From rotor@cmr.uq.edu.au Mon May 10 03:04:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Mon May 10 02:04:04 2004 Subject: [MINC-users] converting one format to minc In-Reply-To: <02c801c41e89$b7398710$0affc30a@quark> References: <02c801c41e89$b7398710$0affc30a@quark> Message-ID: First, sorry about the late reply here, I have been overseas.. On Sat, 10 Apr 2004, Gibby Koldenhof wrote: > I'm writing up some code to convert a number of file formats to minc (I'm > using minc 1.2). For some reason I get strange results. When trying to convert > 16bit signed raw data I get strange results. I first convert the raw data > using minctoraw: > > rawtominc -short -input raw.raw -scan_range -xstep 1.0 -ystep 1.0 -zstep 1.0 > a.mnc 100 100 100 > > GET_VALUE_3D(value, volume, x, y, z); > *voxels++ = value; > > mincinfo says both the files are the same, yet mincdiff tells me that the data > is different. And indeed when I internally compare all the voxels about 1/6th > of the voxels have a difference of 1 (integer, e.g. a voxel from a.mnc is 203 > and from b.mnc is 204 for example) - strangly enough when loading both files > into register they look exactly the same. > > ... how ... why ... I can't understand what is going wrong. I do not do any > floating point conversion anywhere (since it looks like a roundoff error) ... > I tried pretty much everything (e.g. changing the parameters to each call) Gibby, Assuming I can correctly grok what you have done here, I think you are getting caught up with the difference between a real and a voxel range in MINC. Byt simply incrementing the real value of all the voxels you have effectively just changed the scaling of the volume. Also register's precision is limited to byte (0..256) to the point that when a volume is loaded the whole volume is scaled to byte precision and effectively only a scaling and offset value are stored to convert to the "real value". If you are concerned that what you are doing really is "correct" or not, there are a few things you can do: 1: Increment the VOXEL value directly and see that this range is stored correctly (if indeed this is what you are trying to do) 2: Store the volumes in question in float or double precision at which stge the difference between voxel and real ranges is irrelevant. But never fear! keep up the good work writing converters, I'll be more than interested to havea copy of what you have done once you are finished. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From jeremy.johnston-kaye@mail.mcgill.ca Thu May 13 02:16:05 2004 From: jeremy.johnston-kaye@mail.mcgill.ca (Jeremy) Date: Thu May 13 01:16:05 2004 Subject: [MINC-users] MRITOTAL Message-ID: <200405121845.i4CIj2E9024463@viroid.mcgill.ca> This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C4382F.B4FB6850 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit We want to reduce head motion between runs. We need to Talairach each individual run. We were doing this by first aligning it to the anatomical using MRITOSELF and then applying the Talaraich transform matrix from MRITOTAL. However for some subjects we get: Error in /usr/local/mni/bin/minctracc in file init_params.c, line 962 Cannot calculate the COG of volume 1 .mritoself: crashed while running minctracc (exit status=65280) Does anybody know why would be getting this error? Also, is there a better way to Talaraich each of the runs without MRITOSELF? Thanks ------=_NextPart_000_0011_01C4382F.B4FB6850 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

We want to reduce head motion between runs. We need = to Talairach each individual run. We were doing this by first aligning it = to the anatomical using MRITOSELF and then applying the Talaraich transform = matrix from MRITOTAL. However for some subjects we = get:

Error in /usr/local/mni/bin/minctracc in file = init_params.c, line 962

Cannot calculate the COG of volume = 1

.mritoself: crashed while running minctracc (exit status=3D65280)

Does anybody know why would be getting this error? = Also, is there a better way to Talaraich each of the runs without = MRITOSELF?

Thanks

------=_NextPart_000_0011_01C4382F.B4FB6850-- From tguo@imaging.robarts.ca Thu May 13 15:08:04 2004 From: tguo@imaging.robarts.ca ((Jessie) Ting Guo) Date: Thu May 13 14:08:04 2004 Subject: [MINC-users] Problem with fMRISTAT and Emma References: <200405121845.i4CIj2E9024463@viroid.mcgill.ca> Message-ID: <001901c43915$34ecff20$c32914c6@irus.robarts.ca> This is a multi-part message in MIME format. ------=_NextPart_000_0016_01C438F3.AD9B21D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am starting using fMRISTAT on Windows 2000 to analyze fMRI data, but = have some problems. Any help will be greatly appreciated. 1. Looking at the fMRI data using pca_image. input_file=3D'd:\fMRI\fmristat\data\data\brian_ha+19971124_1_100326_mri_M= C.mnc' mask_filel=3Dinput_file; mask_thresh=3Dfmri_mask_thresh(mask_file); Error message: ??? Attempt to execute SCRIPT miinquire as a function. Error in =3D=3D> C:\MATLAB6p5\work\fmris_read_minc.m On line 5 =3D=3D> d.dim =3D fliplr(miinquire(file,'imagesize')'); Error in =3D=3D> C:\MATLAB6p5\work\fmris_read_image.m On line 28 =3D=3D> d =3D fmris_read_minc(file,Z,T); Error in =3D=3D> C:\MATLAB6p5\work\fmri_mask_thresh.m On line 32 =3D=3D> dm=3Dfmris_read_image(fmri_file,0,0); What's the problem and how to resolve it? 2. For installing emma, I put the three .dll files and three .exe files = in matlab/bin/win32 directory. What else should I do? Do I need to = execute the three .exe files and how?=20 Thank you very much in advance. Jessie ------=_NextPart_000_0016_01C438F3.AD9B21D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

I am starting using fMRISTAT on = Windows 2000=20 to analyze fMRI data, but have some problems. Any help will be greatly=20 appreciated.

1. Looking at the fMRI data using=20 pca_image.

input_file=3D'd:\fMRI\fmristat\data\data\brian_ha+19971124_1_100= 326_mri_MC.mnc'

mask_filel=3Dinput_file;
mask_thresh=3Dfmri_mask_thresh(mask_= file);

Error message:

??? Attempt to execute = SCRIPT=20 miinquire as a function.

Error in =3D=3D>=20 C:\MATLAB6p5\work\fmris_read_minc.m
On line 5 =3D=3D> d.dim = =3D=20 fliplr(miinquire(file,'imagesize')');

Error in =3D=3D>=20 C:\MATLAB6p5\work\fmris_read_image.m
On line 28 =20 =3D=3D> d =3D=20 fmris_read_minc(file,Z,T);

Error in =3D=3D>=20 C:\MATLAB6p5\work\fmri_mask_thresh.m
On line 32 =3D=3D>=20 dm=3Dfmris_read_image(fmri_file,0,0);

What's the problem and how to resolve=20 it?

2. For installing emma, = I put the three=20 .dll files and three .exe files in matlab/bin/win32 directory. What = else=20 should I do? Do I need to execute the three .exe files and how? =

Thank you very much in = advance.

