From jhamstra at ucdavis.edu Mon Oct 2 21:10:36 2006 From: jhamstra at ucdavis.edu (Julia Hamstra) Date: Mon, 2 Oct 2006 18:10:36 -0700 Subject: [MINC-users] Install questions Message-ID: Hello, I have successfully instatlled netcdf (v 3.5.0 and 3.6.1). However, when I run configure for minc-1.4.1, I get the following error: creating libtool checking for library m... yes checking for library netcdf... no configure: error: cannot find required library netcdf What needs to be done to resolve this error? Thanks ~julia hamstra From jason at bic.mni.mcgill.ca Tue Oct 3 08:55:38 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 3 Oct 2006 08:55:38 -0400 Subject: [MINC-users] Install questions In-Reply-To: References: Message-ID: <1D3370C5-D516-4DC7-85EF-9A8900277460@bic.mni.mcgill.ca> On 2-Oct-06, at 9:10 PM, Julia Hamstra wrote: > Hello, > I have successfully instatlled netcdf (v 3.5.0 and 3.6.1). However, > when I > run configure for minc-1.4.1, I get the following error: Make sure that configure knows where to find netcdf. The easiest way is by supplying the following flag: ./configure --with-build-path=/path/to/netcdf Jason > > creating libtool > checking for library m... yes > checking for library netcdf... no > configure: error: cannot find required library netcdf > > What needs to be done to resolve this error? Thanks > ~julia hamstra > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From sorench at gmail.com Tue Oct 3 08:58:18 2006 From: sorench at gmail.com (Soren Christensen) Date: Tue, 3 Oct 2006 05:58:18 -0700 Subject: [MINC-users] Install questions In-Reply-To: References: Message-ID: Hi Julia, Did you copy the NetCDF files to /usr/lib or put their location in LD_LIBRARY_PATH? Soren On 10/2/06, Julia Hamstra wrote: > > Hello, > I have successfully instatlled netcdf (v 3.5.0 and 3.6.1). However, when I > run configure for minc-1.4.1, I get the following error: > > creating libtool > checking for library m... yes > checking for library netcdf... no > configure: error: cannot find required library netcdf > > What needs to be done to resolve this error? Thanks > ~julia hamstra > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From biophotoray at yahoo.ca Sat Oct 7 23:06:37 2006 From: biophotoray at yahoo.ca (Raymond Martin) Date: Sun, 8 Oct 2006 03:06:37 +0000 Subject: [MINC-users] Mailing list admins wanted! In-Reply-To: References: Message-ID: <200610080306.38415.biophotoray@yahoo.ca> Hi, I have been trying to help out on the mailing list for quite a while. Someone keeps beating me to it, but there are just way too many spam emails coming in. Is it not possible to use spam software or this? It is pretty much a waste of time doing this by hand! Can Spamassassin or other be used first? Raymond __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From alex at bic.mni.mcgill.ca Tue Oct 10 10:11:56 2006 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Tue, 10 Oct 2006 10:11:56 -0400 Subject: [MINC-users] Mailing list admins wanted! In-Reply-To: <200610080306.38415.biophotoray@yahoo.ca> References: <200610080306.38415.biophotoray@yahoo.ca> Message-ID: <20061010141156.GB468787@bic.mni.mcgill.ca> AFAIK, SpamAssassin is already used on incoming mail, and the spam is flagged accordingly; but I suspect minc-users doesn't check those flags. Somebody with admin access to minc-users should add a spam filter rule that discards everything containing X-Spam-Flag: YES I suspect that will reduce the spam load a good bit (it has for lists that I have control over). -- A On Sun, Oct 08, 2006 at 03:06:37AM +0000, Raymond Martin wrote: > Hi, > > I have been trying to help out on the mailing list for quite a while. > Someone keeps beating me to it, but there are just way too many spam > emails coming in. Is it not possible to use spam software or this? > It is pretty much a waste of time doing this by hand! > > Can Spamassassin or other be used first? > > Raymond > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- ========================================================================= | Alex P. Zijdenbos, Ph.D. | | | McConnell Brain Imaging Centre | Phone: [+1] 514 398-5220 (office) | | Montreal Neurological Institute | [+1] 514 398-1996 (dept.) | | 3801 University St., WB-208 | Fax: [+1] 514 398-8952 (office) | | Montreal, Quebec, H3A 2B4 | [+1] 708 810-3309 (private) | | CANADA | E-mail: alex at bic.mni.mcgill.ca | ========================================================================= From bouffard at bic.mni.mcgill.ca Wed Oct 18 13:02:19 2006 From: bouffard at bic.mni.mcgill.ca (Marc BOUFFARD) Date: Wed, 18 Oct 2006 13:02:19 -0400 Subject: [MINC-users] nlpfit deformation fields and mincblob Message-ID: Hello, When applying mincblob -det to the grid file (produced by nlpfit): what exactly is the result: the determinant of the jacobian of deformation field? What is the meaning of a negative value? How can one get the log of the jacobian? is the result in source or target space? does it make sense to resample the result? Marc From lau at bic.mni.mcgill.ca Wed Oct 18 14:38:39 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Wed, 18 Oct 2006 14:38:39 -0400 Subject: [MINC-users] nlpfit deformation fields and mincblob In-Reply-To: References: Message-ID: Hi Marc, When applying mincblob -det to the grid file (produced by nlpfit): > > what exactly is the result: the determinant of the jacobian of deformation > field? Yes. In case you are interested, there are other operations available in mincblob (use -help for details). What is the meaning of a negative value? The determinant can be a value between -1 and 1. A negative value might be interpreted as a localized decrease in volume, but be careful of this interpretation on a raw output grid file as it will probably be quite noisy. How can one get the log of > the jacobian? In the instance I've seen, it is applied as the following given input_det.mnc mincmath -const 1 -add input_det.mnc output_det_plus1.mnc mincmath -log output_det_plus1.mnc output_log_det.mnc I believe that you add 1 in order to get the range to be >0, but I wonder if there's a better theoretical reason for this. is the result in source or target space? Not too familiar with nlpfit, but I believe that the nonlinear grid would take you from source to target space. does it make sense to resample the result? Not sure what you mean by this? The output_log_det.mnc file is in source space