ./templates/SimpleArray.h:190: error: `_size' undeclared (first use this function) make[1]: *** [FileIO.lo] Error 1 make[1]: Leaving directory `/DISTRIBUTION/MNI_SOFTWARE/EBTKS-1.3' make: *** [all] Error 2 |-----Original Message----- |From: Robert VINCENT [mailto:bert@bic.mni.mcgill.ca] |Sent: Wednesday, March 09, 2005 1:15 AM |To: hpkim@bme.hanyang.ac.kr |Subject: RE: [MINC-users] Running MNI software on SGI Intel 64bits |LinuxMachine (IA64) | |Hi Phil, | |We have already fixed the issue in N3 and are working on a new release |that incorporates this fix. | |I was not aware of any problem in MINC's image_conversion.c. Can you give |me some description of the problem and what changes you had to make? | |If you are having other problems I would be happy to get more of the |details so that we can try to correct them! | | -bert | |On Tue, 8 Mar 2005, ??? wrote: | |> Dear Morgan, |> |> I am trying to build almost every tool from MNI (public or private). And |I |> found that there are numerous problems out there for compiling, |installing, |> and running MNI Software and needed libraries on GNU/Linux/x86/x86_64 |> combinations. I hope that people have more interest in Intel/GNU/Linux |> boxes. :) |> |> ######################################### |> F.Y.I. from my personal correspondence: |> |> We had to patch: |> |> N3 -> extracttag.c |> . "-mintags", ARGV_LONG, (char *) NULL, (char *) &min_tags, . . "- |maxtags", |> ARGV_LONG, . |> |> Also, the following should be patched |> minc 1.3 -> image_conversion.c line 680~ |> /* Check for image dimension properties */ |> if ((icv_property>=MI_ICV_DIM_START) && |> (icv_property idim = icv_property - MI_ICV_DIM_START; |> *value = icvp->derv_dim_start[idim]; |> } |> else if ((icv_property>=MI_ICV_DIM_STEP) && |> (icv_property idim = icv_property - MI_ICV_DIM_STEP; |> *value = icvp->derv_dim_step[idim]; |> } |> else if ((icv_property>=MI_ICV_DIM_SIZE) && |> (icv_property idim = icv_property - MI_ICV_DIM_SIZE; |> *value = icvp->user_dim_size[idim]; |> } |> |> |> ...... |> |> CGAL 2.4 package for mni_surfreg. However I needed additional patch again |to |> work around a problem. That seems to be compatibility problems between |> IRIS(n32? n64?) and GCC/G++. |> |> I had to link following object for building shared library to work around |> 'hidden symbols not found in libCGAL.so error'. This might not be safe. |> |> static void init(){} |> static void fini(){} |> static void preinit(){} |> |> typedef void (*fp)(); |> fp __init_array_start[]={init}; |> fp __init_array_end[]={init}; |> fp __fini_array_start[]={fini}; |> fp __fini_array_end[]={fini}; |> fp __preinit_array_start[]={preinit}; |> fp __preinit_array_end[]={preinit}; |> ############################################ |> |> And some of the software working on x86_32 machine does not work properly |on |> an IA64 machine. |> |> Regards, |> Phil. |> |> |> |-----Original Message----- |> |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |> |admin@bic.mni.mcgill.ca] On Behalf Of Morgan Hough |> |Sent: Friday, March 04, 2005 6:49 PM |> |To: Hyun-Pil Kim |> |Cc: minc-users@bic.mni.mcgill.ca |> |Subject: Re: [MINC-users] Running MNI software on SGI Intel 64bits |> |LinuxMachine (IA64) |> | |> |Phil, |> | |> |You might be the first person to try this as I think MNI only supports |> |IRIX/MIPS builds for SGIs (I could be wrong). I assume you are |> |downloading the source and using the autoconf build process which you |> |say is working without any errors. Can you say anything more about the |> |differences you have been seeing versus Linux/x86? Which tools have you |> |been building? Do you use the Intel compiler or GCC? Is that a 2.4 or |> |2.6 kernel (I have heard they backported 2.6 features to 2.4 for some |> |of their system configurations)? |> | |> |We are thinking about getting one of these systems and I am interested |> |to hear more about the issues you are having. |> | |> |Cheers, |> | |> |-Morgan |> | |> |-- |> |Morgan Hough DPhil student |> |FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK |> |mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 |> |222545 fax +44 (0) 1865 222717 |> | |> |On Tue, 2005-03-01 at 06:14, Hyun-Pil Kim wrote: |> |> |> |> |> |> Recently I've been trying to use MNI tools on a Itanium2 based SGI |> |> Linux machine. |> |> |> |> (SIG Altix 350) All software and firmware are up-to-date but I don't |> |> get it work correctly. |> |> |> |> There seems to be no problems while installation, however, I don't |> |> get consistent results with those of 32bit based Fedora boxes. |> |> Anybody have an idea? |> |> |> |> |> |> |> |> Regards, |> |> |> |> Phil |> |> |> |> *------------------------------------------------* |> |> Hyun-Pil Kim, |> |> Computational Neuroimage Analysis Lab., Dept. of Biomedical |> |> Engineering, Hanyang Univ. |> |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> |> Mobile: +82-19-286-0485 |> |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> |> *------------------------------------------------* |> |> |> |> |> |> |> | |> | |> |_______________________________________________ |> |MINC-users@bic.mni.mcgill.ca |> |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> From minc-users@bic.mni.mcgill.ca Thu Mar 10 20:40:04 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Thu Mar 10 20:40:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: Message-ID: <1110505141973128.25142@webmail> Sure. I'd be happy to test it. I am running Linux, though. Phil |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Robert VINCENT |Sent: Friday, March 11, 2005 7:38 AM |To: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? | |Hi, | |I'm working on a new version of Peter Neelin and Rick Hoge's "dcm2mnc" |utility that may work for Philips files. I would be happy to have you |test it when I'm ready to release a test version (probably in the next |few days). You are running on IRIX, yes? | | -bert | |On Tue, 8 Mar 2005, Hyun-Pil Kim wrote: | |> Is there any working version of dicom to minc converter for Phillips dcm |> files? |> |> The most recent version of dicom3_to_minc utility didn't work for me. |> |> After some googling, I found phil_to_minc but somehow the link is not |> present. |> |> http://www.cmr.uq.edu.au/~rotor/minc/ |> |> |> |> Thanks, |> |> Phil. |> |> *------------------------------------------------* |> Hyun-Pil Kim, |> Computational Neuroimage Analysis Lab., |> Dept. of Biomedical Engineering, Hanyang Univ. |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> Mobile: +82-19-286-0485 |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> *------------------------------------------------* |> |> |> |> | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Mar 11 03:38:05 2005 From: minc-users@bic.mni.mcgill.ca (Kuan H. Kho) Date: Fri Mar 11 03:38:05 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <1110281812181263.19332@webmail> References: <1110281812181263.19332@webmail> Message-ID: --============_-1101592050==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" If you're working with Philips scanners, you might want to reconstruct the scans and have them as raw files, ie *.PAR and *.REC files (instead of the tedious DICOM). This is an option of the scanner software. The *.PAR file serves as a header to the *.REC file (raw) which can easily be converted into minc, or any other file type. (for minc, use rawtominc etc etc), and the parameters (voxelsize, # of dynamics etc) should be checked! This works finereally works well! Keep on the good work, best, Kuan -- Kuan H. Kho, MD Depts. of Psychiatry & Neurosurgery, G03.124 University Medical Center Utrecht Heidelberglaan 100 P.O.Box 85500 3508 GA Utrecht The Netherlands P +31-30-2507969/2507953 F +31-30-2542100 E k.h.kho_'at'_azu.nl >Is there any working version of dicom to minc converter for Phillips >dcm files? >The most recent version of dicom3_to_minc utility didn't work for me. >After some googling, I found phil_to_minc but somehow the link is not present. >http://www.cmr.uq.edu.au/~rotor/minc/ > >Thanks, >Phil. --============_-1101592050==_ma============ Content-Type: text/html; charset="us-ascii" Re: [MINC-users] Dicom to Minc converter for Phillips ?