Jessie

------=_NextPart_000_0016_01C438F3.AD9B21D0-- From ali.soleymani@mail.mcgill.ca Mon May 17 11:27:04 2004 From: ali.soleymani@mail.mcgill.ca (Ali Soleymani) Date: Mon May 17 10:27:04 2004 Subject: [MINC-users] need help for installation of minctools Message-ID: <1084803611.40a8ca1b20a48@www.webmail.mcgill.ca> Hi, I am trying to install minctools and programs on redhat linux 9.0. I used the source code for netcdf. but I think it is not installed successfully, since when I attempt to compile minc-tools 1.2 it gives me following messege: checking for library netcdf... no configure: error: cannot find required library netcdf I assigned new path to find NETCDF_LIB and it didn't work. ( I ' m afraid I' m missing libnetcdf_c++.a, libnetcdf.so, libnetcdf_c++.so , for some reasons.) I appreciate your help. Ali From pgravel@bic.mni.mcgill.ca Mon May 17 15:02:05 2004 From: pgravel@bic.mni.mcgill.ca (Paul GRAVEL) Date: Mon May 17 14:02:05 2004 Subject: [MINC-users] Minc Tools Message-ID: Hi All, Are the minc tools freely distributed or does a research center not affiliated with McGill/MNI/BIC need to purchase a copy of the tools? When using a PC, I assume that Linux would be the OS of choice for the minc tools instead of Windows XP. Am I correct or am I assuming too much? Best Regards, Paul _____________________________ Paul Gravel Neurobiological Psychiatry Unit McGill University 1033 Pine Avenue West Montreal, Quebec, Canada, H3A 1A1 Phone: (514) 398-7301 Fax: (514) 398-4866 From colliot@bic.mni.mcgill.ca Mon May 17 15:15:05 2004 From: colliot@bic.mni.mcgill.ca (Olivier Colliot) Date: Mon May 17 14:15:05 2004 Subject: [MINC-users] need help for installation of minctools References: <1084803611.40a8ca1b20a48@www.webmail.mcgill.ca> Message-ID: <40A90166.3050701@bic.mni.mcgill.ca> When you compiled MINC, did you provide the following options : ./configure --prefix=my_install_dir --with-build-path=my_install_dir where "my_install_dir" is the directory in which you installed netcdf and in which you want to install minc. (netcdf should have been compiled with ./configure --prefix=my_install_dir) Ali Soleymani wrote: >Hi, >I am trying to install minctools and programs on redhat linux 9.0. >I used the source code for netcdf. but I think it is not installed >successfully, >since when I attempt to compile minc-tools 1.2 it gives me following messege: >checking for library netcdf... no >configure: error: cannot find required library netcdf >I assigned new path to find NETCDF_LIB and it didn't work. >( I ' m afraid I' m missing libnetcdf_c++.a, libnetcdf.so, libnetcdf_c++.so , >for some reasons.) > >I appreciate your help. > >Ali > >_______________________________________________ >MINC-users@bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From jason@bic.mni.mcgill.ca Mon May 17 15:38:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Mon May 17 14:38:04 2004 Subject: [MINC-users] Minc Tools In-Reply-To: References: Message-ID: <4BC7C236-A831-11D8-A7DC-000A95DBBFD8@bic.mni.mcgill.ca> Hello Paul, > > Are the minc tools freely distributed or does a research center not > affiliated with McGill/MNI/BIC need to purchase a copy of the tools? Everything you see on the website is freely distributed. For anything else ask first. (the website is: http://www.bic.mni.mcgill.ca/software/distribution) > > When using a PC, I assume that Linux would be the OS of choice for the > minc tools instead of Windows XP. Am I correct or am I assuming too > much? Correct - Linux and IRIX are best supported, followed by OS X, then somewhere down the list windows (though that is getting better, I hear). Cheers, Jason From rotor@cmr.uq.edu.au Mon May 17 21:01:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Mon May 17 20:01:04 2004 Subject: [MINC-users] Minc Tools In-Reply-To: <4BC7C236-A831-11D8-A7DC-000A95DBBFD8@bic.mni.mcgill.ca> References: <4BC7C236-A831-11D8-A7DC-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: On Mon, 17 May 2004, Jason Lerch wrote: > > When using a PC, I assume that Linux would be the OS of choice for the > > minc tools instead of Windows XP. Am I correct or am I assuming too > > much? > > Correct - Linux and IRIX are best supported, followed by OS X, then > somewhere down the list windows (though that is getting better, I > hear). Jason is showwing his own personal bias here.. :) There is a binary w32 installer thanks to Gibby Koldenhof: http://sourceforge.net/projects/mni-minc-win32/ However unless you are running XP then things such as pipes and perl are going to be a bit of a pain. In this case you would be best of to use Cygwin. All the core minc tools compile with no modifications under cygwin. If however you have some trouble compiling for cygwin I can provide a tar.gz of everything that I have compiled for cygwin. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Tue May 18 04:45:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue May 18 03:45:05 2004 Subject: [MINC-users] MRITOTAL In-Reply-To: <200405121845.i4CIj2E9024463@viroid.mcgill.ca> References: <200405121845.i4CIj2E9024463@viroid.mcgill.ca> Message-ID: On Wed, 12 May 2004, Jeremy wrote: > We want to reduce head motion between runs. We need to Talairach each > individual run. We were doing this by first aligning it to the anatomical > using MRITOSELF and then applying the Talaraich transform matrix from > MRITOTAL. However for some subjects we get: > > Error in /usr/local/mni/bin/minctracc in file init_params.c, line 962 > > Cannot calculate the COG of volume 1 > > .mritoself: crashed while running minctracc (exit status=65280) jeremy, Which version of mni_autoreg are you running? An errant build did make it out into the mainstream a while back, this is a known problem. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From jchen@bic.mni.mcgill.ca Tue May 18 21:18:08 2004 From: jchen@bic.mni.mcgill.ca (Jeni Chen) Date: Tue May 18 20:18:08 2004 Subject: [MINC-users] voxel coordinates in native space vs. Message-ID: Hi, I'm just wondering if anyone knew how to convert a set of tal coordinates back into native space (i.e finding the equivalent). For instance, take the Talairach coordinates 6 -8 44. In register we see the corresponding voxel coordinates as 48 59 58. But if I want to look for the exact same peak in the original raw data, how can I find it? Is there a program or mathematical formula to do it? Any insight would be greately appreciated. Thanks! Jen-I Chen Agente de Recherche Centre de Recherche en Sciences Neurologiques Pavillon Paul Desmarais, Universit de Montral C.P. 6128, Succ. A, Montral, QC H3C 3J7 Tel:(514) 343-6111 ext.4359 Fax:(514) 343-2111 From mdesco@cim.mcgill.ca Wed May 19 12:46:04 2004 From: mdesco@cim.mcgill.ca (Maxime Descoteaux) Date: Wed May 19 11:46:04 2004 Subject: [MINC-users] minc history Message-ID: <33019.132.206.73.105.1084981547.squirrel@www.cim.mcgill.ca> Hi all, Is there an easy way to concatinate a new string to the current volume history string when outputting a volume? Thanks -- Maxime Descoteaux phone: (514) 989-8670 Centre for Intelligent Machines phone: (514) 398-5606 Masters in Computer Science McGill University http://www.cim.mcgill.ca/~mdesco From bert@bic.mni.mcgill.ca Wed May 19 13:05:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Wed May 19 12:05:04 2004 Subject: [MINC-users] minc history In-Reply-To: <33019.132.206.73.105.1084981547.squirrel@www.cim.mcgill.ca> Message-ID: Hi, I've added a new function "miappend_history()" to do just this in MINC 2.0. This is checked into CVS but not yet in an official release. The beta for MINC 2.0 is at http://www.bic.mni.mcgill.ca/~bert/minc-2.0.06.tar.gz Volume_io already has a function named "add_minc_history()" which may do what you want. -bert On Wed, 19 May 2004, Maxime Descoteaux wrote: > Hi all, > > Is there an easy way to concatinate a new string to the current volume > history string when outputting a volume? > > Thanks > > > -- > Maxime Descoteaux phone: (514) 989-8670 > Centre for Intelligent Machines phone: (514) 398-5606 > Masters in Computer Science > McGill University > http://www.cim.mcgill.ca/~mdesco > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sylvain@bic.mni.mcgill.ca Wed May 19 13:21:04 2004 From: sylvain@bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed May 19 12:21:04 2004 Subject: [MINC-users] minc history In-Reply-To: <33019.132.206.73.105.1084981547.squirrel@www.cim.mcgill.ca> Message-ID: hello, unless someone has written a litter perl script to do this? use minc_modify_header but you will have to extract the original history value, append to it and overwrite it with minc_modify_header Sylvain On Wed, 19 May 2004, Maxime Descoteaux wrote: > Hi all, > > Is there an easy way to concatinate a new string to the current volume > history string when outputting a volume? > > Thanks > > > -- > Maxime Descoteaux phone: (514) 989-8670 > Centre for Intelligent Machines phone: (514) 398-5606 > Masters in Computer Science > McGill University > http://www.cim.mcgill.ca/~mdesco > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) Positron Imaging Laboratories Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone: (514)-398-4965, 1996 Fax: 8948 From ali.soleymani@mail.mcgill.ca Wed May 19 15:11:04 2004 From: ali.soleymani@mail.mcgill.ca (Ali Soleymani) Date: Wed May 19 14:11:04 2004 Subject: [MINC-users] Installation of Display and Register Message-ID: <1084990217.40aba3096c876@webmail.mcgill.ca> Hi, Well, I have installed netcdf, minctools, and bicpl in /usr/local/mni I am trying to