though. Hope this helps! jon From pgravel at bic.mni.mcgill.ca Thu Oct 19 08:36:10 2006 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 19 Oct 2006 08:36:10 -0400 Subject: [MINC-users] Matlab emma Tools for MAC Message-ID: Hi All, Does anyone know if the emma tools exist for MAC? Thanks in advance, Paul From penhunelab at gmail.com Thu Oct 19 09:23:46 2006 From: penhunelab at gmail.com (Penhune Lab) Date: Thu, 19 Oct 2006 09:23:46 -0400 Subject: [MINC-users] Matlab emma Tools for MAC In-Reply-To: References: Message-ID: I've installed emma in a mac (OS X). If i'm not mistaken (it wasnt an installation for myself) all i did was compiled it from the source available here http://packages.bic.mni.mcgill.ca/tgz/ maybe someone else can confirm if this is possible or not? have you tried this? Alejandro On 10/19/06, Paul GRAVEL wrote: > > Hi All, > > Does anyone know if the emma tools exist for MAC? > > Thanks in advance, > > Paul > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From se at hst.aau.dk Thu Oct 19 03:43:19 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Thu, 19 Oct 2006 09:43:19 +0200 Subject: [MINC-users] minc2dicom ? Message-ID: <45372C97.4010505@hst.aau.dk> I'm stuck with some image conversion problems. I need to convert minc into the vista format. I can convert dicom to vista, but I'm not sure if there is a tool for converting minc into dicom. Maybe I'll have to write some minc2vista code, but I really hope I don't. Any suggestions? Simon From a.janke at gmail.com Thu Oct 19 10:36:38 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 19 Oct 2006 10:36:38 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: <45372C97.4010505@hst.aau.dk> References: <45372C97.4010505@hst.aau.dk> Message-ID: > I'm stuck with some image conversion problems. I need to convert minc > into the vista format. I can convert dicom to vista, but I'm not sure if > there is a tool for converting minc into dicom. > Maybe I'll have to write some minc2vista code, but I really hope I don't. > Any suggestions? Conversion to DICOM is somethat that I myself never plan to support or even implement. The main reason being that there is (paradoxically) no DICOM standard for the sort of thing we do. However my suggestion would be something like this: for i in `seq 0 `; do mincpik infile.mnc tmp.png; dicom2 tmp.png out_$i.dcm; done I dont have the syntax for dicom2 right but you can get it from here: http://www.barre.nom.fr/medical/dicom2/ -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From acveilleux at mrs.mni.mcgill.ca Thu Oct 19 11:29:59 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 19 Oct 2006 11:29:59 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: ; from a.janke@gmail.com on Thu, Oct 19, 2006 at 10:36:38AM -0400 References: <45372C97.4010505@hst.aau.dk> Message-ID: <20061019112959.G13524@mrs.mni.mcgill.ca> On Thu, Oct 19, 2006 at 10:36:38AM -0400, Andrew Janke wrote: > > for i in `seq 0 `; > do > > mincpik infile.mnc tmp.png; > dicom2 tmp.png out_$i.dcm; > done This has the benefit of shredding any last bit of identifiable information for each slice so you'll probably want to also go through the process of including all the DICOM group/element pairs so that the DICOM files can actually be reassembled into something vaguely like the original MINC file. Alex From a.janke at gmail.com Thu Oct 19 11:57:45 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 19 Oct 2006 11:57:45 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: <20061019112959.G13524@mrs.mni.mcgill.ca> References: <45372C97.4010505@hst.aau.dk> <20061019112959.G13524@mrs.mni.mcgill.ca> Message-ID: > This has the benefit of shredding any last bit of identifiable > information for each slice so you'll probably want to also go through > the process of including all the DICOM group/element pairs so that the > DICOM files can actually be reassembled into something vaguely like > the original MINC file. Correct! And anyone out there is more than welcome to write (and support) this! :) -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From Kent.Conover at concordia.ca Thu Oct 19 12:07:43 2006 From: Kent.Conover at concordia.ca (conover) Date: Thu, 19 Oct 2006 12:07:43 -0400 Subject: [MINC-users] Matlab emma Tools for MAC In-Reply-To: References: Message-ID: <3E164232-99DC-4574-9EDC-9807599A7187@concordia.ca> Hi Alejandro, This sounds interesting - but I don't know how to compile code. Is it easy? -Kent On 19-Oct-06, at 9:23 AM, Penhune Lab wrote: > I've installed emma in a mac (OS X). If i'm not mistaken (it wasnt an > installation for myself) all i did was compiled it from the source > available > here > http://packages.bic.mni.mcgill.ca/tgz/ > maybe someone else can confirm if this is possible or not? > have you tried this? > > Alejandro > > > On 10/19/06, Paul GRAVEL wrote: >> >> Hi All, >> >> Does anyone know if the emma tools exist for MAC? >> >> Thanks in advance, >> >> Paul >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > Laboratory for Motor Learning and Neural Plasticity > Dr. Virginia Penhune > Department of Psychology, Concordia University > SP-A 244, 7141 Sherbrooke St. W > Montreal, QC H4B 1R6 Canada > (514)848-2424 ext. 7567 > http://psychology.concordia.ca/fac/penhune/winindex.html > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From se at hst.aau.dk Thu Oct 19 06:09:50 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Thu, 19 Oct 2006 12:09:50 +0200 Subject: [MINC-users] minc2dicom ? In-Reply-To: References: <45372C97.4010505@hst.aau.dk> Message-ID: <45374EEE.5030202@hst.aau.dk> Thanks for the tip Andrew. dicom2 didn't like png input, so I ended up with the following: for i in `seq 0 $slices`; do mincpik -scale 1 $infile tmp.rgb mv tmp.rgb tmp.raw dicom2 -d --size=$cols:$rows tmp.raw dcm2v tmp.raw.dcm -o $prefix\_$i.v done Simon Andrew Janke wrote: >> I'm stuck with some image conversion problems. I need to convert minc >> into the vista format. I can convert dicom to vista, but I'm not sure if >> there is a tool for converting minc into dicom. >> Maybe I'll have to write some minc2vista code, but I really hope I don't. >> Any suggestions? >> > > Conversion to DICOM is somethat that I myself never plan to support or > even implement. The main reason being that there is (paradoxically) > no DICOM standard for the sort of thing we do. > > However my suggestion would be something like this: > > for i in `seq 0 `; > do > > mincpik infile.mnc tmp.png; > dicom2 tmp.png out_$i.dcm; > done > > I dont have the syntax for dicom2 right but you can get it from here: > > http://www.barre.nom.fr/medical/dicom2/ > > > From a.janke at gmail.com Thu Oct 19 12:13:54 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 19 Oct 2006 12:13:54 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: <45374EEE.5030202@hst.aau.dk> References: <45372C97.4010505@hst.aau.dk> <45374EEE.5030202@hst.aau.dk> Message-ID: > for i in `seq 0 $slices`; do > mincpik -scale 1 $infile tmp.rgb > mv tmp.rgb tmp.raw > dicom2 -d --size=$cols:$rows tmp.raw > dcm2v tmp.raw.dcm -o $prefix\_$i.v > done Looks good, although I suspect you will want to add a -slice $i to the mincpik line. Also I think you can do this with Imagemagick: mincpik -slice $1 -scale 1 $infile RGB:tmp.raw and do away with the mv command. 