If you're working with Philips scanners, you might want to reconstruct the scans and have them as raw files, ie *.PAR and *.REC files (instead of the tedious DICOM). This is an option of the scanner software. The *.PAR file serves as a header to the *.REC file (raw) which can easily be converted into minc, or any other file type. (for minc, use rawtominc etc etc), and the parameters (voxelsize, # of dynamics etc) should be checked! This works finereally works well!
Keep on the good work,
best,
Kuan
--
Kuan H. Kho, MD

Depts. of Psychiatry & Neurosurgery, G03.124
University Medical Center Utrecht
Heidelberglaan 100
P.O.Box 85500
3508 GA Utrecht
The Netherlands

P +31-30-2507969/2507953
F +31-30-2542100
E k.h.kho_'at'_azu.nl


Is there any working version of dicom to minc converter for Phillips dcm files?
The most recent version of dicom3_to_minc utility didn't work for me.
After some googling, I found phil_to_minc but somehow the link is not present.
http://www.cmr.uq.edu.au/~rotor/minc/
 
Thanks,
Phil.


--============_-1101592050==_ma============-- From minc-users@bic.mni.mcgill.ca Fri Mar 11 07:37:04 2005 From: minc-users@bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri Mar 11 07:37:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <1110281812181263.19332@webmail> References: <1110281812181263.19332@webmail> Message-ID: <20050311123644.GA2302233@bic.mni.mcgill.ca> Hi, If you have a sample Philips dcm file you can send me, I can look to see what kind of fix to dicom3_to_minc would make it work for you... It's also always useful for us to have "problem" data for testing new versions of the converters. Cheers, Jon On Tue, Mar 08, 2005 at 08:35:08PM +0900, Hyun-Pil Kim wrote: > > Is there any working version of dicom to minc converter for Phillips > dcm files? > > The most recent version of dicom3_to_minc utility didn’t work > for me. > > After some googling, I found phil_to_minc but somehow the link is not > present. > > [1]http://www.cmr.uq.edu.au/~rotor/minc/ > > > > Thanks, > > Phil. > > *------------------------------------------------* > Hyun-Pil Kim, > Computational Neuroimage Analysis Lab., > Dept. of Biomedical Engineering, Hanyang Univ. > Sungdong P.O. Box 55, Seoul, 133-605, KOREA > Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > Mobile: +82-19-286-0485 > E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > *------------------------------------------------* > > References > > 1. http://www.cmr.uq.edu.au/~rotor/minc/ From minc-users@bic.mni.mcgill.ca Fri Mar 11 07:55:04 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Fri Mar 11 07:55:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <20050311123644.GA2302233@bic.mni.mcgill.ca> Message-ID: <1110545650781843.7504@webmail> Hi Jon, I can send you the files only if you remove them after using testing purpose. Just let me know where to upload them. Thanks, Phil |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Jonathan HARLAP |Sent: Friday, March 11, 2005 9:37 PM |To: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? | |Hi, | |If you have a sample Philips dcm file you can send me, I can look to |see what kind of fix to dicom3_to_minc would make it work for you... |It's also always useful for us to have "problem" data for testing new |versions of the converters. | |Cheers, |Jon | | | |On Tue, Mar 08, 2005 at 08:35:08PM +0900, Hyun-Pil Kim wrote: |> |> Is there any working version of dicom to minc converter for Phillips |> dcm files? |> |> The most recent version of dicom3_to_minc utility didn’t work |> for me. |> |> After some googling, I found phil_to_minc but somehow the link is not |> present. |> |> [1]http://www.cmr.uq.edu.au/~rotor/minc/ |> |> |> |> Thanks, |> |> Phil. |> |> *------------------------------------------------* |> Hyun-Pil Kim, |> Computational Neuroimage Analysis Lab., |> Dept. of Biomedical Engineering, Hanyang Univ. |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> Mobile: +82-19-286-0485 |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> *------------------------------------------------* |> |> References |> |> 1. http://www.cmr.uq.edu.au/~rotor/minc/ |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Mar 11 09:25:04 2005 From: minc-users@bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri Mar 11 09:25:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <1110545650781843.7504@webmail> References: <20050311123644.GA2302233@bic.mni.mcgill.ca> <1110545650781843.7504@webmail> Message-ID: <20050311142433.GA2271074@bic.mni.mcgill.ca> It seems that your dcm files have the ImageOrientationPatient (0x20,0x37) field filled in, but not the ImagePositionPatient (0x20,0x32). dicom3_to_minc uses both these fields in order to determine the slice position in the out of slice dimension... There is an option (-ignore_positions) in dicom3_to_minc which lets you tell it to use the image number instead of the slice position, which I had added specifically to handle cases where slice position could not be calculated properly, with the caveat that your step in the out of slice dimension will be 1mm (assuming consecutive image numbers) instead of whatever it should really be, and the start coordinate in that dimension will be wrong. However, a simple header hack could fix that. There also seems to be a field SliceLocation (0x20,0x1041) which your data contains, but the values are not unique across the range of slices, so it would be difficult to use that, as dicom3_to_minc would complain of duplicate slices at a given position, and proceed to ignore all but one slice at each position. I'm open to suggestions if you can think of a sensible way to handle this kind of data... Cheers, Jon On Fri, Mar 11, 2005 at 09:52:48PM +0900, Hyun-Pil Kim wrote: > Hi Jon, > > I can send you the files only if you remove them after using testing > purpose. Just let me know where to upload them. > > Thanks, > Phil > |-----Original Message----- > |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- > |admin@bic.mni.mcgill.ca] On Behalf Of Jonathan HARLAP > |Sent: Friday, March 11, 2005 9:37 PM > |To: minc-users@bic.mni.mcgill.ca > |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? > | > |Hi, > | > |If you have a sample Philips dcm file you can send me, I can look to > |see what kind of fix to dicom3_to_minc would make it work for you... > |It's also always useful for us to have "problem" data for testing new > |versions of the converters. > | > |Cheers, > |Jon > | > | > | > |On Tue, Mar 08, 2005 at 08:35:08PM +0900, Hyun-Pil Kim wrote: > |> > |> Is there any working version of dicom to minc converter for Phillips > |> dcm files? > |> > |> The most recent version of dicom3_to_minc utility didn’t work > |> for me. > |> > |> After some googling, I found phil_to_minc but somehow the link is not > |> present. > |> > |> [1]http://www.cmr.uq.edu.au/~rotor/minc/ > |> > |> > |> > |> Thanks, > |> > |> Phil. > |> > |> *------------------------------------------------* > |> Hyun-Pil Kim, > |> Computational Neuroimage Analysis Lab., > |> Dept. of Biomedical Engineering, Hanyang Univ. > |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA > |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > |> Mobile: +82-19-286-0485 > |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > |> *------------------------------------------------* > |> > |> References > |> > |> 1. http://www.cmr.uq.edu.au/~rotor/minc/ > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Mar 11 11:02:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri Mar 11 11:02:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <1110505141973128.25142@webmail> Message-ID: Hi Phil, Here is a link to the current version of the converter, built for linux: http://www.bic.mni.mcgill.ca/~bert/dcm2mnc-2.0.001-i386-linux.tar.gz Please give it a try and let me know of any problems. The output of the converter run with the -verbose or -debug option will be very useful in the event of problems. -bert On Fri, 11 Mar 2005, Hyun-Pil Kim wrote: > Sure. I'd be happy to test it. I am running Linux, though. > > Phil > > |-----Original Message----- > |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- > |admin@bic.mni.mcgill.ca] On Behalf Of Robert VINCENT > |Sent: Friday, March 11, 2005 7:38 AM > |To: minc-users@bic.mni.mcgill.ca > |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? > | > |Hi, > | > |I'm working on a new version of Peter Neelin and Rick Hoge's "dcm2mnc" > |utility that may work for Philips files. I would be happy to have you > |test it when I'm ready to release a test version (probably in the next > |few days). You are running on IRIX, yes? > | > | -bert > | > |On Tue, 8 Mar 2005, Hyun-Pil Kim wrote: > | > |> Is there any working version of dicom to minc converter for Phillips dcm > |> files? > |> > |> The