install register + display and I run the configure command, which it fails to find netcdf.h !? could you help me out with this ? (or more generally explaination of failing to find an existing file.) Thanks Ali ./configure --prefix=/usr/local/mni --with-build-path=usr/local/mni:/usr [...] checking netcdf.h presence... no checking for netcdf.h... no configure: error: cannot find required header From pgravel@bic.mni.mcgill.ca Wed May 19 18:13:04 2004 From: pgravel@bic.mni.mcgill.ca (Paul GRAVEL) Date: Wed May 19 17:13:04 2004 Subject: [MINC-users] mincblur question Message-ID: Hi All, I guess this should be an easy one. I have a 2x2x2mm MRI image that I would like to smooth to 7mm using mincblur. Should I use: mincblur -fwhm 7 in_image.mnc out_image OR should I divide the 7mm by 2 in order to pass mincblur the voxel size of the fwhm, i.e.: mincblur -fwhm 3.5 in_image.mnc out_image My question is, does mincblur accept voxel size or mm for the fwhm parameters? Thanks, Paul From rotor@cmr.uq.edu.au Wed May 19 22:58:03 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Wed May 19 21:58:03 2004 Subject: [MINC-users] Installation of Display and Register In-Reply-To: <1084990217.40aba3096c876@webmail.mcgill.ca> References: <1084990217.40aba3096c876@webmail.mcgill.ca> Message-ID: On Wed, 19 May 2004, Ali Soleymani wrote: > it fails to find netcdf.h !? > could you help me out with this ? (or more generally explaination of failing > to find an existing file.) > > ./configure --prefix=/usr/local/mni --with-build-path=usr/local/mni:/usr Did you perhaps mean: ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni:/usr ? btw, just --with-build-path=/usr/local/mni should suffice for most GNU installations. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From stever@bic.mni.mcgill.ca Wed May 19 23:27:04 2004 From: stever@bic.mni.mcgill.ca (Steve ROBBINS) Date: Wed May 19 22:27:04 2004 Subject: [MINC-users] Installation of Display and Register In-Reply-To: <1084990217.40aba3096c876@webmail.mcgill.ca>; from ali.soleymani@mail.mcgill.ca on Wed, May 19, 2004 at 02:10:17PM -0400 References: <1084990217.40aba3096c876@webmail.mcgill.ca> Message-ID: <20040519222631.E10187861@shadow.bic.mni.mcgill.ca> On Wed, May 19, 2004 at 02:10:17PM -0400, Ali Soleymani wrote: > > Hi, > Well, I have installed netcdf, minctools, and bicpl in /usr/local/mni So "netcdf.h" appears in directory /usr/local/mni/include, right? > I am trying to install register + display and I run the configure command, which > > it fails to find netcdf.h !? > could you help me out with this ? (or more generally explaination of failing > to find an existing file.) In general, one should look at the file "config.log" for clues as to what has gone wrong. > Thanks > Ali > > ./configure --prefix=/usr/local/mni --with-build-path=usr/local/mni:/usr Two observations: (1) you forgot the leading slash in the first build-path element, and (2) "/usr" is not necessary in the build path -- the build-path is for locations NeOT NORMALLY searched by the compler. You should use ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni > checking netcdf.h presence... no > checking for netcdf.h... no > configure: error: cannot find required header > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From stever@bic.mni.mcgill.ca Thu May 20 00:10:04 2004 From: stever@bic.mni.mcgill.ca (Steve ROBBINS) Date: Wed May 19 23:10:04 2004 Subject: [MINC-users] mincblur question In-Reply-To: ; from pgravel@bic.mni.mcgill.ca on Wed, May 19, 2004 at 05:12:58PM -0400 References: Message-ID: <20040519230913.G10187861@shadow.bic.mni.mcgill.ca> On Wed, May 19, 2004 at 05:12:58PM -0400, Paul GRAVEL wrote: > My question is, does mincblur accept voxel size or mm for the fwhm > parameters? The FWHM is specified in mm, according to the source code. -Steve From rotor@cmr.uq.edu.au Thu May 20 00:29:03 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Wed May 19 23:29:03 2004 Subject: [MINC-users] minc history In-Reply-To: References: Message-ID: On Wed, 19 May 2004, Sylvain MILOT wrote: > unless someone has written a litter perl script to do this? > > use minc_modify_header but you will have to extract the original > history value, append to it and overwrite it with minc_modify_header mni_perllib has this functionality in: update_history() Mind, you I often just roll my own each time when doing such things... ie: # Get and build history string chomp(my($history) = `date`); $history .= '>>>> ' . join(' ', $0, @ARGV) . "\n"; system('minc_modify_header', '-sinsert', ":history='$history'", $mnc_file); -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Fri May 21 06:35:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Fri May 21 05:35:05 2004 Subject: [MINC-users] voxel coordinates in native space vs. In-Reply-To: References: Message-ID: On Tue, 18 May 2004, Jeni Chen wrote: > I'm just wondering if anyone knew how to convert a set of tal coordinates > back into native space (i.e finding the equivalent). For instance, take > the Talairach coordinates 6 -8 44. In register we see the corresponding > voxel coordinates as 48 59 58. But if I want to look for the exact same > peak in the original raw data, how can I find it? Is there a > program or mathematical formula to do it? Jeni, All you need do is find the .xfm file that was generated to register your file to talairach space (assuming you used mritotal to do this). Have a look at this file, it contains a truncated 4x4 affine transformation matrix (assuming you did a linear fit only), the last row (0 0 0 1) is not stored. Then just take your point in talairach space, transform this by the inverse of the Matrix in the .xfm file and you have your point in native space. MATLAB or octave may prove handy to do this matrix calculation. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From jarv0075@umn.edu Fri May 21 10:29:05 2004 From: jarv0075@umn.edu (jarv0075) Date: Fri May 21 09:29:05 2004 Subject: [MINC-users] voxel coordinates in native space vs. Message-ID: <200405211328.i4LDSfrU019713@dingo.software.umn.edu> One easy way is to open the transform file, add the 0,0,0,1, invert it, then use mincresample -like 'native.mnc' with the new transform.. If you do it manually, you have to apply the inverse transform, then apply a transform to account for non-isotropic voxels, then translate it back to its original position in the volume via the mincinfo xstart ystart zstart. On 21 May 2004, Andrew Janke wrote: > On Tue, 18 May 2004, Jeni Chen wrote: > > > I'm just wondering if anyone knew how to convert a set of tal coordinates > > back into native space (i.e finding the equivalent). For instance, take > > the Talairach coordinates 6 -8 44. In register we see the corresponding > > voxel coordinates as 48 59 58. But if I want to look for the exact same > > peak in the original raw data, how can I find it? Is there a > > program or mathematical formula to do it? > > Jeni, > > All you need do is find the .xfm file that was generated to register your > file > to talairach space (assuming you used mritotal to do this). > > Have a look at this file, it contains a truncated 4x4 affine transformation > matrix (assuming you did a linear fit only), the last row (0 0 0 1) is not > stored. > > Then just take your point in talairach space, transform this by the inverse > of > the Matrix in the .xfm file and you have your point in native space. MATLAB > or > octave may prove handy to do this matrix calculation. > > > -- > Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > ------------------------------------- Timothy R. Jarvis email: tjarvis@cs.umn.edu cell: 612-554-4641 ------------------------------------- From alex@bic.mni.mcgill.ca Fri May 21 10:50:05 2004 From: alex@bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Fri May 21 09:50:05 2004 Subject: [MINC-users] voxel coordinates in native space vs. In-Reply-To: References: Message-ID: <20040521134923.GA11396724@shadow.bic.mni.mcgill.ca> Of course, there are also the utilities worldtovoxel and voxeltoworld which do exactly what you want. -- Alex On Fri, May 21, 2004 at 07:34:27PM +1000, Andrew Janke wrote: > On Tue, 18 May 2004, Jeni Chen wrote: > > > I'm just wondering if anyone knew how to convert a set of tal coordinates > > back into native space (i.e finding the equivalent). For instance, take > > the Talairach coordinates 6 -8 44. In register we see the corresponding > > voxel coordinates as 48 59 58. But if I want to look for the exact same > > peak in the original raw data, how can I find it? Is there a > > program or mathematical formula to do it? > > Jeni, > > All you need do is find the .xfm file that was generated to register your file > to talairach space (assuming you used mritotal to do this). > > Have a look at this file, it contains a truncated 4x4 affine transformation > matrix (assuming you did a linear fit only), the last row (0 0 0 1) is not > stored. > > Then just take your point in talairach space, transform this by the inverse of > the Matrix in the .xfm file and you have your point in native space. MATLAB or > octave may prove handy to do this matrix calculation. > > > -- > Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > _______________________________________________ > MINC-users@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@bic.mni.mcgill.ca | ========================================================================= From yves.roy@umontreal.ca Fri May 21 15:25:05 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Fri May 21 14:25:05 2004 Subject: [MINC-users] fMRIstat & EMMA error Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C43F60.DE787073 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, =20 the question was asked before (by (Jessie) Ting Guo, May 13, 2004), but = no answer came out so...