'man ImageMagick' will tell more. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From penhunelab at gmail.com Thu Oct 19 12:23:04 2006 From: penhunelab at gmail.com (Penhune Lab) Date: Thu, 19 Oct 2006 12:23:04 -0400 Subject: [MINC-users] Matlab emma Tools for MAC In-Reply-To: <3E164232-99DC-4574-9EDC-9807599A7187@concordia.ca> References: <3E164232-99DC-4574-9EDC-9807599A7187@concordia.ca> Message-ID: Just read the README file if theres one USUALLY its ./configure, make, make install On 10/19/06, conover wrote: > > Hi Alejandro, > > This sounds interesting - but I don't know how to compile code. Is it > easy? > > -Kent > > > On 19-Oct-06, at 9:23 AM, Penhune Lab wrote: > > > I've installed emma in a mac (OS X). If i'm not mistaken (it wasnt an > > installation for myself) all i did was compiled it from the source > > available > > here > > http://packages.bic.mni.mcgill.ca/tgz/ > > maybe someone else can confirm if this is possible or not? > > have you tried this? > > > > Alejandro > > > > > > On 10/19/06, Paul GRAVEL wrote: > >> > >> Hi All, > >> > >> Does anyone know if the emma tools exist for MAC? > >> > >> Thanks in advance, > >> > >> Paul > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > > > > > > > > -- > > Laboratory for Motor Learning and Neural Plasticity > > Dr. Virginia Penhune > > Department of Psychology, Concordia University > > SP-A 244, 7141 Sherbrooke St. W > > Montreal, QC H4B 1R6 Canada > > (514)848-2424 ext. 7567 > > http://psychology.concordia.ca/fac/penhune/winindex.html > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From Kent.Conover at concordia.ca Thu Oct 19 13:06:39 2006 From: Kent.Conover at concordia.ca (conover) Date: Thu, 19 Oct 2006 13:06:39 -0400 Subject: [MINC-users] Matlab emma Tools for MAC In-Reply-To: References: <3E164232-99DC-4574-9EDC-9807599A7187@concordia.ca> Message-ID: Hi Alejandro, I seem to be missing a library of routines that MINC tools needs (eg- Display) Here is the response when I call display from the terminal: psych-shizgal4:~ conover$ display dyld: Library not loaded: /sw/lib/libnetpbm.10.dylib Referenced from: /usr/local/mni/bin/display Reason: image not found Trace/BPT trap Do I need to download this library? -Kent On 19-Oct-06, at 12:23 PM, Penhune Lab wrote: > Just read the README file if theres one > USUALLY its ./configure, make, make install > > > On 10/19/06, conover wrote: >> >> Hi Alejandro, >> >> This sounds interesting - but I don't know how to compile code. Is it >> easy? >> >> -Kent >> >> >> On 19-Oct-06, at 9:23 AM, Penhune Lab wrote: >> >>> I've installed emma in a mac (OS X). If i'm not mistaken (it >>> wasnt an >>> installation for myself) all i did was compiled it from the source >>> available >>> here >>> http://packages.bic.mni.mcgill.ca/tgz/ >>> maybe someone else can confirm if this is possible or not? >>> have you tried this? >>> >>> Alejandro >>> >>> >>> On 10/19/06, Paul GRAVEL wrote: >>>> >>>> Hi All, >>>> >>>> Does anyone know if the emma tools exist for MAC? >>>> >>>> Thanks in advance, >>>> >>>> Paul >>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>> >>> >>> >>> -- >>> Laboratory for Motor Learning and Neural Plasticity >>> Dr. Virginia Penhune >>> Department of Psychology, Concordia University >>> SP-A 244, 7141 Sherbrooke St. W >>> Montreal, QC H4B 1R6 Canada >>> (514)848-2424 ext. 7567 >>> http://psychology.concordia.ca/fac/penhune/winindex.html >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > Laboratory for Motor Learning and Neural Plasticity > Dr. Virginia Penhune > Department of Psychology, Concordia University > SP-A 244, 7141 Sherbrooke St. W > Montreal, QC H4B 1R6 Canada > (514)848-2424 ext. 7567 > http://psychology.concordia.ca/fac/penhune/winindex.html > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From penhunelab at gmail.com Thu Oct 19 13:29:04 2006 From: penhunelab at gmail.com (Penhune Lab) Date: Thu, 19 Oct 2006 13:29:04 -0400 Subject: [MINC-users] Matlab emma Tools for MAC In-Reply-To: References: <3E164232-99DC-4574-9EDC-9807599A7187@concordia.ca>

Message-ID: yes you do a quick search returned this http://netpbm.sourceforge.net/doc/libnetpbm.html On 10/19/06, conover wrote: > > Hi Alejandro, > > I seem to be missing a library of routines that MINC tools needs (eg- > Display) > Here is the response when I call display from the terminal: > > psych-shizgal4:~ conover$ display > dyld: Library not loaded: /sw/lib/libnetpbm.10.dylib > Referenced from: /usr/local/mni/bin/display > Reason: image not found > Trace/BPT trap > > Do I need to download this library? > > -Kent > > On 19-Oct-06, at 12:23 PM, Penhune Lab wrote: > > > Just read the README file if theres one > > USUALLY its ./configure, make, make install > > > > > > On 10/19/06, conover wrote: > >> > >> Hi Alejandro, > >> > >> This sounds interesting - but I don't know how to compile code. Is it > >> easy? > >> > >> -Kent > >> > >> > >> On 19-Oct-06, at 9:23 AM, Penhune Lab wrote: > >> > >>> I've installed emma in a mac (OS X). If i'm not mistaken (it > >>> wasnt an > >>> installation for myself) all i did was compiled it from the source > >>> available > >>> here > >>> http://packages.bic.mni.mcgill.ca/tgz/ > >>> maybe someone else can confirm if this is possible or not? > >>> have you tried this? > >>> > >>> Alejandro > >>> > >>> > >>> On 10/19/06, Paul GRAVEL wrote: > >>>> > >>>> Hi All, > >>>> > >>>> Does anyone know if the emma tools exist for MAC? > >>>> > >>>> Thanks in advance, > >>>> > >>>> Paul > >>>> _______________________________________________ > >>>> MINC-users at bic.mni.mcgill.ca > >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >>>> > >>> > >>> > >>> > >>> -- > >>> Laboratory for Motor Learning and Neural Plasticity > >>> Dr. Virginia Penhune > >>> Department of Psychology, Concordia University > >>> SP-A 244, 7141 Sherbrooke St. W > >>> Montreal, QC H4B 1R6 Canada > >>> (514)848-2424 ext. 7567 > >>> http://psychology.concordia.ca/fac/penhune/winindex.html > >>> _______________________________________________ > >>> MINC-users at bic.mni.mcgill.ca > >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >>> > >> > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > > > > > > > > -- > > Laboratory for Motor Learning and Neural Plasticity > > Dr. Virginia Penhune > > Department of Psychology, Concordia University > > SP-A 244, 7141 Sherbrooke St. W > > Montreal, QC H4B 1R6 Canada > > (514)848-2424 ext. 7567 > > http://psychology.concordia.ca/fac/penhune/winindex.html > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From se at hst.aau.dk Thu Oct 19 10:08:26 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Thu, 19 Oct 2006 16:08:26 +0200 Subject: [MINC-users] minc2dicom ? In-Reply-To: References: <45372C97.4010505@hst.aau.dk> <45374EEE.5030202@hst.aau.dk> Message-ID: <453786DA.3090303@hst.aau.dk> Ok, this demanded a bit of research. I wrote my own c-code for extracting raw slices from minc so I was completely certain about the number channels and the number of bits pr channel. With the code I generated three different raw files (slice 0 from a t1): t1_1ch1b000.raw (1 channel 1 byte pr channel) t1_1ch2b000.raw (1 channel 2 bytes pr channel) t1_3ch1b000.raw (3 channels 1 byte pr channel) Then I used dicom2 to convert to dicom and back to png: dicom2 -d --modality=MRI --size=181:217 t1_1ch1b000.raw dicom2 -p --size=181:217 t1_1ch1b000.raw.dcm Results: t1_1ch1b000.raw.dcm.png looks good t1_1ch2b000.raw.dcm.png is black (with one white pixel ?) The 3 channel image produces a warning when converted to dicom: "bits allocated 24 > 16 are not fully supported... (email me)" ...and an error when the conversion to png is tried: "missing pixel data (58916 words at least expected, 58915 found)!" Now, running the dcm2v on the three produced dicom images result in black images for the two first and an image where the highest intensities are messed up of the 3 channel image. It looks like it expects a signed 8 bit image. convert -size 181x217 -depth 8 RGB:t1_3ch1b000.raw t1_3ch1b000.png produces a nice image, which shows that the 3 channel raw image is generated ok. Any suggestions to how I trick dicom2 into producing the right format (signed 8bit)? Sorry for the verbosity! Simon Andrew Janke wrote: >> for i in `seq 0 $slices`; do >> mincpik -scale 1 $infile tmp.rgb >> mv tmp.rgb tmp.raw >> dicom2 -d --size=$cols:$rows tmp.raw >> dcm2v tmp.raw.dcm -o $prefix\_$i.v >> done >> > > Looks good, although I suspect you will want to add a > > -slice $i > > to the mincpik line. Also I think you can do this with Imagemagick: > > mincpik -slice $1 -scale 1 $infile RGB:tmp.raw > > and do away with the mv command. 'man ImageMagick' will tell more. > > > From alex at bic.mni.mcgill.ca Thu Oct 19 16:37:04 2006 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Thu, 19 Oct 2006 16:37:04 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: References: <45372C97.4010505@hst.aau.dk> Message-ID: <20061019203704.GB16903@bic.mni.mcgill.ca> You may also want to take a look at MIPAV (http://mipav.cit.nih.gov/) which is able to read MINC and write DICOM. Relating to a specific project, we have recently been helping them to improve their MINC to DICOM conversion, but I am not sure if/when those modifications will make it into an official release. As it is it may work for you - YMMV. -- Alex On Thu, Oct 19, 2006 at 10:36:38AM -0400, Andrew Janke wrote: > > I'm stuck with some image conversion problems. I need to convert minc > > into the vista format. I can convert dicom to vista, but I'm not sure if > > there is a tool for converting minc into dicom. > > Maybe I'll have to write some minc2vista code, but I really hope I don't. > > Any suggestions? > > Conversion to DICOM is somethat that I myself never plan to support or > even implement. The main reason being that there is (paradoxically) > no DICOM standard for the sort of thing we do. > > However my suggestion would be something like this: > > for i in `seq 0 `; > do > > mincpik infile.mnc tmp.png; > dicom2 tmp.png out_$i.dcm; > done > > I dont have the syntax for dicom2 right but you can get it from here: > > http://www.barre.nom.fr/medical/dicom2/ > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From acveilleux at mrs.mni.mcgill.ca Thu Oct 19 18:11:49 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 19 Oct 2006 18:11:49 -0400 Subject: [MINC-users] minc2dicom ? In-Reply-To: ; from a.janke@gmail.com on Thu, Oct 19, 2006 at 12:13:54PM -0400 References: <45372C97.4010505@hst.aau.dk> <45374EEE.5030202@hst.aau.dk> Message-ID: <20061019181149.I13524@mrs.mni.mcgill.ca> On Thu, Oct 19, 2006 at 12:13:54PM -0400, Andrew Janke wrote: > > to the mincpik line. Also I think you can do this with Imagemagick: > > mincpik -slice $1 -scale 1 $infile RGB:tmp.raw mincpik might also cause your output to lose resolution and become a byte-volume. Using mincextract would allow you to preserver the (presumably) 16-bit values in your minc file. Not sure if dicom2 can deal with this however. Using the DICOM.pm that's floating around might also be an option. it has some issues with writing files (I have a version that usually work for bog standard Explicit VR little-endian files.) Going this route, the slices should be extracted through mincextract -short usually. It's a bit of a pain to do however. Depends how often you'd need to generate DICOM files. Alex yup, I've had to deal with a bunch of DICOM files in the past few years... From se at hst.aau.dk Fri Oct 20 03:59:42 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Fri, 20 Oct 2006 09:59:42 +0200 Subject: [MINC-users] minc2dicom ? In-Reply-To: <20061019181149.I13524@mrs.mni.mcgill.ca> References: <45372C97.4010505@hst.aau.dk> <45374EEE.5030202@hst.aau.dk> <20061019181149.I13524@mrs.mni.mcgill.ca> Message-ID: <453881EE.2020705@hst.aau.dk> Alexandre CARMEL-VEILLEUX wrote: > > mincpik might also cause your output to lose resolution and become > a