From yves.roy@umontreal.ca Wed Feb 2 15:38:03 2005 From: yves.roy@umontreal.ca (Roy Yves) Date: Wed Feb 2 15:38:03 2005 Subject: [MINC-users] ana2mnc problem - again Message-ID: Hello: I have this ANALYSE image I want to convert to MINC: $ ana_show sub1_run1_vol1.hdr x outside of string at /usr/local/bin/ana_show line 318. $ ana2mnc sub1_run1_vol1.img sub1_run1_vol1.mnc x outside of string at /usr/local/bin/ana2mnc line 318. FYI, line 318 is... ---------------------------- # No byte swapping required else{ ----> return unpack("x$offset $type", $$stringref); } ------------------------------ I think ana2mnc is version 1.2 (but ana2mnc -version is not a supported option) Also, I downloaded ana2mnc-1.3c from Andrew's site after reading Catherine Ogilvie posting on bic-users Mon Jan 24 13:37:05 2005... (wrongly?) assuming that the problem could be related to byte swapping (but the images were copied from linux to linux...). But here is the behavior, pretty much nothing.... $ ./ana2mnc-1.3c $ ./ana2mnc-1.3c -swap_data sub1_run1_vol1.hdr $ ./ana2mnc-1.3c -swap_data sub1_run1_vol1.hdr sub1_run1_vol1.mnc $ ./ana2mnc-1.3c -version ana2mnc-1.3c version 1.3c no usage information. And if it is indeed a problem due to byte swapping, I am reluctant to correct the situation with dd (dd if=3Dfoo.hdr of=3Dfoo.swap.hdr conv=3Dswab), since this seems to be a low level mean... Thanks Yves From =?ISO-8859-1?Q?Xavier_Tom=E0s?= Fri Feb 4 05:00:05 2005 From: =?ISO-8859-1?Q?Xavier_Tom=E0s?= (=?ISO-8859-1?Q?Xavier_Tom=E0s?=) Date: Fri Feb 4 05:00:05 2005 Subject: [MINC-users] INSECT question Message-ID: <7702fa7d05020401591b5ed7b1@mail.gmail.com> Hello, How can I do to get an image only with the grey matter segmentation using INSECT? Thank you very much for your help, Xavi From vsingh@bic.mni.mcgill.ca Fri Feb 4 08:40:04 2005 From: vsingh@bic.mni.mcgill.ca (Vivek SINGH) Date: Fri Feb 4 08:40:04 2005 Subject: [MINC-users] INSECT question In-Reply-To: <7702fa7d05020401591b5ed7b1@mail.gmail.com> Message-ID: Try: mincmath -eq -const 2 classified.mnc grey.mnc but you will need to skull strip the volume first if you truly only want grey matter... Vivek From Andrew Janke Fri Feb 4 12:18:04 2005 From: Andrew Janke (Andrew Janke) Date: Fri Feb 4 12:18:04 2005 Subject: [MINC-users] MINC OSX packages. Message-ID: For those who like the bleeding edge, here are a number of the MINC tools packaged (individually as opposed to the original OSX MINC installer) up for OSX. http://www.bic.mni.mcgill.ca/~rotor/distro/osx I have included both a native OSX build (.pkg files) and fink dpkg's (.deb files). One of the major fixes is that the register bug of having to click on the window as a file is loading is gone. Comments/usage reports appreciated. Andrew Janke - andrew_janke@iinet.net.au From bert@bic.mni.mcgill.ca Wed Feb 9 09:58:04 2005 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Wed Feb 9 09:58:04 2005 Subject: [MINC-users] Re: [MINC-development] DICOM to minc build errors In-Reply-To: <42093F06.2010409@bic.mni.mcgill.ca> Message-ID: Hi, The old dicom-to-minc conversion tools are a bit out of date. The current best option is the dicom3_to_minc perl script from Jonathan Harlap: http://www.bic.mni.mcgill.ca/~jharlap/dicom/ I am in the process of adding a fully-supported DICOM converter to the MINC core release. I would be happy to provide a beta version of this tool for testing purposes. -bert On Tue, 8 Feb 2005, EJ Nikelski wrote: > Hi, > I initially sent this message to minc-users (perhaps the wrong > mailing list?) and received no response. I really need a response to > this ... since, transitioning to a minc volume format requires a > reliable conversion program and community support. I'm trying to get an > imaging center to start using minc, but I need to demonstrate that they > won't be left high and dry. Any advice on the below problem would be > appreciated. > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am trying to help some people set up a processing pipeline to > convert their DICOM files (from a GE 3T magnet) to minc. A build of > Peter Neelin's DICOM_to_Minc package fails, as it is looking for > "Make_machine_specific" and "Make_configuration" in the minc build > directory ... and these elements do not exist in minc-1.3. Am I trying > to build an old (deprecated) tool? What is currently my best bet for > converting DICOM to Minc? I have tried the PERL implementation of > dicom3_to_minc, but it's a bit slow. Ideas? I am building on Linux (Debian). > > BTW, I have noticed