most recent version of dicom3_to_minc utility didn't work for me. > |> > |> After some googling, I found phil_to_minc but somehow the link is not > |> present. > |> > |> http://www.cmr.uq.edu.au/~rotor/minc/ > |> > |> > |> > |> Thanks, > |> > |> Phil. > |> > |> *------------------------------------------------* > |> Hyun-Pil Kim, > |> Computational Neuroimage Analysis Lab., > |> Dept. of Biomedical Engineering, Hanyang Univ. > |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA > |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 > |> Mobile: +82-19-286-0485 > |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com > |> *------------------------------------------------* > |> > |> > |> > |> > | > |_______________________________________________ > |MINC-users@bic.mni.mcgill.ca > |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Fri Mar 11 18:22:03 2005 From: minc-users@bic.mni.mcgill.ca (Joongnam Yang) Date: Fri Mar 11 18:22:03 2005 Subject: [MINC-users] *.mnc to *.img Message-ID: Hi all, ana2mnc (or rawtominc) turns *.img into *.mnc. Is there a tool that does the opposite? I have a *.mnc file and want to turn it into *.img file. Thanks for comments. Nam. From minc-users@bic.mni.mcgill.ca Fri Mar 11 18:30:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri Mar 11 18:30:04 2005 Subject: [MINC-users] *.mnc to *.img In-Reply-To: Message-ID: Hi, Yes, there is a mnc2ana tool available as part of Andrew Janke's converters for Analyze format: http://www.cmr.uq.edu.au/~rotor/software/ -bert On Fri, 11 Mar 2005, Joongnam Yang wrote: > Hi all, > > ana2mnc (or rawtominc) turns *.img into *.mnc. > Is there a tool that does the opposite? > I have a *.mnc file and want to turn it into *.img file. > > Thanks for comments. > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Fri Mar 11 19:26:04 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Fri Mar 11 19:26:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: Message-ID: <1110587142256375.31702@webmail> This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C526E5.45122330 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi bert, I tested it but it crashed. Here I attach the standard io captured. Also I can send you the dicom files in case you need it for debugging. $ ../../dcm2mnc -debug CM17/*dcm . >& result.txt Thanks, Phil. |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Robert VINCENT |Sent: Saturday, March 12, 2005 1:01 AM |To: minc-users@bic.mni.mcgill.ca |Subject: RE: [MINC-users] Dicom to Minc converter for Phillips ? | |Hi Phil, | |Here is a link to the current version of the converter, built for linux: | |http://www.bic.mni.mcgill.ca/~bert/dcm2mnc-2.0.001-i386-linux.tar.gz | |Please give it a try and let me know of any problems. The output of the |converter run with the -verbose or -debug option will be very useful in |the event of problems. | | -bert | |On Fri, 11 Mar 2005, Hyun-Pil Kim wrote: | |> Sure. I'd be happy to test it. I am running Linux, though. |> |> Phil |> |> |-----Original Message----- |> |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |> |admin@bic.mni.mcgill.ca] On Behalf Of Robert VINCENT |> |Sent: Friday, March 11, 2005 7:38 AM |> |To: minc-users@bic.mni.mcgill.ca |> |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? |> | |> |Hi, |> | |> |I'm working on a new version of Peter Neelin and Rick Hoge's "dcm2mnc" |> |utility that may work for Philips files. I would be happy to have you |> |test it when I'm ready to release a test version (probably in the next |> |few days). You are running on IRIX, yes? |> | |> | -bert |> | |> |On Tue, 8 Mar 2005, Hyun-Pil Kim wrote: |> | |> |> Is there any working version of dicom to minc converter for Phillips |dcm |> |> files? |> |> |> |> The most recent version of dicom3_to_minc utility didn't work for me. |> |> |> |> After some googling, I found phil_to_minc but somehow the link is not |> |> present. |> |> |> |> http://www.cmr.uq.edu.au/~rotor/minc/ |> |> |> |> |> |> |> |> Thanks, |> |> |> |> Phil. |> |> |> |> *------------------------------------------------* |> |> Hyun-Pil Kim, |> |> Computational Neuroimage Analysis Lab., |> |> Dept. of Biomedical Engineering, Hanyang Univ. |> |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> |> Mobile: +82-19-286-0485 |> |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> |> *------------------------------------------------* |> |> |> |> |> |> |> |> |> | |> |_______________________________________________ |> |MINC-users@bic.mni.mcgill.ca |> |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> | |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users ------=_NextPart_000_001C_01C526E5.45122330 Content-Type: application/x-compressed; name="result.txt.tgz" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="result.txt.tgz" H4sIAN4zMkIAA+2c62/bRhbF85l/xaAF+gAchfOeMZAPqdMW6TYPxO2myWJhsBLtcGORLknXyX+/ 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------=_NextPart_000_001C_01C526E5.45122330-- From minc-users@bic.mni.mcgill.ca Fri Mar 11 19:55:04 2005 From: minc-users@bic.mni.mcgill.ca (Hyun-Pil Kim) Date: Fri Mar 11 19:55:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <20050311142433.GA2271074@bic.mni.mcgill.ca> Message-ID: <1110588858550942.14465@webmail> I've tested the -ignore_positions option and it complained about reading slice position but somehow it worked. Besides, I ran tests using Analyze. Import/export module of Analyze told something about SliceLocation order. Guessing by the output images, there might be a trouble with processing interleaved slice orders. I'll send you the captured images using the mni upload gateway. I am sure that you can come with a good way of processing interleaved slices. Thanks, Phil. |-----Original Message----- |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |admin@bic.mni.mcgill.ca] On Behalf Of Jonathan HARLAP |Sent: Friday, March 11, 2005 11:25 PM |To: minc-users@bic.mni.mcgill.ca |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? | |It seems that your dcm files have the ImageOrientationPatient |(0x20,0x37) field filled in, but not the ImagePositionPatient |(0x20,0x32). dicom3_to_minc uses both these fields in order to |determine the slice position in the out of slice dimension... There |is an option (-ignore_positions) in dicom3_to_minc which lets you tell |it to use the image number instead of the slice position, which I had |added specifically to handle cases where slice position could not be |calculated properly, with the caveat that your step in the out of |slice dimension will be 1mm (assuming consecutive image numbers) |instead of whatever it should really be, and the start coordinate in |that dimension will be wrong. However, a simple header hack could fix |that. | |There also seems to be a field SliceLocation (0x20,0x1041) which your |data contains, but the values are not unique across the range of |slices, so it would be difficult to use that, as dicom3_to_minc would |complain of duplicate slices at a given position, and proceed to |ignore all but one slice at each position. | |I'm open to suggestions if you can think of a sensible way to handle |this kind of data... | |Cheers, |Jon | | |On Fri, Mar 11, 2005 at 09:52:48PM +0900, Hyun-Pil Kim wrote: |> Hi Jon, |> |> I can send you the files only if you remove them after using testing |> purpose. Just let me know where to upload them. |> |> Thanks, |> Phil |> |-----Original Message----- |> |From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users- |> |admin@bic.mni.mcgill.ca] On Behalf Of Jonathan HARLAP |> |Sent: Friday, March 11, 2005 9:37 PM |> |To: minc-users@bic.mni.mcgill.ca |> |Subject: Re: [MINC-users] Dicom to Minc converter for Phillips ? |> | |> |Hi, |> | |> |If you have a sample Philips dcm file you can send me, I can look to |> |see what kind of fix to dicom3_to_minc would make it work for you... |> |It's also always useful for us to have "problem" data for testing new |> |versions of the converters. |> | |> |Cheers, |> |Jon |> | |> | |> | |> |On Tue, Mar 08, 2005 at 08:35:08PM +0900, Hyun-Pil Kim wrote: |> |> |> |> Is there any working version of dicom to minc converter for |Phillips |> |> dcm files? |> |> |> |> The most recent version of dicom3_to_minc utility didn’t work |> |> for me. |> |> |> |> After some googling, I found phil_to_minc but somehow the link is |not |> |> present. |> |> |> |> [1]http://www.cmr.uq.edu.au/~rotor/minc/ |> |> |> |> |> |> |> |> Thanks, |> |> |> |> Phil. |> |> |> |> *------------------------------------------------* |> |> Hyun-Pil Kim, |> |> Computational Neuroimage Analysis Lab., |> |> Dept. of Biomedical Engineering, Hanyang Univ. |> |> Sungdong P.O. Box 55, Seoul, 133-605, KOREA |> |> Tel: +82-2-2290-0697; FAX: +82-2-2296-5943 |> |> Mobile: +82-19-286-0485 |> |> E-mail: hpkim at ihanyang.ac.kr; aimtop77 at empal.com |> |> *------------------------------------------------* |> |> |> |> References |> |> |> |> 1. http://www.cmr.uq.edu.au/~rotor/minc/ |> |_______________________________________________ |> |MINC-users@bic.mni.mcgill.ca |> |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |> |> _______________________________________________ |> MINC-users@bic.mni.mcgill.ca |> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users |_______________________________________________ |MINC-users@bic.mni.mcgill.ca |http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Tue Mar 15 17:04:06 2005 From: minc-users@bic.mni.mcgill.ca (Nameeta Lobo) Date: Tue Mar 15 17:04:06 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc Message-ID: <1110920365.42374cad516d4@netmail.bsd.uchicago.edu> Hello all, I am a newbie to this software. I have AFNI datasets which I want to convert to the MNC format. I used the 3dAFNItoMINC command and converted a structural to the mnc format and viewed it using mincview (which needed xv) as well as using Display. I could see all the 3 views with Display which was good but with mincview could see just one view . I want to look at my functional data too. I have been going through your web page and came across Register. My question is how do I view my functional data as an overlay on my structural. Should I be using the 3dAFNItoMINC command, converting this functional data into mnc and then use Register and merge the 2 datasets (structural and functional) or am I totally off on this one. If yes, could you please give me some suggestions as to how to go about working on this data. Any help will be really appreciated. thanks N From minc-users@bic.mni.mcgill.ca Wed Mar 16 11:07:04 2005 From: minc-users@bic.mni.mcgill.ca (Nameeta Lobo) Date: Wed Mar 16 11:07:04 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc In-Reply-To: References: Message-ID: <1110989227.423859ab94d96@netmail.bsd.uchicago.edu> Hi Najmeh, Thank you for that detailed explanation. However, I am having problems trying to find the minc4dim3 command and the xdisp software. We have the 1.3 version of MINC but I dont seem to find the above command anywhere. Also, where could I get xdisp from? The only thing that I could find on google was something that I had to sign up a lot for. Also, is there any other statistical analysis I should be carrying out on my funtional data. I have just used deconvolution in AFNI and as I mentioned in my previous e-mail, used the 3dAFNItoMINC to convert it. My data is in the short format and has 43 sub bricks in AFNI. running the mincinfo command on this minc functional data gives me the following. mincinfo story_motion_new.mnc file: story_motion_new.mnc image: signed__ float -4270.3427734375 to 287392.3125 image dimensions: time xspace zspace yspace dimension name length step start -------------- ------ ---- ----- time 44 unknown unknown xspace 30 5 -71.1 zspace 64 -3.75 118.125 yspace 64 -3.75 133.825 with the original 3dinfo story_motion_new+orig.BRIK command line in AFNI gives me Dataset File: story_motion_new+orig Identifier Code: XYZ_NLmqlhuH1PInWR8tBL7qRg Creation Date: Wed Oct 13 15:46:39 2004 Dataset Type: Func-Bucket (-fbuc) Byte Order: LSB_FIRST [this CPU native = LSB_FIRST] Storage Mode: BRIK file Data Axes Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Left-to-Right [-orient ASL] R-to-L extent: -73.900 [R] -to- 71.100 [L] -step- 5.000 mm [ 30 voxels]A-to-P extent: -133.825 [A] -to- 102.425 [P] -step- 3.750 mm [ 64 voxels]I-to-S extent: -118.125 [I] -to- 118.125 [S] -step- 3.750 mm [ 64 voxels]Number of values stored at each pixel = 44 with values then printed for every sub brick. so far this is all that I have with me as I cannot view the minc funtional data yet. Please do help and thank you for your time. nameeta Quoting "Najmeh Khalili M." : > > Hi Nameeta, > > In order to use register, you need to have your functional data analyzed > and the dimension reduced from 4D to 3D. > > Once you have your functional t-maps or effects in minc you just call > > register structural.mnc functional-tmap.mnc > > In register you can synchronize the functional and the structral and set > the threshold of your t-values, put labels, and obtain stereotaxic > coordinates. > > Of course, display has more functionality but it is poorly documented and > not too trivial to work with. It's very well worth exploring because it > allows you to pain labels and to get 3D views of brain surface and etc. > > If you want to look at your time-series, ie 4D fMRI data, use xdisp. It > allows you to eyeball motion artifacts ans activations, but it does not > ovrlay your functional data on anatomical data. > > Hope this helps, > Naj > > > > > On Tue, 15 Mar 2005, Nameeta Lobo wrote: > > > > > Hello all, > > > > I am a newbie to this software. I have AFNI datasets which I want to > convert to > > the MNC format. I used the 3dAFNItoMINC command and converted a structural > to > > the mnc format and viewed it using mincview (which needed xv) as well as > using > > Display. I could see all the 3 views with Display which was good but with > > mincview could see just one view . I want to look at my functional data > too. I > > have been going through your web page and came across Register. My question > is > > how do I view my functional data as an overlay on my structural. Should I > be > > using the 3dAFNItoMINC command, converting this functional data into mnc > and > > then use Register and merge the 2 datasets (structural and functional) or > am I > > totally off on this one. If yes, could you please give me some suggestions > as to > > how to go about working on this data. Any help will be really > appreciated. > > > > thanks > > N > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > From minc-users@bic.mni.mcgill.ca Wed Mar 16 11:47:05 2005 From: minc-users@bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Wed Mar 16 11:47:05 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc In-Reply-To: <1110989227.423859ab94d96@netmail.bsd.uchicago.edu> Message-ID: > Thank you for that detailed explanation. However, I am having problems trying to > find the minc4dim3 command and the xdisp software. We have the 1.3 version of > MINC but I dont seem to find the above command anywhere. Also, where could I get > xdisp from? The only thing that I could find on google was something that I had > to sign up a lot for. I don't think we have a minc4dim3 command. What I suggested was that after statistical analyses, your 4D fMRI volume will be reduced to a 3D statistical map. Please take a look at visualization tools in www.bic.mni.mcgill.ca/software. postf and xdisp should be a part of minc package. Also, it appears that your afni-to-minc conversion does not specify the temporal dimension of your data. I am not familiar with AFNI format, bt I cannot decipher the time-step/start from the 3dinfo output that you have printed below either. N. > > Also, is there any other statistical analysis I should be carrying out on my > funtional data. I have just used deconvolution in AFNI and as I mentioned in my > previous e-mail, used the 3dAFNItoMINC to convert it. My data is in the short > format and has 43 sub bricks in AFNI. > > running the mincinfo command on this minc functional data gives me the following. > > mincinfo story_motion_new.mnc > file: story_motion_new.mnc > image: signed__ float -4270.3427734375 to 287392.3125 > image dimensions: time xspace zspace yspace > dimension name length step start > -------------- ------ ---- ----- > time 44 unknown unknown > xspace 30 5 -71.1 > zspace 64 -3.75 118.125 > yspace 64 -3.75 133.825 > > with the original 3dinfo story_motion_new+orig.BRIK command line in AFNI gives me > Dataset File: story_motion_new+orig > Identifier Code: XYZ_NLmqlhuH1PInWR8tBL7qRg Creation Date: Wed Oct 13 15:46:39 2004 > Dataset Type: Func-Bucket (-fbuc) > Byte Order: LSB_FIRST [this CPU native = LSB_FIRST] > Storage Mode: BRIK file > Data Axes Orientation: > first (x) = Anterior-to-Posterior > second (y) = Superior-to-Inferior > third (z) = Left-to-Right [-orient ASL] > R-to-L extent: -73.900 [R] -to- 71.100 [L] -step- 5.000 mm [ 30 > voxels]A-to-P extent: -133.825 [A] -to- 102.425 [P] -step- 3.750 mm [ 64 > voxels]I-to-S extent: -118.125 [I] -to- 118.125 [S] -step- 3.750 mm [ 64 > voxels]Number of values stored at each pixel = 44 > > with values then printed for every sub brick. > > so far this is all that I have with me as I cannot view the minc funtional data > yet. Please do help and thank you for your time. > > nameeta > > > > > > > Quoting "Najmeh Khalili M." : > > > > > Hi Nameeta, > > > > In order to use register, you need to have your functional data analyzed > > and the dimension reduced from 4D to 