byte-volume. > > Using mincextract would allow you to preserver the (presumably) 16-bit > values in your minc file. Not sure if dicom2 can deal with this however. > > Using the DICOM.pm that's floating around might also be an option. it > has some issues with writing files (I have a version that usually work for > bog standard Explicit VR little-endian files.) Going this route, the slices > should be extracted through mincextract -short usually. It's a bit of a pain > to do however. Depends how often you'd need to generate DICOM files. > Well I hope I'll only have to generate a few test cases, as I'm testing an algorithm that only takes vista images as input. If I find the algorithm suitable for my purpose I'll have to implement it myself with minc input of course. I actually ended up writing my own minc2vista converter yesterday (skipping the nasty dicom step). Now I can generate 2D vista images, however, the algorithm apparently needs a 3D image. I guess I'll have to do some more coding, unless anyone have an idea how to generate a 3D vista image. Simon From se at hst.aau.dk Fri Oct 20 07:08:00 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Fri, 20 Oct 2006 13:08:00 +0200 Subject: [MINC-users] minc2dicom ? In-Reply-To: <20061019203704.GB16903@bic.mni.mcgill.ca> References: <45372C97.4010505@hst.aau.dk> <20061019203704.GB16903@bic.mni.mcgill.ca> Message-ID: <4538AE10.4080902@hst.aau.dk> Alex ZIJDENBOS wrote: > You may also want to take a look at MIPAV (http://mipav.cit.nih.gov/) > which is able to read MINC and write DICOM. Relating to a specific > project, we have recently been helping them to improve their MINC to > DICOM conversion, but I am not sure if/when those modifications will > make it into an official release. As it is it may work for you - YMMV. > I tried MIPAV. Had to download the nightly build, as the stable version didn't like my shared libc ? Though the feature for saving as dicom is present no output is generated. Also it is quite a big file converter (166M) :-) Simon From evangelouI at ninds.nih.gov Thu Oct 19 15:57:14 2006 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [F]) Date: Thu, 19 Oct 2006 15:57:14 -0400 Subject: [MINC-users] N3 Crashing on Linux Message-ID: <4B9024D294BBEF45A18A1A360E22B242054CA5C8@NIHCESMLBX.nih.gov> I get the following errors when I type: nu_correct uncor.mnc cor.mnc (from miopen): Can't write compressed file ncredef: ncid -1: Not a netCDF id ncattput: ncid -1: Not a netCDF id ncclose: ncid -1: Not a netCDF id nu_evaluate: crashed while running minc_modify_header (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) my machine is Redhat Linux enterprise 2.6.9-42.0.2.ELsmp #1 SMP version of N3 is n3-1.10-linux-2.6-intel.rpm Thanks in advance Iordanis E. Evangelou, D.Phil. Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Diseases and Stroke National Institutes of Health Bethesda, MD 20892 From fristed at bic.mni.mcgill.ca Fri Oct 20 03:48:33 2006 From: fristed at bic.mni.mcgill.ca (Simon Fristed Eskildsen) Date: Fri, 20 Oct 2006 09:48:33 +0200 Subject: [MINC-users] minc2dicom ? In-Reply-To: <20061019203704.GB16903@bic.mni.mcgill.ca> References: <45372C97.4010505@hst.aau.dk> <20061019203704.GB16903@bic.mni.mcgill.ca> Message-ID: <45387F51.8090004@bic.mni.mcgill.ca> I tried MIPAV. Had to download the nightly build, as the stable version didn't like my shared libc ? Though the feature for saving as dicom is present no output is generated. Also it is quite a big file converter (166M) :-) Simon Alex ZIJDENBOS wrote: > You may also want to take a look at MIPAV (http://mipav.cit.nih.gov/) > which is able to read MINC and write DICOM. Relating to a specific > project, we have recently been helping them to improve their MINC to > DICOM conversion, but I am not sure if/when those modifications will > make it into an official release. As it is it may work for you - YMMV. > > -- Alex > > > From syl at bic.mni.mcgill.ca Mon Oct 23 18:12:19 2006 From: syl at bic.mni.mcgill.ca (Sylvia Cox) Date: Mon, 23 Oct 2006 18:12:19 -0400 Subject: [MINC-users] mincrealign - reference point Message-ID: <453D3E43.30505@bic.mni.mcgill.ca> Hi all, Can anyone tell me what the reference point (x,y,z coordinates) is for the rotations and translations of head movement calculated in mincrealign. Thanks, Sylvia From albertleemon at gmail.com Mon Oct 23 06:21:10 2006 From: albertleemon at gmail.com (leemon albert) Date: Mon, 23 Oct 2006 03:21:10 -0700 Subject: [MINC-users] =?gb2312?b?bGVlbW9uIGFsYmVydCDP67j6xPrBxMzs?= Message-ID: <80363be10610230321i4c365b6fj@mail.gmail.com> -----------------------------------------------------------------------leemon albert ???? Google ?????????????????? ?????? Gmail ? Google Talk?????http://mail.google.com/mail/b-1ce655ccab-ce21fed50c-397e7c59641cf9cf??????????? leemon albert ??? ??? Gmail - Google ????? 2,600 ???????????????? - ?? leemon albert ???????http://mail.google.com/mail/a-1ce655ccab-ce21fed50c-a9ba357d55 Gmail ???- ????????????- ?????????????????????"??"?????- ????????????????? - ?????????????????????- ???? Gmail ??????? ??????????????????????????????????? Google Talk? http://www.google.com/talk/ ??????? Windows* ???????????????????????????????????????????????????????? Gmail ? Google Talk???????????????????????????????????????????????????????????????????? ?????Google ???? ????? Gmail ? Google Talk ????????http://mail.google.com/mail/help/intl/zh-CN/about.htmlhttp://www.google.com/talk/about.html ????????????????????????????????????????? *??? Windows ?????????????????????(http://www.google.com/talk/otherclients.html) ???????? Google Talk??? From albertleemon at gmail.com Mon Oct 23 06:25:23 2006 From: albertleemon at gmail.com (leemon albert) Date: Mon, 23 Oct 2006 18:25:23 +0800 Subject: [MINC-users] installation problem of minc-2.0.09 on Linux Message-ID: <80363be10610230325t2bb81ac5o7f44583661c079ae@mail.gmail.com> Hello, Basically, I am trying to install minc-2.0.09 on a Linux system running ununtu 6.06LTS. I have successfully instatlled netcdf (v3.6.1),However, when I run configure for minc-2.0.09 ./configure --with-build-path=/home/leemon/ubuntu/netcdf-3.6.1 I get the following error: checking for library m... yes checking for library netcdf... yes checking for library z... no configure: error: cannot find required library z What needs to be done to resolve this error? If I haven't got something quite right,please let me know.Thanks Thanks, Leemon From jharlap at bic.mni.mcgill.ca Tue Oct 24 10:20:12 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Tue, 24 Oct 2006 10:20:12 -0400 Subject: [MINC-users] installation problem of minc-2.0.09 on Linux In-Reply-To: <80363be10610230325t2bb81ac5o7f44583661c079ae@mail.gmail.com> References: <80363be10610230325t2bb81ac5o7f44583661c079ae@mail.gmail.com> Message-ID: <453E211C.3060504@bic.mni.mcgill.ca> Hi, You need to apt-get install zlib1g-dev. Cheers, Jon leemon albert wrote: > Hello, > Basically, I am trying to install minc-2.0.09 on a Linux system running > ununtu 6.06LTS. I have successfully instatlled netcdf (v3.6.1),However, when > I run configure for minc-2.0.09 > > ./configure --with-build-path=/home/leemon/ubuntu/netcdf-3.6.1 > > I get the following error: > checking for library m... yes > checking for library netcdf... yes > checking for library z... no > configure: error: cannot find required library z > > What needs to be done to resolve this error? If I haven't got something > quite right,please let me know.Thanks > > Thanks, > Leemon > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From muehlboeck at gmail.com Tue Oct 24 10:01:52 2006 From: muehlboeck at gmail.com (J-S Muehlboeck) Date: Tue, 24 Oct 2006 10:01:52 -0400 Subject: [MINC-users] installation problem of minc-2.0.09 on Linux In-Reply-To: <80363be10610230325t2bb81ac5o7f44583661c079ae@mail.gmail.com> References: <80363be10610230325t2bb81ac5o7f44583661c079ae@mail.gmail.com> Message-ID: <783bf6700610240701h7153548fm605ad7541e11d9e8@mail.gmail.com> Hi, these are the packages I usually install before building mincy stuff on ubuntu ... sudo apt-get install build-essential lapack3-dev libnetpbm9-dev fftw-dev libx11-dev freeglut3-dev libgmp3-dev libgnome-perl zlib1g-dev gawk m4 libgnome2-dev libgnome-dev xlibs-dev libcoin40-dev r-base Sebastian On 10/23/06, leemon albert wrote: > > Hello, > Basically, I am trying to install minc-2.0.09 on a Linux system running > ununtu 6.06LTS. I have successfully instatlled netcdf (v3.6.1),However, > when > I run configure for minc-2.0.09 > > ./configure --with-build-path=/home/leemon/ubuntu/netcdf-3.6.1 > > I get the following error: > checking for library m... yes > checking for library netcdf... yes > checking for library z... no > configure: error: cannot find required library z > > What needs to be done to resolve this error? If I haven't got something > quite right,please let me know.Thanks > > Thanks, > Leemon > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Oct 26 01:34:58 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 26 Oct 2006 01:34:58 -0400 Subject: [MINC-users] mincrealign - reference point In-Reply-To: <453D3E43.30505@bic.mni.mcgill.ca> References: <453D3E43.30505@bic.mni.mcgill.ca> Message-ID: On 10/23/06, Sylvia Cox wrote: > Hi all, > Can anyone tell me what the reference point (x,y,z coordinates) is for > the rotations and translations of head movement calculated in mincrealign. I'm afraid you lost me, I have never heard of mincrealign? Where is it and where did you get it? :) -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From abraham.gedamu at gmail.com Thu Oct 26 10:31:01 2006 From: abraham.gedamu at gmail.com (Abraham Gedamu) Date: Thu, 26 Oct 2006 10:31:01 -0400 Subject: [MINC-users] Naming the axis for a 4 Dimensional MNC file Message-ID: I know for a 3D mnc file the value passed as the dim_names array should be the three strings, MIxspace, MIzspace, and MIyspace (order is important, as it defines the order of any subsequent reference to voxel indices). If you have a 4D mnc file, what string name is passed in dim_names array to indicate the 4th dimension? Thanks, Abe From a.janke at gmail.com Thu Oct 26 10:37:00 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 26 Oct 2006 10:37:00 -0400 Subject: [MINC-users] Naming the axis for a 4 Dimensional MNC file In-Reply-To: References: Message-ID: The naming is entirely arbitrary. For example: $ mincconcat -concat_dimension freddy \ ~/data/me/janke_andrew_256x256x256_T1.mnc out.mnc audrey:rotor$ mincinfo out.mnc file: out.mnc image: signed__ short -32768 to 32767 image dimensions: freddy zspace yspace xspace dimension name length step start -------------- ------ ---- ----- freddy 1 1 0 zspace 256 0.9375 -116.135 yspace 256 0.9 -89.0348 xspace 256 0.9375 -118.179 That said, there are a few fairly standard names such as "time" and "vector_dimension". a On 10/26/06, Abraham Gedamu wrote: > I know for a 3D mnc file the value passed as the dim_names array should be > the three strings, MIxspace, MIzspace, and MIyspace (order is important, as > it defines the order of any subsequent reference to voxel indices). If you > have a 4D mnc file, what string name is passed in dim_names array to > indicate the 4th dimension? > > Thanks, > > Abe > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From albertleemon at gmail.com Thu Oct 26 11:31:17 2006 From: albertleemon at gmail.com (leemon albert) Date: Thu, 26 Oct 2006 23:31:17 +0800 Subject: [MINC-users] bicpl cannot find hdf5 during configuration Message-ID: <80363be10610260831o1946b4ccn94440e616470e51c@mail.gmail.com> Hi, Sorry if this issue has already been addressed before. I am trying to compile the basic packages minc2 (minc2.0.11) for Ubuntu. So far, I have been able to successfully install the packages in the following order: netcdf hdf5-1.6.1 minc-2.0.11 However, for bicpl-1.4.2, I get the following problem: .... checking for library m... yes checking for library netcdf... yes checking for library z... yes checking for library hdf5... no configure: error: cannot find required library hdf5 Is there some flag that I need to specify during configuration to get the script to recognize hdf5? I tried defining sudo ./configure --prefix=/usr/local/bin --with-build-path=/usr/local/bin --with-minc2 Thanks Help is appreciated! From a.janke at gmail.com Thu Oct 26 11:39:51 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 26 Oct 2006 11:39:51 -0400 Subject: [MINC-users] bicpl cannot find hdf5 during configuration In-Reply-To: <80363be10610260831o1946b4ccn94440e616470e51c@mail.gmail.com> References: <80363be10610260831o1946b4ccn94440e616470e51c@mail.gmail.com> Message-ID: --with-build-path=/usr/ ? a On 10/26/06, leemon albert wrote: > Hi, > Sorry if this issue has already been addressed before. > I am trying to compile the basic packages minc2 (minc2.0.11) for