=20 =20 I "installed" EMMA (i.e. copied over the .m files, and the 3 .dll and = .exe files into my /matlab6p1/bin/win32 directory) using the port for = Winn 2000/NT (even though I'm running XP Pro...) and I got the following = error:=20 =20 >> mask_thresh=3Dfmri_mask_thresh(mask_file); ??? Attempt to execute SCRIPT miinquire as a function. Error in =3D=3D> C:\MATLAB6p1\toolbox\fmristat\fmris_read_minc.m On line 5 =3D=3D> d.dim =3D fliplr(miinquire(file,'imagesize')'); Error in =3D=3D> C:\MATLAB6p1\toolbox\fmristat\fmris_read_image.m On line 28 =3D=3D> d =3D fmris_read_minc(file,Z,T); Error in =3D=3D> C:\MATLAB6p1\toolbox\fmristat\fmri_mask_thresh.m On line 32 =3D=3D> dm=3Dfmris_read_image(fmri_file,0,0); =20 Any idea what's causing this problem and how to solve it? =20 Thanks Yves ------_=_NextPart_001_01C43F60.DE787073 Content-Type: application/ms-tnef; name="winmail.dat" Content-Transfer-Encoding: base64 eJ8+IiQSAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEAFgAAAGZNUklzdGF0ICYgRU1NQSBl cnJvcgDaBgEFgAMADgAAANQHBQAVAA4AGAAjAAUAQwEBIIADAA4AAADUBwUAFQAOABgAIwAFAEMB AQmAAQAhAAAARUU0QUE4ODEyN0U4OTE0NTg5OTIzQ0M1REJDMjNBNzIAPAcBA5AGAOgNAAA2AAAA AwA2AAAAAABAADkAc3B43mA/xAEeAD0AAQAAAAEAAAAAAAAAAgFHAAEAAAAwAAAAYz1DQTthPSA7 cD1VTW9udHJlYWw7bD1FVE5BLTA0MDUyMTE4MjQzNVotMjQxMTAAHgBJAAEAAAAnAAAATUlOQy11 c2VycyBkaWdlc3QsIFZvbCAxICMxNDUgLSAzIG1zZ3MAAEAATgCAo2bTTD/EAR4AWgABAAAAIwAA AG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAAAIBWwABAAAAYwAAAAAAAACBKx+k vqMQGZ1uAN0BD1QCAAAAAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAU01UUABt aW5jLXVzZXJzLWFkbWluQGJpYy5tbmkubWNnaWxsLmNhAAACAVwAAQAAACgAAABTTVRQOk1JTkMt VVNFUlMtQURNSU5AQklDLk1OSS5NQ0dJTEwuQ0EAHgBdAAEAAAAlAAAAbWluYy11c2Vycy1yZXF1 ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAAAAAIBXgABAAAAZwAAAAAAAACBKx+kvqMQGZ1uAN0BD1QC AAAAAG1pbmMtdXNlcnMtcmVxdWVzdEBiaWMubW5pLm1jZ2lsbC5jYQBTTVRQAG1pbmMtdXNlcnMt cmVxdWVzdEBiaWMubW5pLm1jZ2lsbC5jYQAAAgFfAAEAAAAqAAAAU01UUDpNSU5DLVVTRVJTLVJF UVVFU1RAQklDLk1OSS5NQ0dJTEwuQ0EAAAAeAGYAAQAAAAUAAABTTVRQAAAAAB4AZwABAAAAIwAA AG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAAB4AaAABAAAABQAAAFNNVFAAAAAA HgBpAAEAAAAlAAAAbWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAAAAB4AcAAB AAAAJwAAAE1JTkMtdXNlcnMgZGlnZXN0LCBWb2wgMSAjMTQ1IC0gMyBtc2dzAAACAXEAAQAAABsA AAABxD9M4pyO6C16LAdFN62RBLXqYdzwAASBISoAHgB0AAEAAAAdAAAAbWluYy11c2Vyc0BiaWMu bW5pLm1jZ2lsbC5jYQAAAAAeABoMAQAAAAkAAABSb3kgWXZlcwAAAAAeAB0OAQAAABYAAABmTVJJ c3RhdCAmIEVNTUEgZXJyb3IAAAACAQkQAQAAAKsGAACnBgAAbRcAAExaRnUCfmeEAwAKAHJjcGcx MjWCMgNDaHRtbDEDMD8BAwH3CoACpAPjAgBjaMEKwHNldDAgBxMCgP8QAwBQBFYIVQeyEdUOUQMB 3RDXMgYABsMR1TMERhDZbxLrEeMI7wn3OxjPDjA1OxHSDGBjAFALCQFkMzaTEWALpTQgEAIqXA6y vQGQZxTwCqMR4x3oNBTwADwhRE9DVFlQAEUgSFRNTCBQAFVCTElDICItIC8vVzNDIYBEVCJEIJQz LjIhgEVOnCI+Hu0ejyPBMTgf8G8goiMPJB8mkDMdgCVwRXxBRCXNDvEm7ylvJPQ2QQ7wPE1FVEEH sEExLGA9IkcJ8ASQYXRFBbAiEtBPTlQi0FQTLPAF4UV4EPFuZ2U9BlJ2EzEvQQCQAiAgNvAuMC42 GxAwASL+Ks8JJQM3Nx/wVElUTApFJc40DvBNSU5DjC11ETARICBkaS7goHN0LCBWBvAgDvBAIzE0 NSAtInAgMG1zZ3MkbjaAPC//M08xfyZFNJE4QChPJp88FII1EWA8Qk9EWTVh9HI9PDByO4A78wAh AzA5PpFkbwDgPpEKsVxx/xiwPpEQ8AMwPvURYDurHPERPK9nOTYf8ERJVs8+yQAAQQc7yTY0RD9B UvhIaSw7yQHAPtcKoj7X+wpxJHwwKBEh4EQLSXhBj79Cn0OvRL9Fz1AbO6s4HYBgJm5ic3ACgD7o J/5hAUBQX0hfSW9Kf0uPUq8fTa9Ov1HvUN9d3yB0aJ0u8HEKUDWwL8J3YQQg5WHwawmAIGIBEAWw LvBoKGJ5YuBKB5AAkGUMKSAHYC7QIEd1b8k10E1hYxAxMzXQAdAlWSApNdBidQVAbm8vHZwdgFv0 AHF3EzFjYY0HgCAIYAVAc28uaDD/Vd9W71f/WQ9aH1svXD9dT/9eX19vbP9Tf1SPVZ9pP2pP/2tf bG9tf26Pb59wr3G/frzeSSFQC4A1sAdAbAmALaAIRU1NLJAoaS5l22hQBaBwCJBiYG8vQmES8C5t IGYDEAeQNdAAcOdiYGESNsAuZIIwhNODAP54LvBlz3yyhHNzr3S/dcqvC4AtcDbQYxAvAMB0C2BA YjZwMS9iC4AveQPwbjMU8D5RBZAtcXnvY6A1EGPSYRJwGHGEYAWxPlcLgAOghm98smThMC97LeBi 4GUvQAOgYRAIYGfJQNBJJ4RQcnWOsGPS/FhQIOADYGgxY6CE4YgP54kfdcqBsGdvBUBhEgIQ/YIw b4xRY/CO73yyBJADYPxyOpMvlD91z3bfd+94//96D3sffC99P4Bvf1+jn6C//5nPmt+b75z/ng+f H6AvoT8/ok+jX6lvpX+uj6eWZ3R9qFk+tH+1j7afNtBiIV9jYRAY0HNoPQRQBRBfzbpJKLpDhHIp OyR8LBBtPeFSPssLgGUKgbcXP+e/wBFwAkBlbQUxiwGGIQ5jZWCGT6/0U0NSSfJQkJBtaQuAYVCM wWIR32IQhGCR0IzwL8Euqe+q//+sD60fri+vP7BPsV+yb7N/jckHRZiiitEgPT23r8O4v7nGQzpc XIKwOIB8QUKL0dMQLXAG8AbgeFfTELsCggF01FVfGNBh9mS7QAuAY4RAvM+9377s3k8DoL7CwS/K kzXQX6gf76kq0C/RP7mZZIWAB3C3n7vcD6kbPYRgvsALUHK8AOXDBiiEciwnB3A8UAeQoGl6ZScp 5hA7xH//xY/Gn8evyL/Jz8rfy+/M///OD88f3e/e/9JP01/Ub9Vzv+WD1g/XH9gv2T+PijjyT//i L90v8m/zf+s//d/+7wK//wPPBN8F7wb/CA8JHwovCz//DE8NXw5vD3/gGePh+6+Hc+PVLOUUWixU 5k/nX+hv/+l/6o/rn+yv7b/uz+/f8O//8f8A7/Qf9S/2P7tK+A/5H//6L/s/j4mMgCMfEi//PyM/ +yRP4FVtuvP3SuUQuxLlI/4wNWAXHxgvGT8aTxtfHG//HX8ejx+fIK+0by5PL18+f/82fzePOJ85 rzq/O8883z3vkz7/QA1BbmMQaWT3cPVh0GiLgCfDoGeAjWb2kHuN8CKAYoJAhFCE4pEgd5vAcmgQ bIPAitB0P0Pf/0TvRf9HD0gfSS9KP0tPTF//TW9XL0F/Qo9Dn1NvVH9Vj39Wn1evWL9Zz1rfW+9c +1TxT6Bua3Ngr2G/Ys9j339k72X/Zw9oH2kvaj9wx1n/g8BsL20/bk9vX3BvcX9yjRN9n49yNTh7 AUJPRL5ZKjB+G4yQfw+BkTd7AVBIVE1MKjB9g8AAHgA1EAEAAABBAAAAPEI1ODM1RTFDQzU5NDdE NEY4MUJFQUU2QzY5OTczOThGMDIzRkVCRTJAZXRuYS5zaW0udW1vbnRyZWFsLmNhPgAAAAAeAEcQ AQAAAA8AAABtZXNzYWdlL3JmYzgyMgAACwDyEAEAAAAfAPMQAQAAADgAAABmAE0AUgBJAHMAdABh AHQAIAAlADIANgAgAEUATQBNAEEAIABlAHIAcgBvAHIALgBFAE0ATAAAAAsA9hAAAAAAQAAHMDP3 G+deP8QBQAAIMI++ht5gP8QBAwDeP69vAAADAPE/CRAAAB4A+D8BAAAACQAAAFJveSBZdmVzAAAA AAIB+T8BAAAAXgAAAAAAAADcp0DIwEIQGrS5CAArL+GCAQAAAAAAAAAvTz1VTU9OVFJFQUwvT1U9 RklSU1QgQURNSU5JU1RSQVRJVkUgR1JPVVAvQ049UkVDSVBJRU5UUy9DTj1ST1lZVgAAAB4A+j8B AAAAFQAAAFN5c3RlbSBBZG1pbmlzdHJhdG9yAAAAAAIB+z8BAAAAHgAAAAAAAADcp0DIwEIQGrS5 CAArL+GCAQAAAAAAAAAuAAAAAwD9P+QEAAADABlAAAAAAAMAGkAAAAAAAwAdQAAAAAADAB5AAAAA AB4AMEABAAAABgAAAFJPWVlWAAAAHgAxQAEAAAAGAAAAUk9ZWVYAAAAeADJAAQAAACMAAABtaW5j LXVzZXJzLWFkbWluQGJpYy5tbmkubWNnaWxsLmNhAAAeADNAAQAAACUAAABtaW5jLXVzZXJzLXJl cXVlc3RAYmljLm1uaS5tY2dpbGwuY2EAAAAAHgA4QAEAAAAGAAAAUk9ZWVYAAAAeADlAAQAAAAIA AAAuAAAACwApAAAAAAALACMAAAAAAAMABhDIGviEAwAHEJgCAAADABAQAAAAAAMAERAAAAAAHgAI EAEAAABlAAAASEksVEhFUVVFU1RJT05XQVNBU0tFREJFRk9SRShCWShKRVNTSUUpVElOR0dVTyxN QVkxMywyMDA0KSxCVVROT0FOU1dFUkNBTUVPVVRTT0kiSU5TVEFMTEVEIkVNTUEoSUVDTwAAAAAC AX8AAQAAAEEAAAA8QjU4MzVFMUNDNTk0N0Q0RjgxQkVBRTZDNjk5NzM5OEYwMjNGRUJFMkBldG5h LnNpbS51bW9udHJlYWwuY2E+AAAAAEFj ------_=_NextPart_001_01C43F60.DE787073-- From alee@loni.ucla.edu Mon May 24 14:45:04 2004 From: alee@loni.ucla.edu (Agatha Lee) Date: Mon May 24 13:45:04 2004 Subject: [MINC-users] changing the coordinate in mnc In-Reply-To: <20040521134923.GA11396724@shadow.bic.mni.mcgill.ca> Message-ID: Hello, Does anyone know how to change orientation in mnc? When I open mnc in Display, I am seeing different orientation in different box of window which will interfere when I try to register with average brain. I tried "mincreshape -coronal(transverse)". However, it would not change any orientaion Thank you very much. Agatha ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Agatha Dong-Eun Lee Laboratory of NeuroImaging - UCLA 710 Westwood Plaza agatha.lee@loni.ucla.edu tel: 310 292 4073 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From ali.soleymani@mail.mcgill.ca Tue May 25 02:41:05 2004 From: ali.soleymani@mail.mcgill.ca (Ali Soleymani) Date: Tue May 25 01:41:05 2004 Subject: [MINC-users] Display+Register and glutInit Message-ID: <1085463219.40b2dab3a95b5@www.webmail.mcgill.ca> Hello everyone, After all steps that I have taken to install Display and Register, I could not manage to install them on my computer. Runnig the configure script fails due to the following line: ... checking for glutInit in -lglut... no I have glut installed on my computer and glut libraries are available. I noticed someone had the same probelm before but unfortunately I could not figure out how he had managed to solved it. Thank you From rotor@cmr.uq.edu.au Tue May 25 04:33:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue May 25 03:33:04 2004 Subject: [MINC-users] changing the coordinate in mnc In-Reply-To: References: Message-ID: On Mon, 24 May 2004, Agatha Lee wrote: > Does anyone know how to change orientation in mnc? When I open > mnc in Display, I am seeing different orientation in different box of > window which will interfere when I try to register with average brain. I > tried "mincreshape -coronal(transverse)". However, it would not change any > orientaion Agatha, You appear to be wanting to rotate your MINC volume, mincreshape is not designed to do this, rather it's purpose is to reorganise the data within a MINC file such that reading the data in a coronal or sagittal fashion is faster. What you need to do is either: 1) Figure out what went wrong with the conversion process and fix it 2) rotate your volume To do the second use param2xfm to generate a transformation matrix that will correctly orient your volume remembering to be very carefull that you don't confuse left and right in this process! Then apply this transformation to your volume using mincresample. (and likely with a -nearest_neighbour option) -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Tue May 25 04:34:03 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue May 25 03:34:03 2004 Subject: [MINC-users] Display+Register and glutInit In-Reply-To: <1085463219.40b2dab3a95b5@www.webmail.mcgill.ca> References: <1085463219.40b2dab3a95b5@www.webmail.mcgill.ca> Message-ID: On Tue, 25 May 2004, Ali Soleymani wrote: > After all steps that I have taken to install Display and Register, I could not > manage to install them on my computer. Runnig the configure script fails due to > the following line: > .. > checking for glutInit in -lglut... no > > I have glut installed on my computer and glut libraries are available. I noticed > someone had the same probelm before but unfortunately I could not figure out > how he had managed to solved it. Where is glut installed on your machine? It is likely that it is in /usr/local and thus you may have to add --with-build-path=/usr/local as an option to configure. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From yves.roy@umontreal.ca Thu May 27 11:14:05 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Thu May 27 10:14:05 2004 Subject: [MINC-users] fMRIstat - Emma configuration problem - take 2 Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C443F4.BC55EFAA Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, the question was asked before (by (Jessie) Ting Guo, May 13, 2004) but no answer came out, and by me (but wasn't quite readable), so... I "installed" EMMA (i.e. copied over the .m files, and the 3 .dll and .exe files into my /matlab6p1/bin/win32 directory) using the port for Win 2000/NT as specified at: http://www.math.mcgill.ca/keith/fmristat/ (even though I'm running XP Pro...would that be a problem?) and I got the following error in Matlab: >> mask_thresh=3D3Dfmri_mask_thresh(mask_file); ??? Attempt to execute SCRIPT miinquire as a function. Error in =3D3D=3D3D> C:\MATLAB6p1\toolbox\fmristat\fmris_read_minc.m On line 5 =3D3D=3D3D> d.dim =3D3D = fliplr(miinquire(file,'imagesize')'); Error in =3D3D=3D3D> C:\MATLAB6p1\toolbox\fmristat\fmris_read_image.m On line 28 =3D3D=3D3D> d =3D3D fmris_read_minc(file,Z,T); Error in =3D3D=3D3D> C:\MATLAB6p1\toolbox\fmristat\fmri_mask_thresh.m On line 32 =3D3D=3D3D> dm=3D3Dfmris_read_image(fmri_file,0,0); Any idea what's causing this problem and how to solve would be welcome. Thanks Yves ------_=_NextPart_001_01C443F4.BC55EFAA Content-Type: application/ms-tnef; name="winmail.dat" Content-Transfer-Encoding: base64 eJ8+IgwOAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEALwAAAGZNUklzdGF0IC0gRW1tYSBj b25maWd1cmF0aW9uIHByb2JsZW0gLSB0YWtlIDIABBABBYADAA4AAADUBwUAGwAKAA0ACAAEAB4B ASCAAwAOAAAA1AcFABsACgANAAgABAAeAQEJgAEAIQAAAEJDRTc0OEIxRkMwMTBBNDA5MjdFQ0Y5 MTJCMjg1MkZGAEoHAQOQBgAgCwAANwAAAAMAJgAAAAAAAwA2AAAAAABAADkAqu9VvPRDxAEeAD0A AQAAAAEAAAAAAAAAAgFHAAEAAAAwAAAAYz1DQTthPSA7cD1VTW9udHJlYWw7bD1FVE5BLTA0MDUy NzE0MTMwOFotMzQ2NjcAHgBJAAEAAAAmAAAATUlOQy11c2VycyBkaWdlc3QsIFZvbCAxICMxNDYg LSAxIG1zZwAAAEAATgAAoAb8FUDEAR4AWgABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1u aS5tY2dpbGwuY2EAAAIBWwABAAAAYwAAAAAAAACBKx+kvqMQGZ1uAN0BD1QCAAAAAG1pbmMtdXNl cnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAU01UUABtaW5jLXVzZXJzLWFkbWluQGJpYy5tbmku bWNnaWxsLmNhAAACAVwAAQAAACgAAABTTVRQOk1JTkMtVVNFUlMtQURNSU5AQklDLk1OSS5NQ0dJ TEwuQ0EAHgBdAAEAAAAlAAAAbWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAAA AAIBXgABAAAAZwAAAAAAAACBKx+kvqMQGZ1uAN0BD1QCAAAAAG1pbmMtdXNlcnMtcmVxdWVzdEBi aWMubW5pLm1jZ2lsbC5jYQBTTVRQAG1pbmMtdXNlcnMtcmVxdWVzdEBiaWMubW5pLm1jZ2lsbC5j YQAAAgFfAAEAAAAqAAAAU01UUDpNSU5DLVVTRVJTLVJFUVVFU1RAQklDLk1OSS5NQ0dJTEwuQ0EA AAAeAGYAAQAAAAUAAABTTVRQAAAAAB4AZwABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1u aS5tY2dpbGwuY2EAAB4AaAABAAAABQAAAFNNVFAAAAAAHgBpAAEAAAAlAAAAbWluYy11c2Vycy1y ZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAAAAB4AcAABAAAAJgAAAE1JTkMtdXNlcnMgZGlnZXN0 LCBWb2wgMSAjMTQ2IC0gMSBtc2cAAAACAXEAAQAAABsAAAABxEAWCF3Vscr/GJVOuaV5ZulIOtmC AMzeXD8AHgB0AAEAAAAdAAAAbWluYy11c2Vyc0BiaWMubW5pLm1jZ2lsbC5jYQAAAAAeABoMAQAA AAkAAABSb3kgWXZlcwAAAAAeAB0OAQAAAC8AAABmTVJJc3RhdCAtIEVtbWEgY29uZmlndXJhdGlv biBwcm9ibGVtIC0gdGFrZSAyAAACAQkQAQAAAJMDAACPAwAAqAUAAExaRnVb3O4wAwAKAHJjcGcx MjXiMgNDdGV4BUEBAwH3/wqAAqQD5AcTAoAP8wBQBFY/CFUHshElDlEDAQIAY2jhCsBzZXQyBgAG wxEl9jMERhO3MBIsETMI7wn3tjsYHw4wNREiDGBjAFDzCwkBZDM2FlALpgrjCoAYSGksHPQc9HRo ZUQgcQpQc3RpAiAgLHdhBCAfIGsJgCBiRwEQBbAeYChieSAQSiMHkACQZSkgB2BuZ6AgR3VvLAXQ YSBATDEzIXAB0DA0INBiZHV0HPRubx9AAIB3qRKBY2EHgCAIYHQhcH8AcB+RIEAjwSAgIoAfAm5W JwVAHoBpDrAgGCBhGmQBoGwgwCFwc28u4ybQHYpJICILgB6wB0ABJmBkIiBFTU1BISAQaS5lLiOQ b3AzCJAfkG92EoEeQi5tvCBmAxAHkCQkHkIzKkDeZChAJDIc9CkQeB5gKoOqIAuAdCMQbSBALwDA AnQLYGI2cDEvYiULgC8D8G4zFEBkaaUYIGMtQHJ5INB1AJB7IREeQnAXwSpwBbAc9FfDC4AiAjAv TlQfQSagXnAFkAaQKYItwDodimjxAkBwOi8ugDQQKlAtwJJoKlBjZwMQbC4joOYvH3AlwGgvBFAF ECgR5HQvHYooZSnQA6AeQEEIYGdoIEknKmByDHVuAwAhEVhQIFDrA2Am0XcIYGwrEi3AH6GPH0Aw MANgJlFtPykc9PMkQifAZ28FQB5CAhAoQP5vLpEhIASQA2AFwDExIZCzLdIy2z4+JKAfUV8eQEEY IHNoPTNENaJfbT55KD5zKoIpGTAdAz9/QXAQwAJAOmAFMS1BLIFjgyKAHmBTQ1JJUDHA/G1pC4Al oR/xHyIqcDgQ9y8wHtEm9UU8lj8hPyE+UApDMtBcKMBUTEFC3y4RRmAtQAbwBuB4RmA1pt1HpV8m Aj+QC4BjKlAc9JpPA6BsC4AeYDUgRbd+ZCuQB3BKYypwSgALUHJLQFBDZigqgiwnB3BhgmcHkGl6 ZScpTbB/QQVFP0ZPR19IaU0jSV4yfjhKaFREH5BLc0h8TLRa/CxUTe9O/1APURo/mkle+y7BSnht PyVR2kywP2JMw04wXvBA9hz0QW4gQGnrAQA58Hc5gScEICOgL6Z/BAA6BiQzN2AH4C1BJrBs3ynQ HwA5IznBI2BsBaAHgEUm+1QT4G5rcxz0WRcp0GWVHYp9Z3AAHgA1EAEAAABBAAAAPEI1ODM1RTFD QzU5NDdENEY4MUJFQUU2QzY5OTczOThGMDIzRkVCRjlAZXRuYS5zaW0udW1vbnRyZWFsLmNhPgAA AAAeAEcQAQAAAA8AAABtZXNzYWdlL3JmYzgyMgAACwDyEAEAAAAfAPMQAQAAAGYAAABmAE0AUgBJ AHMAdABhAHQAIAAtACAARQBtAG0AYQAgAGMAbwBuAGYAaQBnAHUAcgBhAHQAaQBvAG4AIABwAHIA bwBiAGwAZQBtACAALQAgAHQAYQBrAGUAIAAyAC4ARQBNAEwAAAAAAAsA9hAAAAAAQAAHMMwOyYFJ Q8QBQAAIMLgWXbz0Q8QBAwDeP69vAAADAPE/CQQAAB4A+D8BAAAACQAAAFJveSBZdmVzAAAAAAIB +T8BAAAAXgAAAAAAAADcp0DIwEIQGrS5CAArL+GCAQAAAAAAAAAvTz1VTU9OVFJFQUwvT1U9RklS U1QgQURNSU5JU1RSQVRJVkUgR1JPVVAvQ049UkVDSVBJRU5UUy9DTj1ST1lZVgAAAB4A+j8BAAAA FQAAAFN5c3RlbSBBZG1pbmlzdHJhdG9yAAAAAAIB+z8BAAAAHgAAAAAAAADcp0DIwEIQGrS5CAAr L+GCAQAAAAAAAAAuAAAAAwD9P+QEAAADABlAAAAAAAMAGkAAAAAAAwAdQAAAAAADAB5AAAAAAB4A MEABAAAABgAAAFJPWVlWAAAAHgAxQAEAAAAGAAAAUk9ZWVYAAAAeADJAAQAAACMAAABtaW5jLXVz ZXJzLWFkbWluQGJpYy5tbmkubWNnaWxsLmNhAAAeADNAAQAAACUAAABtaW5jLXVzZXJzLXJlcXVl c3RAYmljLm1uaS5tY2dpbGwuY2EAAAAAHgA4QAEAAAAGAAAAUk9ZWVYAAAAeADlAAQAAAAIAAAAu AAAACwApAAAAAAALACMAAAAAAAMABhAjT7mFAwAHEDEDAAADABAQAAAAAAMAERAAAAAAHgAIEAEA AABlAAAASEksVEhFUVVFU1RJT05XQVNBU0tFREJFRk9SRShCWShKRVNTSUUpVElOR0dVTyxNQVkx MywyMDA0KUJVVE5PQU5TV0VSQ0FNRU9VVCxBTkRCWU1FKEJVVFdBU05UUVVJVEVSRQAAAAACAX8A AQAAAEEAAAA8QjU4MzVFMUNDNTk0N0Q0RjgxQkVBRTZDNjk5NzM5OEYwMjNGRUJGOUBldG5hLnNp bS51bW9udHJlYWwuY2E+AAAAAOzS ------_=_NextPart_001_01C443F4.BC55EFAA-- From haytham@umich.edu Thu May 27 17:13:05 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Thu May 27 16:13:05 2004 Subject: [MINC-users] Classify and Mritotal Message-ID: <1085688740.40b64ba4875fb@mail.umich.edu> How can I change the default classification method of classify_clean. Also, how can I change the default settings in mritotal (this script calls on minctracc to compute the linear mapping). I am having problems passing options from mritotal to minctracc also from classify_clean to classify. Thanks From neelin@bic.mni.mcgill.ca Fri May 28 01:01:04 2004 From: neelin@bic.mni.mcgill.ca (Peter NEELIN) Date: Fri May 28 00:01:04 2004 Subject: [MINC-users] fMRIstat - Emma configuration problem - take 2 In-Reply-To: Message-ID: On Thu, 27 May 2004, Roy Yves wrote: > (even though I'm running XP Pro...would that be a problem?) > and I got the following error in Matlab: > > >> mask_thresh=3Dfmri_mask_thresh(mask_file); > ??? Attempt to execute SCRIPT miinquire as a function. > Error in =3D=3D> C:\MATLAB6p1\toolbox\fmristat\fmris_read_minc.m > On line 5 =3D=3D> d.dim =3D fliplr(miinquire(file,'imagesize')'); Well, since you aren't getting any answers, I'll give it a shot (I don't use matlab anymore, and I've never used it on Windows, ... be warned). Matlab appears to be confused about the what it is using for miinquire. If you type "which miinquire", you should get a reference to a mex file - on second look that should be a dll. If it finds the .m file, then it may be that the .dll is not in the right place. Other possibilities include permissions on the dll or setting of the Windows PATH variable (though I doubt that one). Another possibility is that the search order has changed and your version of matlab prefers the .m over the .dll. In that case, you can just delete the .m file since it is only there for help. If the "which" command does report the dll file, then I have no idea what the problem is. Note also that this is an older version of emma. I don't know if there is a more recent version ported to windows though. Good hunting. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From yves.roy@umontreal.ca Fri May 28 12:44:04 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Fri May 28 11:44:04 2004 Subject: [MINC-users] RE: fMRIstat - Emma configuration problem - SOLUTION FOUND Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C444CA.8E1366CD Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 The problem is overly simple, and the solution is described at: =20 http://www.mathworks.com/support/tech-notes/1200/1207.html#27 =20 It is just not sufficient to copy the 3 .dll and .exe into the = matlab/bin/win32 directory, but this directory has to be added to the = matlab search path (and before any other directory in the path = containing another --but the one we want to call, script-M file with the = same name. =20 Thanks Yves =20 =20 -----Original Message-----=20 From: minc-users-admin@bic.mni.mcgill.ca on behalf of = minc-users-request@bic.mni.mcgill.ca=20 Sent: Thu 27/05/2004 12:01 PM=20 To: minc-users@bic.mni.mcgill.ca=20 Cc:=20 Subject: MINC-users digest, Vol 1 #148 - 1 msg =09 =09 Send MINC-users mailing list submissions to minc-users@bic.mni.mcgill.ca =09 To subscribe or unsubscribe via the World Wide Web, visit http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request@bic.mni.mcgill.ca =09 You can reach the person managing the list at minc-users-admin@bic.mni.mcgill.ca =09 When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." =09 =09 Today's Topics: =09 1. fMRIstat - Emma configuration problem - take 2 (Roy Yves) =09 --__--__-- =09 Message: 1 Date: Thu, 27 May 2004 10:13:08 -0400 From: "Roy Yves" To: Subject: [MINC-users] fMRIstat - Emma configuration problem - take 2 =09 This is a multi-part message in MIME format. =09 ------_=3D_NextPart_001_01C443F4.BC55EFAA Content-Type: text/plain; charset=3D"iso-8859-1" Content-Transfer-Encoding: quoted-printable =09 =09 Hi, =09 the question was asked before (by (Jessie) Ting Guo, May 13, 2004) but no answer came out, and by me (but wasn't quite readable), so... =09 I "installed" EMMA (i.e. copied over the .m files, and the 3 .dll and .exe files into my /matlab6p1/bin/win32 directory) using the port for Win 2000/NT as specified at: =09 http://www.math.mcgill.ca/keith/fmristat/ =09 (even though I'm running XP Pro...would that be a problem?) and I got the following error in Matlab: =09 >> mask_thresh=3D3D3Dfmri_mask_thresh(mask_file); ??? Attempt to execute SCRIPT miinquire as a function. Error in =3D3D3D=3D3D3D> = C:\MATLAB6p1\toolbox\fmristat\fmris_read_minc.m On line 5 =3D3D3D=3D3D3D> d.dim =3D3D3D =3D fliplr(miinquire(file,'imagesize')'); Error in =3D3D3D=3D3D3D> = C:\MATLAB6p1\toolbox\fmristat\fmris_read_image.m On line 28 =3D3D3D=3D3D3D> d =3D3D3D fmris_read_minc(file,Z,T); Error in =3D3D3D=3D3D3D> = C:\MATLAB6p1\toolbox\fmristat\fmri_mask_thresh.m On line 32 =3D3D3D=3D3D3D> dm=3D3D3Dfmris_read_image(fmri_file,0,0); =09 Any idea what's causing this problem and how to solve would be welcome. =09 Thanks Yves =09 =09 =09 =09 ------_=3D_NextPart_001_01C443F4.BC55EFAA Content-Type: application/ms-tnef; name=3D"winmail.dat" Content-Transfer-Encoding: base64 =09 = eJ8+IgwOAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5Na= WNy = b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEALwAAAGZNUklzdGF0IC0gRW1tY= SBj = b25maWd1cmF0aW9uIHByb2JsZW0gLSB0YWtlIDIABBABBYADAA4AAADUBwUAGwAKAA0ACAAEA= B4B = ASCAAwAOAAAA1AcFABsACgANAAgABAAeAQEJgAEAIQAAAEJDRTc0OEIxRkMwMTBBNDA5MjdFQ= 0Y5 = MTJCMjg1MkZGAEoHAQOQBgAgCwAANwAAAAMAJgAAAAAAAwA2AAAAAABAADkAqu9VvPRDxAEeA= D0A = AQAAAAEAAAAAAAAAAgFHAAEAAAAwAAAAYz1DQTthPSA7cD1VTW9udHJlYWw7bD1FVE5BLTA0M= DUy = NzE0MTMwOFotMzQ2NjcAHgBJAAEAAAAmAAAATUlOQy11c2VycyBkaWdlc3QsIFZvbCAxICMxN= DYg = LSAxIG1zZwAAAEAATgAAoAb8FUDEAR4AWgABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljL= m1u = aS5tY2dpbGwuY2EAAAIBWwABAAAAYwAAAAAAAACBKx+kvqMQGZ1uAN0BD1QCAAAAAG1pbmMtd= XNl = cnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAU01UUABtaW5jLXVzZXJzLWFkbWluQGJpYy5tb= mku = bWNnaWxsLmNhAAACAVwAAQAAACgAAABTTVRQOk1JTkMtVVNFUlMtQURNSU5AQklDLk1OSS5NQ= 0dJ = TEwuQ0EAHgBdAAEAAAAlAAAAbWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhA= AAA = AAIBXgABAAAAZwAAAAAAAACBKx+kvqMQGZ1uAN0BD1QCAAAAAG1pbmMtdXNlcnMtcmVxdWVzd= EBi = aWMubW5pLm1jZ2lsbC5jYQBTTVRQAG1pbmMtdXNlcnMtcmVxdWVzdEBiaWMubW5pLm1jZ2lsb= C5j = YQAAAgFfAAEAAAAqAAAAU01UUDpNSU5DLVVTRVJTLVJFUVVFU1RAQklDLk1OSS5NQ0dJTEwuQ= 0EA = AAAeAGYAAQAAAAUAAABTTVRQAAAAAB4AZwABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljL= m1u = aS5tY2dpbGwuY2EAAB4AaAABAAAABQAAAFNNVFAAAAAAHgBpAAEAAAAlAAAAbWluYy11c2Vyc= y1y = ZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAAAAB4AcAABAAAAJgAAAE1JTkMtdXNlcnMgZGlnZ= XN0 = LCBWb2wgMSAjMTQ2IC0gMSBtc2cAAAACAXEAAQAAABsAAAABxEAWCF3Vscr/GJVOuaV5ZulIO= tmC = AMzeXD8AHgB0AAEAAAAdAAAAbWluYy11c2Vyc0BiaWMubW5pLm1jZ2lsbC5jYQAAAAAeABoMA= QAA = AAkAAABSb3kgWXZlcwAAAAAeAB0OAQAAAC8AAABmTVJJc3RhdCAtIEVtbWEgY29uZmlndXJhd= Glv = biBwcm9ibGVtIC0gdGFrZSAyAAACAQkQAQAAAJMDAACPAwAAqAUAAExaRnVb3O4wAwAKAHJjc= Gcx = MjXiMgNDdGV4BUEBAwH3/wqAAqQD5AcTAoAP8wBQBFY/CFUHshElDlEDAQIAY2jhCsBzZXQyB= gAG = wxEl9jMERhO3MBIsETMI7wn3tjsYHw4wNREiDGBjAFDzCwkBZDM2FlALpgrjCoAYSGksHPQc9= HRo = ZUQgcQpQc3RpAiAgLHdhBCAfIGsJgCBiRwEQBbAeYChieSAQSiMHkACQZSkgB2BuZ6AgR3VvL= AXQ = YSBATDEzIXAB0DA0INBiZHV0HPRubx9AAIB3qRKBY2EHgCAIYHQhcH8AcB+RIEAjwSAgIoAfA= m5W = JwVAHoBpDrAgGCBhGmQBoGwgwCFwc28u4ybQHYpJICILgB6wB0ABJmBkIiBFTU1BISAQaS5lL= iOQ = b3AzCJAfkG92EoEeQi5tvCBmAxAHkCQkHkIzKkDeZChAJDIc9CkQeB5gKoOqIAuAdCMQbSBAL= wDA = AnQLYGI2cDEvYiULgC8D8G4zFEBkaaUYIGMtQHJ5INB1AJB7IREeQnAXwSpwBbAc9FfDC4AiA= jAv = TlQfQSagXnAFkAaQKYItwDodimjxAkBwOi8ugDQQKlAtwJJoKlBjZwMQbC4joOYvH3AlwGgvB= FAF = ECgR5HQvHYooZSnQA6AeQEEIYGdoIEknKmByDHVuAwAhEVhQIFDrA2Am0XcIYGwrEi3AH6GPH= 0Aw = MANgJlFtPykc9PMkQifAZ28FQB5CAhAoQP5vLpEhIASQA2AFwDExIZCzLdIy2z4+JKAfUV8eQ= EEY = IHNoPTNENaJfbT55KD5zKoIpGTAdAz9/QXAQwAJAOmAFMS1BLIFjgyKAHmBTQ1JJUDHA/G1pC= 4Al = oR/xHyIqcDgQ9y8wHtEm9UU8lj8hPyE+UApDMtBcKMBUTEFC3y4RRmAtQAbwBuB4RmA1pt1Hp= V8m = Aj+QC4BjKlAc9JpPA6BsC4AeYDUgRbd+ZCuQB3BKYypwSgALUHJLQFBDZigqgiwnB3BhgmcHk= Gl6 = ZScpTbB/QQVFP0ZPR19IaU0jSV4yfjhKaFREH5BLc0h8TLRa/CxUTe9O/1APURo/mkle+y7BS= nht = PyVR2kywP2JMw04wXvBA9hz0QW4gQGnrAQA58Hc5gScEICOgL6Z/BAA6BiQzN2AH4C1BJrBs3= ynQ = HwA5IznBI2BsBaAHgEUm+1QT4G5rcxz0WRcp0GWVHYp9Z3AAHgA1EAEAAABBAAAAPEI1ODM1R= TFD = QzU5NDdENEY4MUJFQUU2QzY5OTczOThGMDIzRkVCRjlAZXRuYS5zaW0udW1vbnRyZWFsLmNhP= gAA = AAAeAEcQAQAAAA8AAABtZXNzYWdlL3JmYzgyMgAACwDyEAEAAAAfAPMQAQAAAGYAAABmAE0AU= gBJ = AHMAdABhAHQAIAAtACAARQBtAG0AYQAgAGMAbwBuAGYAaQBnAHUAcgBhAHQAaQBvAG4AIABwA= HIA = bwBiAGwAZQBtACAALQAgAHQAYQBrAGUAIAAyAC4ARQBNAEwAAAAAAAsA9hAAAAAAQAAHMMwOy= YFJ = Q8QBQAAIMLgWXbz0Q8QBAwDeP69vAAADAPE/CQQAAB4A+D8BAAAACQAAAFJveSBZdmVzAAAAA= AIB = +T8BAAAAXgAAAAAAAADcp0DIwEIQGrS5CAArL+GCAQAAAAAAAAAvTz1VTU9OVFJFQUwvT1U9R= klS = U1QgQURNSU5JU1RSQVRJVkUgR1JPVVAvQ049UkVDSVBJRU5UUy9DTj1ST1lZVgAAAB4A+j8BA= AAA = FQAAAFN5c3RlbSBBZG1pbmlzdHJhdG9yAAAAAAIB+z8BAAAAHgAAAAAAAADcp0DIwEIQGrS5C= AAr = L+GCAQAAAAAAAAAuAAAAAwD9P+QEAAADABlAAAAAAAMAGkAAAAAAAwAdQAAAAAADAB5AAAAAA= B4A = MEABAAAABgAAAFJPWVlWAAAAHgAxQAEAAAAGAAAAUk9ZWVYAAAAeADJAAQAAACMAAABtaW5jL= XVz = ZXJzLWFkbWluQGJpYy5tbmkubWNnaWxsLmNhAAAeADNAAQAAACUAAABtaW5jLXVzZXJzLXJlc= XVl = c3RAYmljLm1uaS5tY2dpbGwuY2EAAAAAHgA4QAEAAAAGAAAAUk9ZWVYAAAAeADlAAQAAAAIAA= AAu = AAAACwApAAAAAAALACMAAAAAAAMABhAjT7mFAwAHEDEDAAADABAQAAAAAAMAERAAAAAAHgAIE= AEA = AABlAAAASEksVEhFUVVFU1RJT05XQVNBU0tFREJFRk9SRShCWShKRVNTSUUpVElOR0dVTyxNQ= Vkx = MywyMDA0KUJVVE5PQU5TV0VSQ0FNRU9VVCxBTkRCWU1FKEJVVFdBU05UUVVJVEVSRQAAAAACA= X8A = AQAAAEEAAAA8QjU4MzVFMUNDNTk0N0Q0RjgxQkVBRTZDNjk5NzM5OEYwMjNGRUJGOUBldG5hL= nNp bS51bW9udHJlYWwuY2E+AAAAAOzS =09 ------_=3D_NextPart_001_01C443F4.BC55EFAA-- =09 =09 --__--__-- =09 _______________________________________________ MINC-users mailing list MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users =09 =09 End of MINC-users Digest =09 ------_=_NextPart_001_01C444CA.8E1366CD Content-Type: application/ms-tnef; name="winmail.dat" Content-Transfer-Encoding: base64 eJ8+IiwPAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEAOwAAAFJFOiBmTVJJc3RhdCAtIEVt bWEgY29uZmlndXJhdGlvbiBwcm9ibGVtIC0gU09MVVRJT04gRk9VTkQAFxMBBYADAA4AAADUBwUA HAALACsAKwAFAGIBASCAAwAOAAAA1AcFABwACwArACsABQBiAQEJgAEAIQAAADVDMjRENTM5RUEz NzMwNDc4NTY5QTMzMzgwQkU3NDdDAAsHAQOQBgC4KQAANgAAAAMANgAAAAAAQAA5AM1mE47KRMQB HgA9AAEAAAAFAAAAUkU6IAAAAAACAUcAAQAAADAAAABjPUNBO2E9IDtwPVVNb250cmVhbDtsPUVU TkEtMDQwNTI4MTU0MzQzWi0zNzk4MgAeAEkAAQAAACYAAABNSU5DLXVzZXJzIGRpZ2VzdCwgVm9s IDEgIzE0OCAtIDEgbXNnAAAAQABOAACNSNEDRMQBHgBaAAEAAAAjAAAAbWluYy11c2Vycy1hZG1p bkBiaWMubW5pLm1jZ2lsbC5jYQAAAgFbAAEAAABjAAAAAAAAAIErH6S+oxAZnW4A3QEPVAIAAAAA bWluYy11c2Vycy1hZG1pbkBiaWMubW5pLm1jZ2lsbC5jYQBTTVRQAG1pbmMtdXNlcnMtYWRtaW5A YmljLm1uaS5tY2dpbGwuY2EAAAIBXAABAAAAKAAAAFNNVFA6TUlOQy1VU0VSUy1BRE1JTkBCSUMu TU5JLk1DR0lMTC5DQQAeAF0AAQAAACUAAABtaW5jLXVzZXJzLXJlcXVlc3RAYmljLm1uaS5tY2dp bGwuY2EAAAAAAgFeAAEAAABnAAAAAAAAAIErH6S+oxAZnW4A3QEPVAIAAAAAbWluYy11c2Vycy1y ZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAFNNVFAAbWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmku bWNnaWxsLmNhAAACAV8AAQAAACoAAABTTVRQOk1JTkMtVVNFUlMtUkVRVUVTVEBCSUMuTU5JLk1D R0lMTC5DQQAAAB4AZgABAAAABQAAAFNNVFAAAAAAHgBnAAEAAAAjAAAAbWluYy11c2Vycy1hZG1p bkBiaWMubW5pLm1jZ2lsbC5jYQAAHgBoAAEAAAAFAAAAU01UUAAAAAAeAGkAAQAAACUAAABtaW5j LXVzZXJzLXJlcXVlc3RAYmljLm1uaS5tY2dpbGwuY2EAAAAAHgBwAAEAAAAmAAAATUlOQy11c2Vy cyBkaWdlc3QsIFZvbCAxICMxNDggLSAxIG1zZwAAAAIBcQABAAAAGwAAAAHERAPeFDWVXVn96E2Z oimuHoxRh7UAMXZnggAeAHQAAQAAAB0AAABtaW5jLXVzZXJzQGJpYy5tbmkubWNnaWxsLmNhAAAA AB4AGgwBAAAACQAAAFJveSBZdmVzAAAAAB4AHQ4BAAAANwAAAGZNUklzdGF0IC0gRW1tYSBjb25m aWd1cmF0aW9uIHByb2JsZW0gLSBTT0xVVElPTiBGT1VORAAAAgEJEAEAAAAJIgAABSIAAAVjAABM WkZ14sqYAAMACgByY3BnMTI1gjIDQ2h0bWwxAzA/AQMB9wqAAqQD4wIAY2jBCsBzZXQwIAcTAoD/ EAMAUARWCFUHshHVDlEDAd0Q1zIGAAbDEdUzBEYQ2W8S6xHjCO8J9zsYzw4wNTsR0gxgYwBQCwkB ZDM2kxFgC6U0IBACKlwOsr0BkGcU8AqjEeMd6DQU8AA8IURPQ1RZUABFIEhUTUwgUABVQkxJQyAi LSAvL1czQyGARFQiRCCUMy4yIYBFTpwiPh7tHo8jwTE4H/BvIKIjDyQfJpAzHYAlcEV8QUQlzQ7x Ju8pbyT0NkEO8DxNRVRBB7BBMSxgPSJHCfAEkGF0RQWwIhLQT05UItBUEyzwBeFFeBDxbmdlPQZS dhMxL0EAkAIgIDbwLjAuNhsQMAEi/irPCSUDNzcf8FRJVEwKRSXONA7wTUlOQ4wtdREwESAgZGku 4KBzdCwgVgbwIA7wKCMxNCVQLTYhbXPqZyRuNR/wLzNPMX8mRV80kTgwKE8mnzwENRFgPJBCT0RZ NWFyPTwgPnI7cDvjACEDMD6BZG/nAOA+gQqxXHEYsD6BEPA/AzA+5RFgO5sc8TyfZzniNh/wRElW PrkAAED3WTu5NjREL0FPOB2AJjBuYnNwAoA+2Cdh/wFARO88MQHAPscKoj7HCnH9JHwwKBEh4EP7 TBhBf0KPh0OTIRAgMEtRVU8t8EU+NiA1sHlsZS4xQYRSRzTQLVJJRyCg4DogMHB4IvE+2Aqx/xAC P+VAg0BBQN9P/x8bEWB/WdBQ30PfSe9F/1b3P2BpZxzSJHw2cTxGLdFTEGk6elNgMltbC+JW2VRo jS7wcANgAmBlbSAEAKQgby9BbHlgoW0LUEZlNdAAcGQgdGLhc3kG8HV0L8JjkQEABPJifwmAHZwd gFh/SENZ4S1gOv8kfDBgOCFgYk4/Si9LP0xP/01fau9Xb2ePWY9an13PXL//dV9e31/vYP9iC2lP al9wj/9H/0kPdg9sz23fbu9+H3EP/3Ifcy90P3dvdl+Lb3h/f+WuPCyQCqOJoGgY0GYs8FEOsHRw OiGAd5GALosAwGTwdwWwa3MuBaBAbS9zdXBwGHEvQnQFkGgtbm+TIHOSLw4gMDCTwjcuDrI4IzI3 