3D. > > > > Once you have your functional t-maps or effects in minc you just call > > > > register structural.mnc functional-tmap.mnc > > > > In register you can synchronize the functional and the structral and set > > the threshold of your t-values, put labels, and obtain stereotaxic > > coordinates. > > > > Of course, display has more functionality but it is poorly documented and > > not too trivial to work with. It's very well worth exploring because it > > allows you to pain labels and to get 3D views of brain surface and etc. > > > > If you want to look at your time-series, ie 4D fMRI data, use xdisp. It > > allows you to eyeball motion artifacts ans activations, but it does not > > ovrlay your functional data on anatomical data. > > > > Hope this helps, > > Naj > > > > > > > > > > On Tue, 15 Mar 2005, Nameeta Lobo wrote: > > > > > > > > Hello all, > > > > > > I am a newbie to this software. I have AFNI datasets which I want to > > convert to > > > the MNC format. I used the 3dAFNItoMINC command and converted a structural > > to > > > the mnc format and viewed it using mincview (which needed xv) as well as > > using > > > Display. I could see all the 3 views with Display which was good but with > > > mincview could see just one view . I want to look at my functional data > > too. I > > > have been going through your web page and came across Register. My question > > is > > > how do I view my functional data as an overlay on my structural. Should I > > be > > > using the 3dAFNItoMINC command, converting this functional data into mnc > > and > > > then use Register and merge the 2 datasets (structural and functional) or > > am I > > > totally off on this one. If yes, could you please give me some suggestions > > as to > > > how to go about working on this data. Any help will be really > > appreciated. > > > > > > thanks > > > N From minc-users@bic.mni.mcgill.ca Wed Mar 16 12:00:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Wed Mar 16 12:00:04 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc In-Reply-To: Message-ID: Hi, Andrew Janke and I are working to get postf and xdisp in distributable form. They are not currently available on the website. I'm also working on a new version of Register which will allow viewing of 4D and 3D data alongside one another. -bert On Wed, 16 Mar 2005, Najmeh Khalili M. wrote: > > > Thank you for that detailed explanation. However, I am having problems trying to > > find the minc4dim3 command and the xdisp software. We have the 1.3 version of > > MINC but I dont seem to find the above command anywhere. Also, where could I get > > xdisp from? The only thing that I could find on google was something that I had > > to sign up a lot for. > > I don't think we have a minc4dim3 command. What I suggested was that after > statistical analyses, your 4D fMRI volume will be reduced to a 3D > statistical map. > > Please take a look at visualization tools in > www.bic.mni.mcgill.ca/software. postf and xdisp should be a part of minc > package. > > Also, it appears that your afni-to-minc conversion does not specify the > temporal dimension of your data. I am not familiar with AFNI format, bt I > cannot decipher the time-step/start from the 3dinfo output that you > have printed below either. > > N. > > > > > Also, is there any other statistical analysis I should be carrying out on my > > funtional data. I have just used deconvolution in AFNI and as I mentioned in my > > previous e-mail, used the 3dAFNItoMINC to convert it. My data is in the short > > format and has 43 sub bricks in AFNI. > > > > running the mincinfo command on this minc functional data gives me the following. > > > > mincinfo story_motion_new.mnc > > file: story_motion_new.mnc > > image: signed__ float -4270.3427734375 to 287392.3125 > > image dimensions: time xspace zspace yspace > > dimension name length step start > > -------------- ------ ---- ----- > > time 44 unknown unknown > > xspace 30 5 -71.1 > > zspace 64 -3.75 118.125 > > yspace 64 -3.75 133.825 > > > > with the original 3dinfo story_motion_new+orig.BRIK command line in AFNI gives me > > Dataset File: story_motion_new+orig > > Identifier Code: XYZ_NLmqlhuH1PInWR8tBL7qRg Creation Date: Wed Oct 13 15:46:39 2004 > > Dataset Type: Func-Bucket (-fbuc) > > Byte Order: LSB_FIRST [this CPU native = LSB_FIRST] > > Storage Mode: BRIK file > > Data Axes Orientation: > > first (x) = Anterior-to-Posterior > > second (y) = Superior-to-Inferior > > third (z) = Left-to-Right [-orient ASL] > > R-to-L extent: -73.900 [R] -to- 71.100 [L] -step- 5.000 mm [ 30 > > voxels]A-to-P extent: -133.825 [A] -to- 102.425 [P] -step- 3.750 mm [ 64 > > voxels]I-to-S extent: -118.125 [I] -to- 118.125 [S] -step- 3.750 mm [ 64 > > voxels]Number of values stored at each pixel = 44 > > > > with values then printed for every sub brick. > > > > so far this is all that I have with me as I cannot view the minc funtional data > > yet. Please do help and thank you for your time. > > > > nameeta > > > > > > > > > > > > > > Quoting "Najmeh Khalili M." : > > > > > > > > Hi Nameeta, > > > > > > In order to use register, you need to have your functional data analyzed > > > and the dimension reduced from 4D to 3D. > > > > > > Once you have your functional t-maps or effects in minc you just call > > > > > > register structural.mnc functional-tmap.mnc > > > > > > In register you can synchronize the functional and the structral and set > > > the threshold of your t-values, put labels, and obtain stereotaxic > > > coordinates. > > > > > > Of course, display has more functionality but it is poorly documented and > > > not too trivial to work with. It's very well worth exploring because it > > > allows you to pain labels and to get 3D views of brain surface and etc. > > > > > > If you want to look at your time-series, ie 4D fMRI data, use xdisp. It > > > allows you to eyeball motion artifacts ans activations, but it does not > > > ovrlay your functional data on anatomical data. > > > > > > Hope this helps, > > > Naj > > > > > > > > > > > > > > > On Tue, 15 Mar 2005, Nameeta Lobo wrote: > > > > > > > > > > > Hello all, > > > > > > > > I am a newbie to this software. I have AFNI datasets which I want to > > > convert to > > > > the MNC format. I used the 3dAFNItoMINC command and converted a structural > > > to > > > > the mnc format and viewed it using mincview (which needed xv) as well as > > > using > > > > Display. I could see all the 3 views with Display which was good but with > > > > mincview could see just one view . I want to look at my functional data > > > too. I > > > > have been going through your web page and came across Register. My question > > > is > > > > how do I view my functional data as an overlay on my structural. Should I > > > be > > > > using the 3dAFNItoMINC command, converting this functional data into mnc > > > and > > > > then use Register and merge the 2 datasets (structural and functional) or > > > am I > > > > totally off on this one. If yes, could you please give me some suggestions > > > as to > > > > how to go about working on this data. Any help will be really > > > appreciated. > > > > > > > > thanks > > > > N > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Wed Mar 16 12:46:03 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Wed Mar 16 12:46:03 2005 Subject: [MINC-users] postf for X Message-ID: Hello intrepid MINC users, A few of you are still using Gabriel Leger's "postf" program for visualization of dynamic PET or fMRI data. I've just placed a new version of the program here: http://www.bic.mni.mcgill.ca/~bert/postf-1.0.02-test.tar.gz This code has been ported to the X Window System and should now compile and run on 32-bit Linux, SGI, and Mac OS X. A handy man page has been added to the distribution as well. If you're feeling brave, please download this code and give it a try. Let me know how it goes... -bert From cjb@pet.auh.dk Thu Mar 17 06:21:05 2005 From: cjb@pet.auh.dk (Christopher Bailey) Date: Thu Mar 17 06:21:05 2005 Subject: [MINC-users] postf for X In-Reply-To: References: Message-ID: <1111058403.24021.14.camel@kafka.pet.auh.dk> Hi, Thanks for postf; it is to my knowledge the only tool for visual inspection of dynamic minc data. Great that us linuces can also benefit! I had a compilation problem, which was solved by commenting out line 2696 in postf.c: postf.c: In function `main': postf.c:2696: error: `ARGV_VERINFO' undeclared (first use in this function) postf.c:2696: error: (Each undeclared identifier is reported only once postf.c:2696: error: for each function it appears in.) postf.c:2696: error: initializer element is not constant postf.c:2696: error: (near initialization for `argTable[0].type') ... all the way to `argTable[21].type'. My gcc is at 3.3.5. I never could really figure out the colormap scaling using the mouse; always end up getting inf's or nan's (rescued by 'r'). But in my linux compilation things seem to be even more difficult. I can get the lower limit to rise using the right mouse button, but nothing happens when using the left (apart from the occasional inf...). I went around this by using the (free) 't'-key to ask for limits manually (a la Display; can send diff of postf.c if anyone interested) since I couldn't figure out the X-commands... A related matter is that of the time-activity curve ('d'): Would it be possible to apply the scaling chosen in the colormap to that graph too? In the data I've been looking at there are huge recon artefacts at the edges, which then make the full range of the data ridiculous. A third feature I want to comment on is the ROI selector. In my compilation the centre of the ROI shifts as I increase it's radius. Actually, I think it's only the ROI displayed on screen that's "off", whereas the actual ROI applied to the data is "on-centre". This could be a simple thing to fix (but I couldn't see it...). Thanks again, -Chris -- Christopher Bailey PET Centre and Center for Functionally Integrative Neuroscience Aarhus University Hospital, Denmark http://www.cfin.au.dk/ On Wed, 2005-03-16 at 12:45 -0500, Robert VINCENT wrote: > Hello intrepid MINC users, > > A few of you are still using Gabriel Leger's "postf" program for > visualization of dynamic PET or fMRI data. I've just placed a new > version of the program here: > > http://www.bic.mni.mcgill.ca/~bert/postf-1.0.02-test.tar.gz > > This code has been ported to the X Window System and should now compile > and run on 32-bit Linux, SGI, and Mac OS X. A handy man page has been > added to the distribution as well. > > If you're feeling brave, please download this code and give it a try. Let > me know how it goes... > > -bert > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Thu Mar 17 09:50:03 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Mar 17 09:50:03 2005 Subject: [MINC-users] postf for X In-Reply-To: <1111058403.24021.14.camel@kafka.pet.auh.dk> Message-ID: Hi Christopher, Thanks for the comments. Actually, we have another tool for visualizing dynamic data, xdisp, which Andrew is close to releasing, and I have a preliminary dynamic version of Register which I will release shortly. The ARGV_VERINFO thing is a new (MINC 1.3 and after) thing for reporting program versions. You must still have MINC 1.2 or earlier installed. I'll add a protective #ifdef to avoid this problem in the future. The ROI and colormap issues you describe could be a result of my rewrite from GL to X - the rewrite required flipping the sense of the screen's Y coordinate, so some inconsistencies may have crept in. Thanks for you other suggestions, I'll take a look at them today. -bert On Thu, 17 Mar 2005, Christopher Bailey wrote: > > Hi, > > Thanks for postf; it is to my knowledge the only tool for visual > inspection of dynamic minc data. Great that us linuces can also benefit! > > I had a compilation problem, which was solved by commenting out line > 2696 in postf.c: > > postf.c: In function `main': > postf.c:2696: error: `ARGV_VERINFO' undeclared (first use in this > function) > postf.c:2696: error: (Each undeclared identifier is reported only once > postf.c:2696: error: for each function it appears in.) > postf.c:2696: error: initializer element is not constant > postf.c:2696: error: (near initialization for `argTable[0].type') > ... > > all the way to `argTable[21].type'. My gcc is at 3.3.5. > > I never could really figure out the colormap scaling using the mouse; > always end up getting inf's or nan's (rescued by 'r'). But in my linux > compilation things seem to be even more difficult. I can get the lower > limit to rise using the right mouse button, but nothing happens when > using the left (apart from the occasional inf...). > > I went around this by using the (free) 't'-key to ask for limits > manually (a la Display; can send diff of postf.c if anyone interested) > since I couldn't figure out the X-commands... A related matter is that > of the time-activity curve ('d'): Would it be possible to apply the > scaling chosen in the colormap to that graph too? In the data I've been > looking at there are huge recon artefacts at the edges, which then make > the full range of the data ridiculous. > > A third feature I want to comment on is the ROI selector. In my > compilation the centre of the ROI shifts as I increase it's radius. > Actually, I think it's only the ROI displayed on screen that's "off", > whereas the actual ROI applied to the data is "on-centre". This could be > a simple thing to fix (but I couldn't see it...). > > > Thanks again, > > -Chris > -- > Christopher Bailey > PET Centre and > Center for Functionally Integrative Neuroscience > Aarhus University Hospital, Denmark > http://www.cfin.au.dk/ > > > > > On Wed, 2005-03-16 at 12:45 -0500, Robert VINCENT wrote: > > Hello intrepid MINC users, > > > > A few of you are still using Gabriel Leger's "postf" program for > > visualization of dynamic PET or fMRI data. I've just placed a new > > version of the program here: > > > > http://www.bic.mni.mcgill.ca/~bert/postf-1.0.02-test.tar.gz > > > > This code has been ported to the X Window System and should now compile > > and run on 32-bit Linux, SGI, and Mac OS X. A handy man page has been > > added to the distribution as well. > > > > If you're feeling brave, please download this code and give it a try. Let > > me know how it goes... > > > > -bert > > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Thu Mar 17 13:14:04 2005 From: minc-users@bic.mni.mcgill.ca (Nameeta Lobo) Date: Thu Mar 17 13:14:04 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc In-Reply-To: References: Message-ID: <1111083221.4239c8d5bdb52@netmail.bsd.uchicago.edu> Hi I want to actually use the MNI-ROIs instead of manually drawing ROIs. I work with AFNI and so thought I could convert my AFNI structurals and functionals into the MNC format. I have 43 sub bricks in my functional dataset which I know are present too in the mnc format as the mincinfo: time gives me the number 43. Also, to check the data I converted from AFNI to MINC and then back to AFNI. I had all my 43 sub bricks with the same values in AFNI (the activation map looked a little smooth though). I just cannot figure out how to see these 43 sub bricks in MINC. xdisp is still not available and I havent downloaded postf yet. Also, the functional dataset (statistical map) is a 4D and not a 3D. 1. How do I make this 3D? 2. I guess to see 4D data I should be using postf as xdisp is not available. Can I see it using any other software? 3. You also mentioned that > > > In register you can synchronize the functional and the structral and > set > > > the threshold of your t-values, put labels, and obtain stereotaxic > > > coordinates. As of now, I managed to upload the 4D functional data in the register window. Besides moving that intensity bar, is there any other way to adjust thresholds. Besides I guess this step does not help me right now as I still dont know how to adjust the threshold for 44 sub bricks (this probably gives the same threshold for all sub bricks) 5. How do I identify tag points. Is there some web page that I could read this up? I just tried registering 2 volumes (test and retest) and played safe by marking 4 equidistant points on the brain. I am sorry to be so confused at this moment but it has been just 2 days ago that I have been asked to manage this task and so am just googling and reading up matter on your website and asking you so many questions. Thank you all for your time and patience. Nameeta Quoting "Najmeh Khalili M." : > > > Thank you for that detailed explanation. However, I am having problems > trying to > > find the minc4dim3 command and the xdisp software. We have the 1.3 version > of > > MINC but I dont seem to find the above command anywhere. Also, where could > I get > > xdisp from? The only thing that I could find on google was something that I > had > > to sign up a lot for. > > I don't think we have a minc4dim3 command. What I suggested was that after > statistical analyses, your 4D fMRI volume will be reduced to a 3D > statistical map. > > Please take a look at visualization tools in > www.bic.mni.mcgill.ca/software. postf and xdisp should be a part of minc > package. > > Also, it appears that your afni-to-minc conversion does not specify the > temporal dimension of your data. I am not familiar with AFNI format, bt I > cannot decipher the time-step/start from the 3dinfo output that you > have printed below either. > > N. > > > > > Also, is there any other statistical analysis I should be carrying out on > my > > funtional data. I have just used deconvolution in AFNI and as I mentioned > in my > > previous e-mail, used the 3dAFNItoMINC to convert it. My data is in the > short > > format and has 43 sub bricks in AFNI. > > > > running the mincinfo command on this minc functional data gives me the > following. > > > > mincinfo story_motion_new.mnc > > file: story_motion_new.mnc > > image: signed__ float -4270.3427734375 to 287392.3125 > > image dimensions: time xspace zspace yspace > > dimension name length step start > > -------------- ------ ---- ----- > > time 44 unknown unknown > > xspace 30 5 -71.1 > > zspace 64 -3.75 118.125 > > yspace 64 -3.75 133.825 > > > > with the original 3dinfo story_motion_new+orig.BRIK command line in AFNI > gives me > > Dataset File: story_motion_new+orig > > Identifier Code: XYZ_NLmqlhuH1PInWR8tBL7qRg Creation Date: Wed Oct 13 > 15:46:39 2004 > > Dataset Type: Func-Bucket (-fbuc) > > Byte Order: LSB_FIRST [this CPU native = LSB_FIRST] > > Storage Mode: BRIK file > > Data Axes Orientation: > > first (x) = Anterior-to-Posterior > > second (y) = Superior-to-Inferior > > third (z) = Left-to-Right [-orient ASL] > > R-to-L extent: -73.900 [R] -to- 71.100 [L] -step- 5.000 mm [ 30 > > voxels]A-to-P extent: -133.825 [A] -to- 102.425 [P] -step- 3.750 mm [ > 64 > > voxels]I-to-S extent: -118.125 [I] -to- 118.125 [S] -step- 3.750 mm > [ 64 > > voxels]Number of values stored at each pixel = 44 > > > > with values then printed for every sub brick. > > > > so far this is all that I have with me as I cannot view the minc funtional > data > > yet. Please do help and thank you for your time. > > > > nameeta > > > > > > > > > > > > > > Quoting "Najmeh Khalili M." : > > > > > > > > Hi Nameeta, > > > > > > In order to use register, you need to have your functional data > analyzed > > > and the dimension reduced from 4D to 3D. > > > > > > Once you have your functional t-maps or effects in minc you just call > > > > > > register structural.mnc functional-tmap.mnc > > > > > > In register you can synchronize the functional and the structral and > set > > > the threshold of your t-values, put labels, and obtain stereotaxic > > > coordinates. > > > > > > Of course, display has more functionality but it is poorly documented > and > > > not too trivial to work with. It's very well worth exploring because it > > > allows you to pain labels and to get 3D views of brain surface and etc. > > > > > > If you want to look at your time-series, ie 4D fMRI data, use xdisp. It > > > allows you to eyeball motion artifacts ans activations, but it does not > > > ovrlay your functional data on anatomical data. > > > > > > Hope this helps, > > > Naj > > > > > > > > > > > > > > > On Tue, 15 Mar 2005, Nameeta Lobo wrote: > > > > > > > > > > > Hello all, > > > > > > > > I am a newbie to this software. I have AFNI datasets which I want to > > > convert to > > > > the MNC format. I used the 3dAFNItoMINC command and converted a > structural > > > to > > > > the mnc format and viewed it using mincview (which needed xv) as well > as > > > using > > > > Display. I could see all the 3 views with Display which was good but > with > > > > mincview could see just one view . I want to look at my functional > data > > > too. I > > > > have been going through your web page and came across Register. My > question > > > is > > > > how do I view my functional data as an overlay on my structural. Should > I > > > be > > > > using the 3dAFNItoMINC command, converting this functional data into > mnc > > > and > > > > then use Register and merge the 2 datasets (structural and functional) > or > > > am I > > > > totally off on this one. If yes, could you please give me some > suggestions > > > as to > > > > how to go about working on this data. Any help will be really > > > appreciated. > > > > > > > > thanks > > > > N > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > From minc-users@bic.mni.mcgill.ca Thu Mar 17 14:16:05 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Mar 17 14:16:05 2005 Subject: [MINC-users] Update: postf for X Message-ID: Hi everyone, I've placed a new source release of postf, the simple visualization tool for MINC dynamic data, on : http://www.bic.mni.mcgill.ca/~bert/postf-1.0.02-test.tar.gz This corrects all of the errors pointed out today by Christopher Bailey. I have checked that this version builds and runs on RedHat Linux (2.4.X kernel), Mac OS X, and IRIX 6.5. Please give it a try and let me know if you find any additional problems. -bert From minc-users@bic.mni.mcgill.ca Mon Mar 21 06:43:03 2005 From: minc-users@bic.mni.mcgill.ca (Daniel Schwarz) Date: Mon Mar 21 06:43:03 2005 Subject: [MINC-users] mritotal non-gradient option Message-ID: <423EB320.6060907@feec.vutbr.cz> Dear minc-users, is there any way to force mritotal not to register gradient data, but original subsampeled data? Is it possible to do it by an option/switch or does one have to remake the mritotal script manually? Thank you. Daniel Schwarz From Andrew Janke Mon Mar 21 11:12:04 2005 From: Andrew Janke (Andrew Janke) Date: Mon Mar 21 11:12:04 2005 Subject: [MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc In-Reply-To: <1111083221.4239c8d5bdb52@netmail.bsd.uchicago.edu> References: <1111083221.4239c8d5bdb52@netmail.bsd.uchicago.edu> Message-ID: On Thu, 17 Mar 2005 12:13:41 -0600, Nameeta Lobo wrote > > I just cannot figure out how to see these 43 sub bricks > in MINC. xdisp is still not available and I havent downloaded postf yet. Also, > the functional dataset (statistical map) is a 4D and not a 3D. xdisp will soon be availble. > 1. How do I make this 3D? You can at least view one slice of the 4D by extracting a frame as such: mincreshape -dimrange time=10,0 fmri_4d.mnc out_frame_10.mnc a From Andrew Janke Mon Mar 21 11:31:04 2005 From: Andrew Janke (Andrew Janke) Date: Mon Mar 21 11:31:04 2005 Subject: [MINC-users] mritotal non-gradient option In-Reply-To: <423EB320.6060907@feec.vutbr.cz> References: <423EB320.6060907@feec.vutbr.cz> Message-ID: On Mon, 21 Mar 2005 12:42:24 +0100, Daniel Schwarz wrote: > > is there any way to force mritotal not to register gradient data, but > original subsampeled data? Is it possible to do it by an option/switch > or does one have to remake the mritotal script manually? There is a -noblur option, given that the gradient data is generated as bart of the blurring step, I suspect by turning off this option that you will skip the step you wish. However, there may be other side-effects. The most obvious question is: Why would you want to skip this step? -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Mon Mar 21 17:35:04 2005 From: minc-users@bic.mni.mcgill.ca (D. Louis Collins) Date: Mon Mar 21 17:35:04 2005 Subject: [MINC-users] mritotal non-gradient option In-Reply-To: <423EB320.6060907@feec.vutbr.cz> References: <423EB320.6060907@feec.vutbr.cz> Message-ID: <3a33f19b2e85aa8d74da063f1548c417@mcgill.ca> Daniel, If you really want to use the original subsampled, but unblurred data, then the option is '-noblur'. If you want to use blurred data (and not gradient data), then you would need to modify the mritotal script in the subroutine SetUpFits (~lines 1387-1625). You should change the array @initial_fits and @final_fits, changing the filenames from _dxyz to _blur. This will use only the blurred original data. In either case, this will affect the fitting to stereotaxic space. If you then use this modified script in a publication, it will be important to list the changes you've made since it will no longer correspond to the previously published and described version. good luck! -Louis On Mar 21, 2005, at 6:42 AM, Daniel Schwarz wrote: > Dear minc-users, > > is there any way to force mritotal not to register gradient data, but > original subsampeled data? Is it possible to do it by an option/switch > or does one have to remake the mritotal script manually? > > Thank you. > > Daniel Schwarz > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From Andrew Janke Thu Mar 24 09:40:04 2005 From: Andrew Janke (Andrew Janke) Date: Thu Mar 24 09:40:04 2005 Subject: [MINC-users] OSX conglomerate package. Message-ID: For those who are (likely blissfully) unaware, conglomerate is a veritable kitchen sink of minc processing tools mainly written by Dave McDonald. Anyhow, you can get a nice shiny OSX binary package for it here: http://packages.bic.mni.mcgill.ca/osx/conglomerate-1.4.pkg.tar.gz Let us know if there are any problems with it. Given the number of executables in it, murphys law would dictate that there should be a problem or two..) -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Sat Mar 26 03:11:04 2005 From: minc-users@bic.mni.mcgill.ca (Roger Luechinger) Date: Sat Mar 26 03:11:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: References: <1110281812181263.19332@webmail> Message-ID: <42411FDC.1010605@biomed.ee.ethz.ch> Hi, Sorry for the delayed contribution to this topic. Kuan H. Kho wrote: > If you're working with Philips scanners, you might want to reconstruct > the scans and have them as raw files, ie *.PAR and *.REC files (instead > of the tedious DICOM). This is an option of the scanner software. The > *.PAR file serves as a header to the *.REC file (raw) which can easily > be converted into minc, or any other file type. (for minc, use rawtominc > etc etc), and the parameters (voxelsize, # of dynamics etc) should be > checked! This works finereally works well! It's true that using rawtominc will convert the rec-File (raw-Format from Philips) easily to minc. However the major problem are the geometry infos in the par-File contains the following infos for each slice: . Angulation midslice(ap,fh,rl)[degr]: .17 -1.62 -24.5 . Off Centre midslice(ap,fh,rl) [mm] : 4.94 16.44 .97 (here the info for the stack), whereas the minc-Files wants to have the direction cosines for the 3 directions. And this conversion is not trivial. However for most applications the orientations are not of such an importance. I started with a perlscript using rawtominc to make a cnoversion of the rec-files to minc. However the orientation part is not yet correctly implemented and since there was at our group no need for this part I stop to implemented it.If there is some interest in such a conversion tool I could implement it. In the meantime I had to perform the coordination transformation in the other direction for an other project. (Philips switch in the database on the scanner from the angulations along the ap, fh, rl direction to the cosines like used in the minc-Files.) Therefore it would even be the easiest just to take the infos directly from the database and create directly the minc-File. However such an tool would only be of benefit for sites with deeper knowledge of the scanner. If there is real interest in a conversion tool rec2minc, please let me know. Roger -- ^ ^ o o ------------------------OOO----(_)----OOO--------------------- Dr. Roger Luechinger E-Mail: luechinger@biomed.ee.ethz.ch Universitaetsspital MR-Zentrum VMR30 www/PGP: http://www.mr.ethz.ch/~rluchin/ CH-8091 Zuerich Tel: ++41 1 255 30 64 Fax: ++41 1 255 45 06 -------------------------oooO-------Oooo---------------------- From mperry@ucsd.edu Sat Mar 26 03:11:40 2005 From: mperry@ucsd.edu (Michele Perry) Date: Sat Mar 26 03:11:40 2005 Subject: [MINC-users] problem with MNI tools in Freesurfer Message-ID: <34891.137.110.172.6.1111621415.squirrel@acs-webmail.ucsd.edu> Hi, I have been using Freesurfer for about 5 months now. It was working normally for most of that time. About 2 weeks ago, I started having problems with one of the processing steps. I posted questions to the Freesurfer mailing list and they said I should contact MNI because the problems I was having involved MNI tools. When I run recon-all -stage1 -subjid , it exits after the following: --------------------------------------------- Nu Intensity Correction Fri Mar 18 17:19:49 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip06://mri/] [2005-03-18 17:19:59] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_31180/ nu0.mnc nu1.imp Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on 693727244 310617732 347870136 48% ------------------------------------------ recon-all exited with errors at Fri Mar 18 17:19:59 PST 2005 vi /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33 is: use MNI::Startup qw(nocputimes); That's the first line after all the initial comments. Any advice? Thank you for your help, Michele Perry From k.h.kho@azu.nl Sun Mar 27 23:30:04 2005 From: k.h.kho@azu.nl (Kuan H. Kho) Date: Sun Mar 27 23:30:04 2005 Subject: [MINC-users] Dicom to Minc converter for Phillips ? In-Reply-To: <42411FDC.1010605@biomed.ee.ethz.ch> References: <1110281812181263.19332@webmail> <42411FDC.1010605@biomed.ee.ethz.ch> Message-ID: Hi Roger, I think you're right about the slice info: that's very important to most imagers. As we make whole 3D scans instead of slices (both structural and functional images), the simple rawtominc conversion suffices. But I indeed did not realize that there may be a bunch of people that indeed do need that information! About a rectominc tool: I can work with the rawtominc, but I heard that on the newest Phillips scanner software (release ..? I can't keep count anymore), the PAR/REC format changed a bit. I could be wrong, but one may have to check that. Best, Kuan -- Kuan H. Kho, MD Depts. of Psychiatry & Neurosurgery, G03.124 University Medical Center Utrecht Heidelberglaan 100 P.O.Box 85500 3508 GA Utrecht The Netherlands P +31-30-2507969/2507953 F +31-30-2542100 E k.h.kho_'at'_azu.nl On Wed, 23 Mar 2005 08:50:52 +0100, Roger Luechinger wrote: > Hi, > > Sorry for the delayed contribution to this topic. > > > It's true that using rawtominc will convert the rec-File (raw-Format from > Philips) easily to minc. However the major problem are the geometry infos > in the par-File contains the following infos for each slice: > . Angulation midslice(ap,fh,rl)[degr]: .17 -1.62 -24.5 > . Off Centre midslice(ap,fh,rl) [mm] : 4.94 16.44 .97 > (here the info for the stack), whereas the minc-Files wants to have the > direction cosines for the 3 directions. > And this conversion is not trivial. However for most applications the > orientations are not of such an importance. > I started with a perlscript using rawtominc to make a cnoversion of the > rec-files to minc. However the orientation part is not yet correctly > implemented and since there was at our group no need for this part I stop > to implemented it.If there is some interest in such a conversion tool I > could implement it. In the meantime I had to perform the coordination > transformation in the other direction for an other project. (Philips > switch in the database on the scanner from the angulations along the ap, > fh, rl direction to the cosines like used in the minc-Files.) Therefore it > would even be the easiest just to take the infos directly from the > database and create directly the minc-File. However such an tool would > only be of benefit for sites with deeper knowledge of the scanner. > > If there is real interest in a conversion tool rec2minc, please let me know. > > Roger > > -- > ^ ^ > o o > ------------------------OOO----(_)----OOO--------------------- > Dr. Roger Luechinger E-Mail: luechinger@biomed.ee.ethz.ch > Universitaetsspital > MR-Zentrum VMR30 www/PGP: http://www.mr.ethz.ch/~rluchin/ > CH-8091 Zuerich > Tel: ++41 1 255 30 64 Fax: ++41 1 255 45 06 > -------------------------oooO-------Oooo---------------------- From minc-users@bic.mni.mcgill.ca Tue Mar 29 16:41:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue Mar 29 16:41:04 2005 Subject: [MINC-users] New dcm2mnc test code for Linux Message-ID: Hi all, I've got a new binary release of my dcm2mnc converter available for Linux at: http://www.bic.mni.mcgill.ca/~bert/dcm2mnc-2.0.002-i386-linux.tar.gz If you have any "problem data", please give this new code a try. I have added some support for Philips and GE proprietary fields to this version. It should handle functional data from either manufacturer, and may handle PET as well as MRI data in some cases. Please let me know of any interesting successes or problems! I'm still working towards a source release of this code sometime reasonably soon. Ultimately it will be folded into the MINC distributions. Thanks, -bert From minc-users@bic.mni.mcgill.ca Thu Mar 31 01:07:05 2005 From: minc-users@bic.mni.mcgill.ca (Steve M. Robbins) Date: Thu Mar 31 01:07:05 2005 Subject: [MINC-users] problem with MNI tools in Freesurfer In-Reply-To: <34891.137.110.172.6.1111621415.squirrel@acs-webmail.ucsd.edu> References: <34891.137.110.172.6.1111621415.squirrel@acs-webmail.ucsd.edu> Message-ID: <20050331060608.GD5459@nyongwa.montreal.qc.ca> On Wed, Mar 23, 2005 at 03:43:35PM -0800, Michele Perry wrote: > I have been using Freesurfer for about 5 months now. It was working > normally for most of that time. About 2 weeks ago, I started having > problems with one of the processing steps. When something suddenly stops working, it's a good bet that one of the pieces of software has been changed. Perhaps Freesurfer, the MNI tools, or perl has been upgraded between 5 months ago and 2 weeks ago? Another possibility is that your PERL5LIB has changed. > Can't locate MNI/Startup.pm in @INC (@INC contains: > /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at > /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. > BEGIN failed--compilation aborted at > /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. The error message means what it says: perl cannot find the file "MNI/Startup.pm". The quick hack is to find that file and set your PERL5LIB appropriately. -Steve