Ubuntu. > So far, I have been able to successfully install the packages in the > following order: > > netcdf > hdf5-1.6.1 > minc-2.0.11 > > However, for bicpl-1.4.2, I get the following problem: > .... > checking for library m... yes > checking for library netcdf... yes > checking for library z... yes > checking for library hdf5... no > configure: error: cannot find required library hdf5 > > Is there some flag that I need to specify during configuration to get > the script to recognize hdf5? > I tried defining sudo ./configure --prefix=/usr/local/bin > --with-build-path=/usr/local/bin --with-minc2 > Thanks > > Help is appreciated! > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From jharlap at bic.mni.mcgill.ca Thu Oct 26 11:44:37 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Thu, 26 Oct 2006 11:44:37 -0400 Subject: [MINC-users] bicpl cannot find hdf5 during configuration In-Reply-To: <80363be10610260831o1946b4ccn94440e616470e51c@mail.gmail.com> References: <80363be10610260831o1946b4ccn94440e616470e51c@mail.gmail.com> Message-ID: <4540D7E5.3000503@bic.mni.mcgill.ca> You should probably have both prefix and build path set to /usr/local rather than /usr/local/bin, otherwise it will look for (and install) libraries in /usr/local/bin/lib, binaries in /usr/local/bin/bin and so on. Cheers, J leemon albert wrote: > Hi, > Sorry if this issue has already been addressed before. > I am trying to compile the basic packages minc2 (minc2.0.11) for Ubuntu. > So far, I have been able to successfully install the packages in the > following order: > > netcdf > hdf5-1.6.1 > minc-2.0.11 > > However, for bicpl-1.4.2, I get the following problem: > .... > checking for library m... yes > checking for library netcdf... yes > checking for library z... yes > checking for library hdf5... no > configure: error: cannot find required library hdf5 > > Is there some flag that I need to specify during configuration to get > the script to recognize hdf5? > I tried defining sudo ./configure --prefix=/usr/local/bin > --with-build-path=/usr/local/bin --with-minc2 > Thanks > > Help is appreciated! > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From syl at bic.mni.mcgill.ca Thu Oct 26 12:17:39 2006 From: syl at bic.mni.mcgill.ca (Sylvia Cox) Date: Thu, 26 Oct 2006 12:17:39 -0400 Subject: [MINC-users] mincrealign - reference point In-Reply-To: References: <453D3E43.30505@bic.mni.mcgill.ca> Message-ID: <4540DFA3.3040900@bic.mni.mcgill.ca> Hey Andrew, thanks for your reply....mincrealign was developed by Anthonin Reilhac and Sebastien Sechet..to correct for motion in our PET (raclopride) images....it's in /data/disk2/anthonin/bin/mincrealign... Cheers, Syl Andrew Janke wrote: > On 10/23/06, Sylvia Cox wrote: >> Hi all, >> Can anyone tell me what the reference point (x,y,z coordinates) is for >> the rotations and translations of head movement calculated in mincrealign. > > I'm afraid you lost me, I have never heard of mincrealign? Where is > it and where did you get it? :) > > From cmark at bic.mni.mcgill.ca Thu Oct 26 12:23:56 2006 From: cmark at bic.mni.mcgill.ca (Clarisse MARK) Date: Thu, 26 Oct 2006 12:23:56 -0400 Subject: [MINC-users] Installing MINC & X-term Message-ID: <4540E11C.7040807@bic.mni.mcgill.ca> Hi, I downloaded the MINC package on my MAC and was wondering how to use it ? Any paths I need to define ? Also, if I wanted to run xdisp/mincview/register on an ssh connection from home, how would I do it ? Inserting '-X' on the command line does not seem to work. Thanks ! Clarisse -- Clarisse Mark, M.Sc., P.Eng. PhD Candidate McConnell Brain Imaging Center Montreal Neurological Institute 3801 University Street, WB-325 Montreal, Quebec CANADA, H3A 2B4 tel:(514)398-8547 fax:(514)398-2975 email: cmark at bic.mni.mcgill.ca From jharlap at bic.mni.mcgill.ca Thu Oct 26 12:36:19 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Thu, 26 Oct 2006 12:36:19 -0400 Subject: [MINC-users] Installing MINC & X-term In-Reply-To: <4540E11C.7040807@bic.mni.mcgill.ca> References: <4540E11C.7040807@bic.mni.mcgill.ca> Message-ID: <4540E403.8080702@bic.mni.mcgill.ca> To run gui stuff using X with ssh you'd need to be using an X11 server on your mac rather than the standard Terminal. If you're running Panther (10.3) you can use the Apple X11 server at http://www.apple.com/downloads/macosx/apple/x11formacosx.html, while if you're running Tiger the X11 server is on the Tiger install DVD. I can't comment on the minc package for mac as it isn't clear which minc package you're using (Andrew's recent binaries from packages.bic..., the source tarball, Jason's outdated binaries from www/software/distribution/). If you don't want to compile your own stuff, you should probably use Andrew's binaries from packages.bic. Cheers, Jon Clarisse MARK wrote: > Hi, > > I downloaded the MINC package on my MAC and was wondering > how to use it ? Any paths I need to define ? > > Also, if I wanted to run xdisp/mincview/register on an ssh > connection from home, how would I do it ? Inserting '-X' on the command line > does not seem to work. > > Thanks ! > Clarisse > From mhough at fmrib.ox.ac.uk Thu Oct 26 12:39:05 2006 From: mhough at fmrib.ox.ac.uk (Morgan G. Hough) Date: Thu, 26 Oct 2006 17:39:05 +0100 Subject: [MINC-users] Installing MINC & X-term In-Reply-To: <4540E11C.7040807@bic.mni.mcgill.ca> References: <4540E11C.7040807@bic.mni.mcgill.ca> Message-ID: <1161880745.4932.26.camel@dhania.fmrib.ox.ac.uk> Clarrise, You might try -Y instead of -X for tunneling X-Windows over ssh. I personally find VNC a faster way to work remotely but OpenGL applications will need real X-windows. Hope that helps. Cheers, -Morgan On Thu, 2006-10-26 at 12:23 -0400, Clarisse MARK wrote: > Hi, > > I downloaded the MINC package on my MAC and was wondering > how to use it ? Any paths I need to define ? > > Also, if I wanted to run xdisp/mincview/register on an ssh > connection from home, how would I do it ? Inserting '-X' on the command line > does not seem to work. > > Thanks ! > Clarisse > -- Morgan Hough DPhil candidate FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK mhough at fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 From acveilleux at mrs.mni.mcgill.ca Thu Oct 26 13:30:28 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 26 Oct 2006 13:30:28 -0400 Subject: [MINC-users] Installing MINC & X-term In-Reply-To: <1161880745.4932.26.camel@dhania.fmrib.ox.ac.uk>; from