VKoB8QiQbGSdO7JmlfALgDWwe0ggYfJSISBOSyFQkR+SL5M//5RJF+AB8ZXwESA8IBgwAEH+dVbK l4+Yn5mvlEiGH45yy6Efhz05H+EvQTtwgj//g0+EX4Vvoq+Hj4ifia+Kv/+Lz4zfje+O/4BPgV+l D6Yf/6cvqD+pT6pfq2+sf62PtA/br6+wvkkFQGORajUQBUD7n5FTEHUBIA3gCJACMGTgNG8gBaBw ZBBk8jMgGC5kbAMgZLIuZXj/LvALgMMRZPJmn7rPaLSd4XELYGIvYguAnZALgDOvFPA+QQWQLXF5 NdBiZWDvZOFlwskGkKBhBCDDEWZQ/WSgZAEAZNHFBMfkxV/Gbz9opREwCsBAsQqwZPAgKP9ksmZQ AhAY0GShZBCfoGLg/wXAyjgLgGTjz6MFoAIwC3F9C4BnZKHQ9My/zc9otC3eLcmkLvACIC7wd9ch AHAbwvQHQGw10AT0LU0gt5XAU1DXMGnPwWTzYQeA+8IQ2dEutJ+1r7a/t8+43/+577r/vA+9H74v vz/AT7Gf/7Kvs7/an9uv3L/dz97f3+//4P/iD+Mf6Z/lP+ZOYtAAcP+eUOov6z/sT+1f7m/vf/CP v/Gf8q/zv/TP9d8RYFkvQP/3X/hv+X/6j/uf/K/9v/7P///fAO8B/wMPeM9533rvCR//fQ8Ib38v 6C/pPwSvBb8Gz/8H3xcPCf8LDwwfDS8aDw9P/xBfEW8SfxOPH28Vrx6/F8//GN8Z7xr/HA8dHx4v LV8gT/8hXyJvI38wXyWfJq8nvyjPrynfNbHWYEExT9hwZ9MgmdgAIE2fwNnAZ2VBM/U9nTFRwlJU uj1A1xA14Ls1T4+IQjm7zJBFSEZjIP5taTykU0b6NTnT3zbvx3aZ0yBjLcHgY+BzLctwdU4BQMhQ Y53Q0xCd0GP3QbDEEJ5wYS3vLv8wCmWRe8tAytBsVUBLj0yf1gRvPmZQL1E/MApOCZDAcXX1n8B0 Tw9hQt9D70T/Rg/7Rx9eBVPC0UjfSe9K9/cAhHUglMAvMDUvmlEf1hBTr1S/1gSf8DowMfwgUNjA W39cj12fXq9fv/lqtFRvYW9if0r3TghaTz9bX2kPah9rL2w/dOZDY/9t727/Sv9lj8b9cm9zf3SP x3Wfdq9gxXViaspheD/reU96V02XMENORMohQmCzwfDJgFZvnHBnwCM+cuNCwGfAbXNnfW9+f3+P /4i/ic+K2YTvMJ8xrzK/M8//jr83PT6RLDU173v/OA87k/2kcFCMypdxjc88Tz1fPm//P39gfMuw hjnMQNjw0yKdINvB8cJgYk4AQjBp1wDKEP9675eP1gTKgIuPjJ+Kr1Z//1ePqL+pz6rfq++s/64P rx//sC+xP7JPs1+0b7V/to+3n/+4ry/7o5+kr02fcT9QHKcf/6gvi3/Cv8PNbcCi0thSy0GZ0HAg daNwx/d2aXJA9cwCV9BwbMuwvX++j9YEyFdpZMnRZWLYMMlw/Z7wdMS/xc/D37q/u8/QP//RT9Jf 02/Uf9WP1p/Xr9i//9nP2t/b79z/3g/fH+AvvJ8tgJxByzSYwGhZ0GY9AiLjgHRwOi8vdzXnYC7A ry+iEqIQbi+zopJO4GZv6LBOFyKfXOxpZcogl+JmyiBO4KKwgHtIWVBFUkyGQDxLIObv5//pD+oV fX0PoAHKIE6AmFBcY2Yx/Fx1QfDhaO0f7i/vP4aD75Ovjl/hr4RFQZZdzp/Pr7/Icc1Qyl/Lb2ck yXJlohIvzVCGkKExckBtQiQgdx3NoGii0oNCyHJib2SIeSAnycBscCf8///+D6W/+k/7X/gf4r/j zwh//wmPCp8Lrwy/Dc8O3w/vEP//Eg8THxQvFT8WTxdfGG/kn/8Dn78/WX/A3wW/Bs8H3yHf8yLv I/ZZb2QwUABTEB/g7GFjAVDJsnBOcVMB9IF/mHCiUhy/Hc8FBcnBopNh/82/JX8jjxnvGv8vLzA/ MU//Ml8zbzR/NY82nzevOL85z/863zvvPP8+Dz8fG88pvyrP/03PTt8hPy2fLq8kb0mfSq3GV8nA J9JwbHmiUc1Qv08AKACGkP+whuCiwHkngP/IkEP/RQ9nJIMVooFKsJ7gf8fAUBHNgFkQygBTwSiQ Y/pp61BjS59Mr0q8ybAnwbAiUmU6eACjYHRhMf2h8G9AAIY5UJ9Rr2ckhuT6Ll0wIlVPVl9Kv12v Xr8PX89g32HvbUhkYXkn66Hwx7BwR5Bzg4xkT2Vf/2NvaG9pf0EvQj9sz23fbu8BQ5QxLiBmTVJJ 56KwLKCIAUVt/9BaT1tf7UYFY6Ng61BnUGAsoKNR0SiAcm9iT5BtiAGXEEZryGCEcChSbwJQWfp2 hxApam9rf2yPea96v+F7yS0tX19/dHx/fY/ve5+AT4FfgmlNALRYwHRvu3V/UrQxgx+EL4I8RCyg kVixVGh1zVAyN6FQG2ageKAwkwGS8DoxM/Q6MJ5wLZMAjWCJP4pPdYI8RnfQbVjAWJB49SK/hp+H r4i1cE+YUHGZPIJ4inl5MS530HlAdVRwr1kAJ/FIX3ESZ5Y6PoJ//47/kA9mB4aPk4+Un5Wvlr3/ v/9H75lfmm+bf5yPgi1TFfVYwFtZqF1zX57Pn992j/93n3igqC+pP4I/sh+zL8cKvmhUQVRBAIHx oO+QLa6Bz1AgAKZHUFmRTUWtf66P+4i16aBy/9BdILTvtf+0Dw+9X75vfsvDIl89X05QZXh0ULjx X45gMQHEMDFDNDQzRjQALkJDNTVFRkEeQcAvwT+/TFjlLVR53yiQnq+7LwTnw8EvTwD0UPxuO8Wf xq+/T3B/cY/PH//QL9E/0k/TX9Rv1X/Wj9ef/9iv2b/az9vf3O/d/98PQx8fya/Kv6/SWFBG8GV0 PQIiLGBvLTg4NTl8LTFdb82vx6/ItbBwbuRzZkbgLUVGkGaATzGvyV/kz4imIABvWRBkuND+ckdQ 6DB38eef6K/Oz+//H/EP8h/zL/Q/9UZIaSz/9c/23/Tv+S/6P1ebKHAgA62wondPsCyQc3iAZAIQ 5mW8sShwKGICUOxP7V+JUrQoSoYhaWUpnnD9KVJH7tCMwI0SjdCMwY1huQQAYnUsv/z/+w1uU/D9 6zF3RuAnobkwWWAFsIzA/yfAAEGNMAmRANAFsAEPAh/ziLX/wW4nUCAgAFAQKHD3J/FmkHfxKYzA U+BdMQXf3wbv+x8PjxCfEalJWIBHUA+swaVAT/CScEVNTUF7eMCk4GVzQLAAZxAAMW//eTAMICwS Cw8MH1K0pPCscA+lMF0ACfQsEjMgLmS/pUAKAhJfE28RfBageChwqxqTuaF0U/BtjTAvvOFBzFBi NnAxL6SAbvQvd0dQM3iwF+8Y/1x2907gq3C8wHkEAEbAKVIoU/+8wFAgvLEcLx0/Tb25sY1R8DAv TlT/8VS2ADEsoH9nXyb/EW8q3yvvLP+ISTzXFmAik6EAaE7gZubA4mDwdHA6LyEwMyCk8KzgGmik +C94gFQQaC9m5m3vQKzCLyIu+S3QKjE0bGQt0mY2UBWCe0igWVBFUkxZsEtYgOcyvzPPNNZ9fTYB NlBG8MEiMFxjZjFcuJAvkP8wJzfvOP801aKX4kctkD7vxS2OOXiwPC9BLvAtv58uzy/fQu9D/0UJ KGV5MC+wwCGvIr/LlWhQUGdoxRVAJ3ggcnVupNAEQbBYUCBQd9BdMXdQUL82UFgyUCAAYLhRd8U/ eW/vRr9EzQoSFVBn7uAXn0nf+7wLpUBvIUEEUKRAd9BT4P+5siBzKq9P70TPVw9YH1kv/6Xvpv9c z13f4z9TP4guvOANABBfTbAOUHNoPTPWRGVQNLJfZJkoZJMaki4pzJ9a71v9P2pQIEG7PGCxMHBS YSAAHzFjBbDpJVBTQ6ygUCmQYh9jL/1kNWmj4A3xAKH/0qxwTFDfq3CwoQ9PaF9b/UVV9mVDP2VD X39gj2GfbM+ITEM6hFxcFlBUTEFCIMHHeaAf8FVQYm94eaA0tv165V8OUmXQo+Gk8HA/cU/NXAxP sMBb4iA1dG/h/3/jD3dPeF+EYHPPdN917yD6ZBugaXysgR+CL2VDgy+/hD+FRny/fc9cDDawacxA lnJmkG7GKBqSLCeJIMO5cQPQemUnKZQgZ0//kC9yT3NfiU+Hb4K/jS94r/95v3rPe9aTk3yflW9+ v3/F/DI4mK+KX4Jvm4+cn4Wf/5j/mg9fX6Wf4A+tf66Pr5//sK+xv7LPs9+077X/tw+4H/+5L7o/ iIaML6g/VHx7vJMk+FosVJRfof+Wf5ePqq//q7+nD7+fnN+d757/Zbyg7//EL6MPf8UhcMdvvL+m z8pP38tfqf/Hv8jPiMJtZUegKveTIGWikzMw3iDDH9C/W+8n3p/fr+C7QW4A8Glk9w5g/7BNwSf/ 4NZf128DNL8JcCTWNOBORgoDS6B3awL9DwBsF2D/sE1jTgHlj+af/w0lNkAW4AmQcC/ij+Cf7h+L 7y/wOlRNwG5rc/D/+/IP8BxZF2D0T/Vf8A/3v//4z/nf+u/7//0P/h//LwA/FwFPAl8DYS0Gk189 X5JOHzB0UOwAdF8pUAIxB6AxQzQ0M0YANC5CQzU1RUbcQUEDnwSvArxDcABqsNEf4C1UeSnwOurv 6//p2GVhcJJQaegAb+IgUOhzLXQCsGbefwoPAq//04/UnxMPFB8VLxY/F08YX/8Zbxp/G48cnx2v Hr8fzyDfPyHvIv/Vbw0PDh+O0m5hf+3AMpBVkT0APYCJAE3QIi8QrxG/Cy8MNHJR4HNmqVXgLUVv wG820WcMz4soz9hWYm9QZTY0K38fLI8SzzM/NE81WWVKOAArSWd3T0FRYbRRQwjgRQjgOgNCOdOA UWVRQmdBSToCZjU5gDoFRG850TlAQQhjQUc6AkVsUVSAUzVOYVdOeTYPAzcfNSxiM052Wm6AUWdU V0ZwYgiQck9AwFJsPBA8YDmAMt86YjnBOgE7EDnCRTsQOfAETHc6AUdaTlVrAGx6ZEdGMElDADBn UlcxdFlTnEJqPc8+3z/tMjWgoGBXZDFjbUSgPYA5IHVJSEJ5SIBKcxRaV0TgTEVQMFlXaVaQSUQ7 MEI6cEsAWQs8EAjgNDvyVUJ3VWs8sEPQSwjgMEMjzQA0/kJFj0af461rwAjgQ9A5cM06ATE8kAjQ QnNCoDsQlk5C8jpxZTmARUpDggZJO6JSYERSVGMwAk88YHhSa013TQpUSwBOS3A1TWpkvEZRSnCA PE4fTy8gVACMSkNUgFXATWtaPMAoRW9IOYBPOvJnQ/VD0U5D0kHMwFJxOgRD0CNCYDomRGtBbvA5 VmB2UFJEeDngUjBEf0ygVQ9WH+OtO6M59kLiRodY8DnkWdNZejFEPTAB6IBQU0E3Y0QxhlZBQElg ZEhKbEqACHc3YmKQRlZFNehCTFRMkE1L4D2/Xc9RNR1OekVkMFRT4E8gRm90TXpCUE5qoTygSGdC SjnVbToCKFRVbFkgeWVQYzLAVnljeUJrSMHtkIAzUXNJRlp2QYAkQXhEwE14VEBZZx9kj2WfNSxK QGuhRzF6NlpD0jnxVFpRPDBiOKRGVUIQQVJLoFdR4xUI4ElD0zFBcG1NdGhkWE7tkG5yYEqAUhVs 4Fc7gFkmgGpMbdwxdWxPbV81LGE9UEUwbDJkQXBMQHV3QDnySTZCY1BxZFlZ0zoCQ0IAS3gra3Zx TVHnRBBz4FGgMEJikDmycey/dA91HzUscs9z0XcOVQfAmlVMIEJzMnOwWFZvsBBYSnpMQVBrYleE bHV58EpwWXl3IH1yQGtz/3zPP949kCpQVyR4c3PATmh5MkFWD0PRO6JRgTpRVFRWUiFZEGsxSlRT 0HRWFFZOcMBscmBRVVKYTlNVO4FEUERMiNDMT1M9UVTAZEqDj4SfvfMdRXegVMA58GjBZDnVn0Hw OgGCgoMAaiYxeYIA/EYxggB6UILKho1cv4xP+17eeBFYcVVvw3kfei9yOyFJAFZ4ZFeB4GRFnEJp kw+UH3YtV02R8QQ1cHPBaloybHP5QYFqWTrwiHOZD5oZnc+/ntGaz5vf9n07omDQZjnV5nE6AoED RHCJ8opwiUDYVFJWiPCngEpwwIlA+XDAMVKKP45Goo+jn5Uu/VIhR0tQO5RMIIhGOiRLoP9vwXF/ co9zn6rvq/92z3fSHa8RYTpTOlE7okZOTveoYDoEaMFwjw+QGbIPsx9/NSyQz5HfruQ8oK9kWkNF y4jksIVnWKBsbr0Cuc8Xut9ubZdgV0iAd2dN/WJQalQAQlBEwsUAgWBqQHu/QUKSWDqiOkJRYDpC eAE58FdDRjNWc2Mkci+C0FZPf/BWNdJa6oBJTyZwQ8GPwp/DXu1oQGVYRDhoskyg/znkjvG4rZhg oT+exDoDUjD8Qm9aIDuhyU/KX5UuW6AFOlFTQMBrZ1dYWn9q8JbU0HFTcIfEzKA6UW2JiIBKSmsA UmhkmLDQdElFVoMwV0Nwd0B9SWBasZDpYIIQ1vDBEHY30Q/SHz/taUwASQA5aU93gNdgRMJEgXJa YlB5b4dDikA7oDuiSmRAQpFQB2FipnCuIUV4YVJu8lZAwE80Q9BMUmMQaJA4R2N42M/Z31ctaliu acDgVEBEgFZNIFWakCFawEgzL3emcXFRGkQ7gGNkEDwwUDh3IbbAQkZZL8fAVUhEc2g9EERsRVRQ UYM7MHdAamhDc0KB8btqADsBR+CP4Z81LHfHgBRsOcUwRdbgTzNNEEJJc0Vn0Ek3dwBuM3Rqc1lI d4HfoE5SRWlER0VgCbcARHpZgGtCWkQITTJGQfBMcGdyJmoMAGGwU0f0MEhQwFFjOUhSb+hP6V/F u+1VQSBjUXDvoEHQhbfwaUMATEhkaAiANEFmb4BzUnCXYGlSFHdFOvBiUiBZQ2ikaWViUFFT47BI W6CMQ1HdANSgQjJC1/BKNkMAUsfgdkzGgFE/8A/xH6StRVBpsEIQekkuWNWBVFBEsE6aoFpIlFYw 74BSvfB4OXgC8DNxUktLQHfQaMCYsEJJ7PBRaGNIzKBjWEIrUtdAxSB3YlBnxkk8MKXwbTVX98/4 31E1LEp3Vmiwb7fgRIpyQwBHl2BoR2068B5vTEA5UMfA2/AyOHWCNEmwUUhZcEpEwHRJTGjQNuXQ TKBo4G3VaqBJ29BGacAx7BD10fG1AWxMaVkg/48Anz/uhkHt8GjwZmtHOXfQ0m9cYFFpdyB2l2Bp cBdcQPYw9mBr9jBJekvwa0RlWvWQWjBK0O+wAkPdoGVCNWdLb7xPcTswmDDXAJfgYvrRP0PAVFAH TwhfXu1BEExZDEdJxhBCEHZZaVWHBTDWEMyQRzR6RpqQcWqwYVVZb4CJoWMQNcP7wVEASkI3Se1Q OuD2bsaA/sBw5dD1UO+wpeD8RENLoPPQ7bDYvxAPjV7tPSBm9fAXcFgVUIJgtjA0UUsT8HQO0C+x bWrXXEDuIDlgaQRgZ2HwGrD3QfAa8NagbxxARWBvwA5hZRZAag3QWXbkoLhgd/hHZ3bmALcAFs8X 3zUsMkVRgFI1/dAdsFlv9m/dAEEQQfcQOuBDYP2wiEdkb9dAa25LBdA8eUT8EJgwQ9DmkFZoD+cQ 7dADEFrwbTBYYxki8Xdy7WAKUEg2R/RQSFygdx6PH59XLVGggmdjIEZ0UHlr77B+UFiAC0Cl8J6A cLA68DVDmLCSsG9RUDX3cHD0RWg7MFM7oFrwBCBCEAdrsAzAgjBkSXkyeqg0K0pMcGaoQDgish5Z Jk8nXzUsSYBOb1AIVE5FPXBKZmJUODU1S+UwDHAjMHBHQ2QQjvB6OS9R+1BRa0PQaPBPaXBGxQAG YEx7a0BYUHnf8QXQxVCI4Er/cNBY8MgwsCAWQXu/Lw/yHQBvUi94SHlJcSFigGdROXnlwEh0VkXc EIEwOLGgOGIweRxFK0wgAvCwYEJjSwXsAFWOQEZDM3k0vFJSaXCJsHCQ5dB1TRBDPAGwIHQxSHAt kG1nNc82317taiuYoE0gau8cQe+wguDecDZRUBZB9XDjS+BE8GJkKwzAgrD84FeXcIMAFaBTWlBM 5mBKCExRRphwWmlncYxnaeyQQsFoZ23+ADkKwGw2PY8+n/ItU2NQcFRiQjLwUahgUEQwWlwQMTlJ E9AwJGpT5CB5ZudgS2GaRu1QSGPhU2BoOKfwFFJh5jB4O3BlOU9KL1EAUInQby+DUGzQZSt5N9Rg bkawRU8PRl/yLCnAiJAya3l3pFAy3hB3MN+gWB4wkEE5aHq9MFc0OWAMR24DEK6wNThIYycNoEhQ IuBDT/PwNlqGL7ZxQZBpUXpOWvDISDRDBmBKckGgO8D/EhBND04f8iztAFIgDGBEcBsSYEGgQrZA aMBFVW2CK5iQVDRHNXLgYGdRYLEQSGAwR5pQBME5vloKUGixPODNIM0iQrZz3lAi4Iqg7lCokFTt 0FTPf1Xf8ixToIoQ4+ExcC3gNExNVaggicBVMlOgWeA1T1RjemEAA3BkQIEMYFJrVkNSau6Qn7zA /GDvMDIgasAwdZpAcjFrcG5SkLCCUIbzUN9wUVyPXZ+sb9VwRfNArcSd1iN0vQFg0GrRTDMFwPxZ ejRAwODdUQ7QOpDNFP+l8CoQ3bStktZRzRDM8EIg7wWwZE9lXz+tSClAzXADYN+OsK6wK8DXIN1h QYiggWD/rYDM8KWB6BEpQDxirYIaoOpCFVBIOsBjzNBvc3HB/natgK8gK8Db4I6wK8BsD/9tH4Wt 5dDz0APQKnBwUpix30OwcOFvkZ8BAxBHOsBvwffdMBZBcEFOzRCW1scgUUAPlvSusW8QULBPeVlG N2v/dM9enjgDoK6xSU17BTDUwGJRYX6R3oAMoFD8Njly8GQg3jBbwOYwHCA9rvMrzJC2c/ZgtuJK duv1wO4wZJoQepb0liB7j3N8n/IsK1SBZJZBlvVE11nhDRD1EEmX8HIG0JixOHJMKwNArcSW83ZU dHoxp6BVS6C3QGBid8uJcKbgOWHAbFODT4Rf7/IsqIDzIGCAUqcyNPCokLcr4J9QyFBrQiHAIFCo UNsWoKmANDoAYdBEScAFsAZSp1Cm8Hk5RFRqxDFTioBsWla/0oESfzpQtnOLD4wf8iwqsLbjNd3W wWwOge4wsBNsmnAUUOfYcTmAgsYreoFkWsGG//+IBpLPk9/DrYicDiCY8g7Q7yoAQKDNIt4wQrhz mPEpQPfvUJj1V9BkiNWfcbFgrsZ/mo+bn+KtzSC2dL/Se2BQaVogbFeYhXiusM0jR72t42tacFog ayKtYUQzYN/VxClAaEKxQbGwWIKgok/bo1+77kossGOQa83CvU//vliocXlw1cTe4alZrQPYUP/A sKnQNb+rD/Id1sHnMNgQr6mwz1DIgAbQdOdAZJbw3wPQYnD9UJjzWsE0pw+oF/+fodATb8GeUbHP