that netcdf-3.6 is out. The build process seems > to be a bit more robust and up-to-date than under 3.5. Initial build on > Debian was magic. If nobody knows of any incompatibility problems with > minc-1.3, I shall build it on Mac OS X as well. > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > Thanks, > > Jim > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From yangjo@upstate.edu Sun Feb 13 17:24:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Sun Feb 13 17:24:04 2005 Subject: [MINC-users] alignment between aMRI.mnc and fMRI.mnc Message-ID: Hi, Would someone let me know how to align aMRI.mnc and fMRI.mnc using "mincresample"? Thanks. Nam. From mdesco@cim.mcgill.ca Mon Feb 14 08:04:04 2005 From: mdesco@cim.mcgill.ca (Maxime Descoteaux) Date: Mon Feb 14 08:04:04 2005 Subject: [MINC-users] problem MINC + fedora Message-ID: <33272.138.96.80.33.1108386185.squirrel@www.cim.mcgill.ca> Hi, I have just installed with success the NetCDF and MINC rpm's on a Fedora OS. However, when I try to recompile my program that use to run at the MNI I get the following error: /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function `NC_check_name': : undefined reference to `__ctype_b' Any ideas? From steven.robbins@videotron.ca Mon Feb 14 08:25:04 2005 From: steven.robbins@videotron.ca (Steve M. Robbins) Date: Mon Feb 14 08:25:04 2005 Subject: [MINC-users] problem MINC + fedora In-Reply-To: <33272.138.96.80.33.1108386185.squirrel@www.cim.mcgill.ca> References: <33272.138.96.80.33.1108386185.squirrel@www.cim.mcgill.ca> Message-ID: <20050214132417.GA13674@nyongwa.montreal.qc.ca> On Mon, Feb 14, 2005 at 08:03:05AM -0500, Maxime Descoteaux wrote: > Hi, > > I have just installed with success the NetCDF and MINC rpm's on a Fedora > OS. However, when I try to recompile my program that use to run at the > MNI I get the following error: > > /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function > `NC_check_name': > : undefined reference to `__ctype_b' > > Any ideas? My recollection is that it means your libnetcdf.a is built with a different C library than you currently have. I expect the problem will go away if you rebuild NetCDF from source. You might have to do the same with MINC, too. -Steve From yangjo@upstate.edu Mon Feb 14 18:01:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Mon Feb 14 18:01:04 2005 Subject: [MINC-users] mni register manual or instructions? Message-ID: Hi, Is there a manual or instructions on how to use mni register to create an xfm file manually? Nam. From sylvain@bic.mni.mcgill.ca Tue Feb 15 15:07:04 2005 From: sylvain@bic.mni.mcgill.ca (Sylvain MILOT) Date: Tue Feb 15 15:07:04 2005 Subject: [MINC-users] mni register manual or instructions? In-Reply-To: Message-ID: Hello, none that I'm aware of, aside from the man page and it's not very explicit on this feature. I would suggest reading this first if you haven't already done so. The recipe is somewhat simple in terms of the actions to take. The difficulty resides in identifying homologous points in each volume - this comes with practice! Knowing something about anatomy as seen thru MRI and/or PET is helpful but ultimately, its all about pattern recognition. I suggest saving a tag file though as opposed to just a xfm file - do both if you like and/or use tagtoxfm to convert the tag file. You must also select the appropriate Transform type. Use the right button on your mouse or the "Record Tag" button to select homologous tag point pairs and you will see them appear on the bottom window pane. The "Record Tag" button is also useful for overwriting a tag point pair. Use the navigation elements on the bottom of the viewport for the merged volumes or the up/down arrows on your keyboard to navigate thru the point-pairs to either overwrite a point pair with the "Record Tag" button or delete one with the "Delete Tag" button. Hope this helps a little, Sylvain On Mon, 14 Feb 2005, Joongnam Yang wrote: > Hi, > > Is there a manual or instructions on how to use mni register to create an > xfm file manually? > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) (trinity@bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From yangjo@upstate.edu Tue Feb 15 18:56:04 2005 From: yangjo@upstate.edu (Joongnam Yang) Date: Tue Feb 15 18:56:04 2005 Subject: [MINC-users] mni register manual or instructions? Message-ID: Hi Sylvain Someone already sent me email about how to do it. Thanks, anyway. Why, though, is there NOT a simple a-few-line insturction available on how to use it? Something developers have to take care of....? Nam. >>> Sylvain MILOT 02/15/05 6:44 PM >>> Hello, none that I'm aware of, aside from the man page and it's not very explicit on this feature. I would suggest reading this first if you haven't already done so. The recipe is somewhat simple in terms of the actions to take. The difficulty resides in identifying homologous points in each volume - this comes with practice! Knowing something about anatomy as seen thru MRI and/or PET is helpful but ultimately, its all about pattern recognition. I suggest saving a tag file though as opposed to just a xfm file - do both if you like and/or use tagtoxfm to convert the tag file. You must also select the appropriate Transform type. Use the right button on your mouse or the "Record Tag" button to select homologous tag point pairs and you will see them appear on the bottom window pane. The "Record Tag" button is also useful for overwriting a tag point pair. Use the navigation elements on the bottom of the viewport for the merged volumes or the up/down arrows on your keyboard to navigate thru the point-pairs to either overwrite a point pair with the "Record Tag" button or delete one with the "Delete Tag" button. Hope this helps a little, Sylvain On Mon, 14 Feb 2005, Joongnam Yang wrote: > Hi, > > Is there a manual or instructions on how to use mni register to create an > xfm file manually? > > Nam. > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) (trinity@bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From Andrew Janke Sun Feb 20 05:29:04 2005 From: Andrew Janke (Andrew Janke) Date: Sun Feb 20 05:29:04 2005 Subject: [MINC-users] mincfft Message-ID: For those who are interested, I have places a small package for doing fft's on minc volumes here: http://www.bic.mni.mcgill.ca/~rotor/distro/tgz/mincfft-1.1.tar.gz I have also built a debian sarge package for it here: http://www.bic.mni.mcgill.ca/~rotor/distro/deb/mincfft-1.1-linux-2.6-intel.deb I'd be interested in usage/wants-needs reports for those who use it. Thanks Andrew From Andrew Janke Sun Feb 20 09:13:04 2005 From: Andrew Janke (Andrew Janke) Date: Sun Feb 20 09:13:04 2005 Subject: [MINC-users] MNI Models. Message-ID: Thanks to some work by Louis Collins, I am happy to annouce that three of the MNI average models are now downloable as autoconfigured packages, the average_305, icbm152 and the colin27. THe original source packages are here: http://www.bic.mni.mcgill.ca/~rotor/distro/tgz/mni-models_average305-lin-1.0.tar.gz http://www.bic.mni.mcgill.ca/~rotor/distro/tgz/mni-models_colin27-lin-1.0.tar.gz http://www.bic.mni.mcgill.ca/~rotor/distro/tgz/mni-models_icbm152-lin-1.0.tar.gz and debian packages are here: http://www.bic.mni.mcgill.ca/~rotor/distro/deb/mni-models-average305-lin-1.0-linux-2.6-intel.deb http://www.bic.mni.mcgill.ca/~rotor/distro/deb/mni-models-colin27-lin-1.0-linux-2.6-intel.deb http://www.bic.mni.mcgill.ca/~rotor/distro/deb/mni-models-icbm152-lin-1.0-linux-2.6-intel.deb The ICBM model package contains T1, T2 and PD models, thus when pre-compiled it is sizeable (200MB). Thus it may be best to download the source pacakges and compile them yourself. I provide the debian packages for those who do site-wide distribution. If there is sufficient call/need I can provide OSX packages for these also. The make process is very simple for all three of these (presuming you have mni_autoreg already installed): ./configure --with-build-path=/usr/local/mni (presuming this is where MINC is) make make install Let us know of any problems a From patrick@bic.mni.mcgill.ca Mon Feb 28 14:23:06 2005 From: patrick@bic.mni.mcgill.ca (patrick@bic.mni.mcgill.ca) Date: Mon Feb 28 14:23:06 2005 Subject: [MINC-users] autocrop question Message-ID: <42236F55.3020209@bic.mni.mcgill.ca> 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 From Kopchyk@etang.com Mon Feb 28 17:28:05 2005 From: Kopchyk@etang.com (Walker Spider) Date: Mon Feb 28 17:28:05 2005 Subject: [MINC-users] Re[1]: talk thread about your health Message-ID: <6da701c51d5e$05d10c24$421a153e@wawasan2020.com> This is a multi-part message in MIME format. ------=_NextPart_000_89AB_CDEF0123.456789AB Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Expe ce thr es lon gas rien ee tim ger or ms Wor de shi g wit hou ld Wi ppin hin 24 rs SP -M UR The we and Saf Wa Ph acy is Ne st The est y of arm Inc e Yo xual Des Spe ume by % reas ur Se ire and rm vol 500 100 ural and de Eff - in con t to wel wn bra % Nat No Si ects tras l-kno nds. 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