mhough@fmrib.ox.ac.uk on Thu, Oct 26, 2006 at 05:39:05PM +0100 References: <4540E11C.7040807@bic.mni.mcgill.ca> <1161880745.4932.26.camel@dhania.fmrib.ox.ac.uk> Message-ID: <20061026133028.D23776@mrs.mni.mcgill.ca> Also, some of the newer Minc packages for Mac have a native version of Display and register that does not use X and so can't be used remotely that way. Alex On Thu, Oct 26, 2006 at 05:39:05PM +0100, Morgan G. Hough wrote: > From: "Morgan G. Hough" > To: MINC users mailing list > Date: Thu, 26 Oct 2006 17:39:05 +0100 > X-Mailer: Evolution 2.2.3 (2.2.3-4.fc4) > Subject: Re: [MINC-users] Installing MINC & X-term > > Clarrise, > > You might try -Y instead of -X for tunneling X-Windows over ssh. I > personally find VNC a faster way to work remotely but OpenGL > applications will need real X-windows. Hope that helps. > > Cheers, > > -Morgan > > On Thu, 2006-10-26 at 12:23 -0400, Clarisse MARK wrote: > > Hi, > > > > I downloaded the MINC package on my MAC and was wondering > > how to use it ? Any paths I need to define ? > > > > Also, if I wanted to run xdisp/mincview/register on an ssh > > connection from home, how would I do it ? Inserting '-X' on the command line > > does not seem to work. > > > > Thanks ! > > Clarisse > > > -- > Morgan Hough DPhil candidate > FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > mhough at fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough > tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From se at hst.aau.dk Thu Oct 26 14:25:42 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Thu, 26 Oct 2006 14:25:42 -0400 Subject: [MINC-users] Naming the axis for a 4 Dimensional MNC file In-Reply-To: References: Message-ID: <4540FDA6.8020507@hst.aau.dk> Andrew Janke wrote: > The naming is entirely arbitrary. For example: > > $ mincconcat -concat_dimension freddy \ > ~/data/me/janke_andrew_256x256x256_T1.mnc out.mnc > > audrey:rotor$ mincinfo out.mnc > file: out.mnc > image: signed__ short -32768 to 32767 > image dimensions: freddy zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > freddy 1 1 0 > zspace 256 0.9375 -116.135 > yspace 256 0.9 -89.0348 > xspace 256 0.9375 -118.179 > > That said, there are a few fairly standard names such as "time" and > "vector_dimension". From minc.h: /* Dimension names and names of associated variables */ #define MIxspace "xspace" #define MIyspace "yspace" #define MIzspace "zspace" #define MItime "time" #define MItfrequency "tfrequency" #define MIxfrequency "xfrequency" #define MIyfrequency "yfrequency" #define MIzfrequency "zfrequency" #define MIvector_dimension "vector_dimension" #define MIxspace_width "xspace-width" #define MIyspace_width "yspace-width" #define MIzspace_width "zspace-width" #define MItime_width "time-width" #define MItfrequency_width "tfrequency-width" #define MIxfrequency_width "xfrequency-width" #define MIyfrequency_width "yfrequency-width" #define MIzfrequency_width "zfrequency-width" I'm also somewhat confused about when to use other names than x,y,z space names. I have a vector image that I need to write as a 4D minc volume. Should I use the vector_dimension, and if so what is the dimension order? vector,z,y,x or z,y,x,vector ? Simon From a.janke at gmail.com Fri Oct 27 01:52:51 2006 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 27 Oct 2006 01:52:51 -0400 Subject: [MINC-users] Naming the axis for a 4 Dimensional MNC file In-Reply-To: <4540FDA6.8020507@hst.aau.dk> References: <4540FDA6.8020507@hst.aau.dk> Message-ID: > I'm also somewhat confused about when to use other names than x,y,z > space names. I have a vector image that I need to write as a 4D minc > volume. Should I use the vector_dimension, and if so what is the > dimension order? vector,z,y,x or z,y,x,vector ? In this case, vector_dimension would seem the most likely candidate. As for the order it is entirely up to you. You can always re-order it later should you wish with mincreshape -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From bert at bic.mni.mcgill.ca Sun Oct 29 08:55:07 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Sun, 29 Oct 2006 08:55:07 -0500 Subject: [MINC-users] Naming the axis for a 4 Dimensional MNC file In-Reply-To: Message-ID: Hi, One thing to keep in mind is that some tools expect vector_dimension to be the fastest-varying (i.e. last) dimension in the file. This is true of mincmakescalar in particular. At least some versions of this tool will fail silently if used on a file that has a vector_dimension that is _not_ the last dimension in the file. -bert On Fri, 27 Oct 2006, Andrew Janke wrote: > > I'm also somewhat confused about when to use other names than x,y,z > > space names. I have a vector image that I need to write as a 4D minc > > volume. Should I use the vector_dimension, and if so what is the > > dimension order? vector,z,y,x or z,y,x,vector ? > > In this case, vector_dimension would seem the most likely candidate. > As for the order it is entirely up to you. You can always re-order it > later should you wish with mincreshape > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From albertleemon at gmail.com Sun Oct 29 20:43:21 2006 From: albertleemon at gmail.com (leemon albert) Date: Mon, 30 Oct 2006 09:43:21 +0800 Subject: [MINC-users] Motion Correction problem about fmr_preprocess Message-ID: <80363be10610291743q1516a460k6c03d77678898144@mail.gmail.com> Hi, As a beginner, I'm somewhat confused about how to run motion correction by fmr_preprocess. For example,I load a fMRI file:"003.mnc",then run fmr_preprocess,I get the another file "003-SM.mnc" in the current direction.But if applied Motion Correction to a mnc file, the motion-corrected series should appear with suffix"-MC.mnc"? So what is the "003-SM.mnc"? "003-SM.mnc = 003-MC.mnc"? yes or no.if no,how can I get the right 003-MC.mnc. Thanks! From Kent.Conover at concordia.ca Tue Oct 31 12:48:56 2006 From: Kent.Conover at concordia.ca (conover) Date: Tue, 31 Oct 2006 12:48:56 -0500 Subject: [MINC-users] EMMA mireadimages read file error Message-ID: <00C0A179-8323-48EB-A6E2-3BB2406F6DE1@concordia.ca> The Matlab EMMA function mireadimages.m crashes Matlab when I attempt to read one slice (64x64) over more than 250 frames at once. Has anyone encountered this error before? If so, can this error be resolved? Regards, Kent Conover, Ph. D. Centre for Studies in Behavioral Neurobiology, Concordia University, Montreal, Quebec, Canada