st9mb2mxPzrQmPX3gKkTn+RvYWpU/DdtHlBzcebg5uGfU4jG/ylA67CY9FrB/oHNILmPup/L0y6f lFMjUHNWK6DmUIePwOZQjtBKVDA159B2VhSQSZB0SlFgYGHAOZZTjuDncFfHEEtSxhAaVI6AVT1A 5qBPUjCiZImweXhOSNBr4H/fwk8oXlBgaXD7kUtgUI/AnEU175COkNaAMFYr4HYwlhCQwDmPwEtQ NKBrZlLHMI7ARkvGkMVRZP/GMZDhj8CPMNdQxvCI1HeQ/ljWIMkPyh8/rbjSItBn4+hRalVgMHqK AGBAX8BRx6BrME5RcDBiAGcXpvBh0NHgVO5ATmprOV+wek1g8C3gHRBqTsJHkMBKR09Vn5DcwMA1 aExuTnDQz9Hfa3XtBtAxroA5YvAUUGzLaMC2IyuY8096iv/Zjy/yHd1P3l+FbC3jQ189UF9OZXgp sGHh8F8oMDAx5FAxFkA0M/hGNC70QDHgO5CSoONA/+BP4V/fb+YP5x/oL+k/6k/54shfX+7U69/s 7+r/76//8L+sWe7w9Y/2n/dZ8n/zjwMobRSAQy11c2VyKnPybDT6QHDkICB9DfhrOPzg/lB9bWFp 6dLBZyDSwHNM//lv+n8B+4ZAYmljLm1uDmkDMHJA/rBsLmNhz/9fAG/xn/2bPEH89P5QQGhyZWY9 IgWAdKBwOi8vdwmALgMPZ0ww/qH+kG4v/xKsEGZrTCGsEGP7pCIFWQQwZuxpZdfwBDJm1/CsEP8w FnsiAICQUjQATksgzwkPCh8LLww1fX0NUdfwA/vgBKBcY2YxXHX+bAXwrHcPPxBPEV/7swV3TwVn buAYH/JOOTIFEC/+QQVQBB8FLwY/HB8dLx4/xx9PIF+shkVuZPwP/R+t/iVvI7D7aUREEGX/Pxci 3yDvKPs1KdEvRk//x6AqKRivKqAmEi4IrEgmA+srLyk2NxtyUBvOkBAbgbFKoE9DS2CAYQBFLV/9 MX9nGTEmLzcPKWNSMDQSvVwAWRvNG3A4jzsRNxuBLEhUfwAqIH09QAAAAB4ANRABAAAAQQAAADxC NTgzNUUxQ0M1OTQ3RDRGODFCRUFFNkM2OTk3Mzk4RjAyM0ZFQzBDQGV0bmEuc2ltLnVtb250cmVh bC5jYT4AAAAAHgBHEAEAAAAPAAAAbWVzc2FnZS9yZmM4MjIAAAsA8hABAAAAHwDzEAEAAACCAAAA UgBFACUAMwBBACAAZgBNAFIASQBzAHQAYQB0ACAALQAgAEUAbQBtAGEAIABjAG8AbgBmAGkAZwB1 AHIAYQB0AGkAbwBuACAAcAByAG8AYgBsAGUAbQAgAC0AIABTAE8ATABVAFQASQBPAE4AIABGAE8A VQBOAEQALgBFAE0ATAAAAAAACwD2EAAAAABAAAcwCSuvt8lExAFAAAgwbXkmjspExAEDAN4/r28A AAMA8T8JEAAAHgD4PwEAAAAJAAAAUm95IFl2ZXMAAAAAAgH5PwEAAABeAAAAAAAAANynQMjAQhAa tLkIACsv4YIBAAAAAAAAAC9PPVVNT05UUkVBTC9PVT1GSVJTVCBBRE1JTklTVFJBVElWRSBHUk9V UC9DTj1SRUNJUElFTlRTL0NOPVJPWVlWAAAAHgD6PwEAAAAVAAAAU3lzdGVtIEFkbWluaXN0cmF0 b3IAAAAAAgH7PwEAAAAeAAAAAAAAANynQMjAQhAatLkIACsv4YIBAAAAAAAAAC4AAAADAP0/5AQA AAMAGUAAAAAAAwAaQAAAAAADAB1AAAAAAAMAHkAAAAAAHgAwQAEAAAAGAAAAUk9ZWVYAAAAeADFA AQAAAAYAAABST1lZVgAAAB4AMkABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dp bGwuY2EAAB4AM0ABAAAAJQAAAG1pbmMtdXNlcnMtcmVxdWVzdEBiaWMubW5pLm1jZ2lsbC5jYQAA AAAeADhAAQAAAAYAAABST1lZVgAAAB4AOUABAAAAAgAAAC4AAAALACkAAAAAAAsAIwAAAAAAAwAG EGtYJd4DAAcQvhkAAAMAEBAAAAAAAwAREAAAAAAeAAgQAQAAAGUAAABUSEVQUk9CTEVNSVNPVkVS TFlTSU1QTEUsQU5EVEhFU09MVVRJT05JU0RFU0NSSUJFREFUOkhUVFA6Ly9XV1dNQVRIV09SS1ND T00vU1VQUE9SVC9URUNILU5PVEVTLzEyMDAvAAAAAAIBfwABAAAAQQAAADxCNTgzNUUxQ0M1OTQ3 RDRGODFCRUFFNkM2OTk3Mzk4RjAyM0ZFQzBDQGV0bmEuc2ltLnVtb250cmVhbC5jYT4AAAAAzO4= ------_=_NextPart_001_01C444CA.8E1366CD-- From adamt-pub@fmrif.nimh.nih.gov Sun May 30 12:55:05 2004 From: adamt-pub@fmrif.nimh.nih.gov (adamt-pub@fmrif.nimh.nih.gov) Date: Sun May 30 11:55:05 2004 Subject: [MINC-users] "Not implemented yet in cache_volume_range_has_chang ed()" Message-ID: Was there a solution posted for the problem Max posted back in January (attached below)? I am encountering the same problem with minctracc: [adamt@aurum sk-2004-05-27]$ minctracc -verbose 5 -lsq6 -tricubic -step 0.4 0.4 0.4 -mi sk-2004-05-27_3.mnc sk-2004-05-27_2.mnc sk-2004-05-27_3to2.xfm COG of v1: 0.191217 29.691250 2.433900 COG of v2: -0.619259 27.213451 1.950602 [trans] = -0.810476 -2.477798 -0.483299 (snip) rotation angles are: 0.888762 -0.610462 -0.611639 translation mm : -0.810476 -2.477798 -0.483299 WARNING: source volume not UNSIGNED_BYTE, will do conversion now. Converting: ................................................................... Not implemented yet in cache_volume_range_has_changed() WARNING: target volume not UNSIGNED_BYTE, will do conversion now. Converting: ................................................................... Not implemented yet in cache_volume_range_has_changed() Segmentation fault [adamt@aurum sk-2004-05-27]$ [adamt@aurum sk-2004-05-27]$ minctracc -version The program was built from: Package MNI AutoReg, version 0.98k, compiled by adamt@antimony.nimh.nih.gov (i686-pc-linux-gnu) on 2004-01-09 at 13:19:13 [adamt@aurum sk-2004-05-27]$ mincinfo sk-2004-05-27_2.mnc file: sk-2004-05-27_2.mnc image: signed__ short 0 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 188 0.7 -55.499 yspace 512 -0.391 125.658 xspace 512 -0.391 101.561 [adamt@aurum sk-2004-05-27]$ thanks, --- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 On Tue, 13 Jan 2004, Maxime Descoteaux wrote: > Hi all, > > My program has always run fine on minc volumes up to 181 x 217 x 181. > But today, I tried to run on a 256 x 256 x 181 and on a 384 x 512 x 90 > volumes I get this weird output and finally a bus error: > > Outputting Volume: 46% done. (41/90) Time: 20.8 sec out of approx > 45.4 sec > Outputting Volume: DONE in 29.9 sec > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > writing /tmp/max/I_yy.mnc ... > Bus error > > > Any idea what is causing this. As the process runs, I do a top and > watch > the %mem and how big it is and everything seems as expected. > > Thanks > > Max > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From crioux@student.cs.uwaterloo.ca Sun May 30 18:49:03 2004 From: crioux@student.cs.uwaterloo.ca (crioux) Date: Sun May 30 17:49:03 2004 Subject: [MINC-users] Problems installing Display on Fedora -- undefined reference to `__ctype_b' Message-ID: Hi, I've been trying to configure Display. I've installed all required libraries, however, when running ./configure --with-build-path=/usr/local/mni I get: [...] checking netcdf.h usability... yes checking netcdf.h presence... yes checking for netcdf.h... yes checking for ncopen in -lnetcdf... no configure: error: cannot find required library config.log reveals: [...] configure:20894: checking for ncopen in -lnetcdf configure:20924: gcc -o conftest -g -O2 -I/usr/local/mni/include -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function `NC_check_name': : undefined reference to `__ctype_b' collect2: ld returned 1 exit status configure:20930: $? = 1 configure: failed program was: | /* confdefs.h. */ [...] Now I've looked around for similar problems, and have found this: http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=86465#c1 http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=86465#c24 ----- Undefined __ctype_b using glibc with ncurses __ctype_b is gone for *__ctype_b_loc() because of the new locale model. In libc.so, __ctype_b is exported as compatibility symbol, but for the 8.0 errata it should be readded to libc.a. On RHL9 and later it is going to stay the way it is, ie. forcing all incompatible objects to be recompiled. The reason is e.g. libstdc++, which extensively uses uselocale these days, and __ctype_b using objects don't work together with uselocale (that's why __ctype_b_loc etc. were introduced). Binary compatibility is maintained for shared libraries and binaries only accross releases, so what you're trying to accomplish was never guaranteed to work between any releases. ----- and this fix: http://oss.sgi.com/archives/info-inventor-dev/2004-02/msg00004.html Is this my problem? Do I have to build such a workaround? Anyone else using these tools on Fedora? Thanks for any help, Caroline From stever@bic.mni.mcgill.ca Sun May 30 22:38:04 2004 From: stever@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sun May 30 21:38:04 2004 Subject: [MINC-users] Problems installing Display on Fedora -- undefined reference to `__ctype_b' In-Reply-To: ; from crioux@student.cs.uwaterloo.ca on Fri, May 28, 2004 at 02:53:22PM -0400 References: Message-ID: <20040530213746.E11627907@shadow.bic.mni.mcgill.ca> On Fri, May 28, 2004 at 02:53:22PM -0400, crioux wrote: > configure:20894: checking for ncopen in -lnetcdf > configure:20924: gcc -o conftest -g -O2 -I/usr/local/mni/include > -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 > /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function > `NC_check_name': > : undefined reference to `__ctype_b' > collect2: ld returned 1 exit status [...] > Now I've looked around for similar problems, and have found this: > and this fix: > http://oss.sgi.com/archives/info-inventor-dev/2004-02/msg00004.html > Is this my problem? I'm not using Redhat myself, but I suspect that is your problem. Do I have to build such a workaround? I would guess so. Or perhaps it suffices to recompile netcdf. -S From bert@bic.mni.mcgill.ca Mon May 31 12:20:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Mon May 31 11:20:04 2004 Subject: [MINC-users] Problems installing Display on Fedora -- undefined reference to `__ctype_b' In-Reply-To: <20040530213746.E11627907@shadow.bic.mni.mcgill.ca> Message-ID: I believe that the preferred workaround for this problem is to recompile netCDF from the sources. See the following reference from the netCDF website: http://www.unidata.ucar.edu/cgi-bin/msgout?/glimpse/netcdf/5327 -bert On Sun, 30 May 2004, Steve ROBBINS wrote: > On Fri, May 28, 2004 at 02:53:22PM -0400, crioux wrote: > > > configure:20894: checking for ncopen in -lnetcdf > > configure:20924: gcc -o conftest -g -O2 -I/usr/local/mni/include > > -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 > > /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function > > `NC_check_name': > > : undefined reference to `__ctype_b' > > collect2: ld returned 1 exit status > [...] > > > Now I've looked around for similar problems, and have found this: > > > and this fix: > > http://oss.sgi.com/archives/info-inventor-dev/2004-02/msg00004.html > > > > Is this my problem? > > I'm not using Redhat myself, but I suspect that is your problem. > > Do I have to build such a workaround? > > I would guess so. Or perhaps it suffices to recompile netcdf. > > -S > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >