From minc-users@bic.mni.mcgill.ca Wed Jun 1 17:49:04 2005 From: minc-users@bic.mni.mcgill.ca (Don Bigler) Date: Wed Jun 1 16:49:04 2005 Subject: [MINC-users] Unable to Locate Various Perl Scripts Message-ID: <429E1F34.8050908@psu.edu> MINC-Users, I am a new user to the MINC tools. I'm in the process of building and testing the tools on a Fedora Core 1 Linux system. However, I am unable to find a number of tools that are referenced on the web pages. Below is a list of tools: cortical_surface smooth_mask stx_segment sulcus_graph Where can I find these tools? Thanks, Don Bigler -- Don Bigler The Pennsylvania State University NMR Building H066 Radiology Hershey Medical Center Hershey, PA 17033 Phone: (717)531-5858 Fax: (717)531-8486 Hershey Confidentiality Statement: This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. From minc-users@bic.mni.mcgill.ca Thu Jun 2 05:53:07 2005 From: minc-users@bic.mni.mcgill.ca (Fornito, Alexander) Date: Thu Jun 2 04:53:07 2005 Subject: [MINC-users] MNI tools in Freesurfer Message-ID: <98A56869DA8D624C9869D012AE807A3D0225E486@whmail.ssg.org.au> Hi all, I've been having trouble with the MNI tools packaged together with Freesurfer. We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables. When I run Freesurfer's segmentation algorithm, I get the following error messages: segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' On their own some of the MNI tools work (eg., Display), whereas others don't (eg., mritotal, which returns with the mincinfo: error while loading shared libraries: libvolume_io.so.0 message). Any help would be greatly appreciated!!! Thanks, Alex From Andrew Janke Thu Jun 2 06:17:04 2005 From: Andrew Janke (Andrew Janke) Date: Thu Jun 2 05:17:04 2005 Subject: [MINC-users] MNI tools in Freesurfer In-Reply-To: <98A56869DA8D624C9869D012AE807A3D0225E486@whmail.ssg.org.au> References: <98A56869DA8D624C9869D012AE807A3D0225E486@whmail.ssg.org.au> Message-ID: Wierd, I had thought all the packages from now on were using static libraries. Anyhow, I presume you got the .deb packages from packages.bic.mni.mcgill.ca/deb? If so, then I'd still like to know why they are using shared libraries but the fix is to simply add: /usr/local/mni/lib to your LD_LIBRARY_PATH andrew On 01/06/05, Fornito, Alexander wrote: > Hi all, > I've been having trouble with the MNI tools packaged together with Freesurfer. We are running a linux kernel 2.4.26 debian 3.0 (woody). > We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables. > When I run Freesurfer's segmentation algorithm, I get the following error messages: > > segment_subject 190 > cp: cannot stat > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' > : No such file or directory > /data/flanders/work/alex/freesurfer/subjects/190/scripts > /data/flanders/work/ale > x/freesurfer/subjects > registering 190 > mri_convert orig orig/orig.mnc > reading from orig... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to orig/orig.mnc... > mincinfo: error while loading shared libraries: libvolume_io.so.0: > cannot open shared object file: No such file or directory > Error executing mincinfo on orig/orig.mnc > Error: could not open file > "/data/flanders/work/alex/freesurfer/subjects/190/mr > i/transforms/talairach.xfm". > System message: No such file or directory > mri_add_xform_to_header: could not read xform file > '/data/flanders/work/alex/fre > esurfer/subjects/190/mri/transforms/talairach.xfm' > > On their own some of the MNI tools work (eg., Display), whereas others don't (eg., mritotal, which returns with the mincinfo: error while loading shared libraries: libvolume_io.so.0 message). > Any help would be greatly appreciated!!! > Thanks, > Alex > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From Andrew Janke Thu Jun 2 06:32:03 2005 From: Andrew Janke (Andrew Janke) Date: Thu Jun 2 05:32:03 2005 Subject: [MINC-users] MINC 1.4 In-Reply-To: References: Message-ID: On 26/05/05, Robert VINCENT wrote: > So I've officially "released" MINC 1.4. The source code is available for > download here: > > http://www.bic.mni.mcgill.ca/software/distribution/packages/minc-1.4.tar.gz There is now also an OSX packages of this here: http://packages.bic.mni.mcgill.ca/osx/ linux versions to follow when I get my hands on a linux box again. (2 weeks time) -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Thu Jun 2 18:01:17 2005 From: minc-users@bic.mni.mcgill.ca (Don Bigler) Date: Thu Jun 2 17:01:17 2005 Subject: [MINC-users] Another Missing File Message-ID: <429F7376.1020000@psu.edu> MINC-Users, While testing the various built and installed MINC tools I came across a problem with 'classify_clean.pl'. It is trying to use a .mnc file called 'icbm_atlas_cerebellum_avg_53_mask_1mm.mnc', but the file is not located anywhere on my system. I did a search for the file on the internet and I couldn't find it there either. Any help would be greatly appreciated. It appears that 'classify_clean' is used by INSECT. Thanks, Don Bigler -- Don Bigler The Pennsylvania State University NMR Building H066 Radiology Hershey Medical Center Hershey, PA 17033 Phone: (717)531-5858 Fax: (717)531-8486 Hershey Confidentiality Statement: This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. From minc-users@bic.mni.mcgill.ca Thu Jun 2 22:45:05 2005 From: minc-users@bic.mni.mcgill.ca (Steve M. Robbins) Date: Thu Jun 2 21:45:05 2005 Subject: [MINC-users] MNI tools in Freesurfer In-Reply-To: <98A56869DA8D624C9869D012AE807A3D0225E486@whmail.ssg.org.au> References: <98A56869DA8D624C9869D012AE807A3D0225E486@whmail.ssg.org.au> Message-ID: <20050603014307.GA12330@nyongwa.montreal.qc.ca> On Wed, Jun 01, 2005 at 02:42:30PM +1000, Fornito, Alexander wrote: > Hi all, > I've been having trouble with the MNI tools packaged together with Freesurfer. Chances are you'd get a more informed response from a Freesurfer mailing list. > We are running a linux kernel 2.4.26 debian 3.0 (woody). > We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables. > When I run Freesurfer's segmentation algorithm, I get the following error messages: > > segment_subject 190 > cp: cannot stat > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' > : No such file or directory Not finding a script suggests an install problem. > On their own some of the MNI tools work (eg., Display), whereas > others don't (eg., mritotal, which returns with the mincinfo: error > while loading shared libraries: libvolume_io.so.0 message). Any > help would be greatly appreciated!!! That suggests you have a mix: some tools compiled with shared MINC libraries and some with static libraries. One source of the former is the "official" Debian packages, i.e. the ones from packages.debian.org. Best idea is to ask the person who built your binaries. -Steve From minc-users@bic.mni.mcgill.ca Fri Jun 3 08:35:03 2005 From: minc-users@bic.mni.mcgill.ca (Simon Fristed Eskildsen) Date: Fri Jun 3 07:35:03 2005 Subject: [MINC-users] error running mincmath In-Reply-To: <94d149057afdb0f1c504973f2c726b9d@mcgill.ca> References: <1114039381.4266e455c959d@web.mail.umich.edu> <94d149057afdb0f1c504973f2c726b9d@mcgill.ca> Message-ID: <42A04062.908@hst.aau.dk> I have encountered the same problem: Package MNI N3 Command: nu_correct native/t1_native.mnc.gz temp/t1_nuc.mnc -clobber -keeptmp Error message: Files /usr/tmp/nu_correct_28314//t1_nuc_field.mnc and native/t1_native.mnc.gz have different coordinate spacings (zspace) nu_evaluate: crashed while running mincmath (termination status=256) nu_correct: crashed while running nu_evaluate (termination status=256) Same output on mincinfo: image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 160 1 -30.4761 yspace 256 -0.9375 148.799 xspace 256 -0.9375 119.531 Same direction cosines: mincheader /usr/tmp/nu_correct_28314//t1_nuc_field.mnc | grep direction_cosine zspace:direction_cosines = 0., 0., 1. ; yspace:direction_cosines = -0., 1., -0. ; xspace:direction_cosines = 1., -0., -0. ; Maybe the -0 entries in the cosines are causing the problem? This is the first time I have encountered this problem. The input minc file have been converted from dicom using dcm2mnc (minc-1.4, netcdf -3.5.1) Any ideas? Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student Denmark->Aalborg->HST->MI (se@hst.aau.dk || +45 9635 9823) D. Louis Collins wrote: > Haytham, > > If the mincinfo output for the two volumes is the same, (ie, same > starts, steps and number of elements _and_ same dimension ordering), > then I suspect that the two volumes have different direction cosines. > Check with 'mincheader file.mnc | grep direction_cosine'. > > you could rerun with '-nocheck_dimensions' - this will force the code > to do voxel-to-voxel manipulations, without checking against the > dimension information. > > -Louis > > > On Apr 20, 2005, at 7:23 PM, haytham@umich.edu wrote: > >> Command: (executed during nu_evaluate) >> >> mincmath -clobber -verbose -copy_header -zero -div in.mnc.gz >> in_nuc_field.mnc >> out.mnc >> >> >> Error message: >> Files in_nuc_field.mnc and in.mnc.gz have different coordinate >> spacings (zspace) >> nu_evaluate: crashed while running mincmath (termination status=256) >> >> >> When I run mincinfo on the two volumes, I get the same output: >> >> image dimensions: zspace yspace xspace >> dimension name length step start >> -------------- ------ ---- ----- >> zspace 112 1.5 -86.396 >> yspace 256 -1.48438 178.728 >> xspace 256 -1.48438 190 >> >> >> any ideas on what causing? >> >> Thank you. >> _______________________________________________ >> MINC-users@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From Andrew Janke Fri Jun 3 08:48:05 2005 From: Andrew Janke (Andrew Janke) Date: Fri Jun 3 07:48:05 2005 Subject: [MINC-users] error running mincmath In-Reply-To: <42A04062.908@hst.aau.dk> References: <1114039381.4266e455c959d@web.mail.umich.edu> <94d149057afdb0f1c504973f2c726b9d@mcgill.ca> <42A04062.908@hst.aau.dk> Message-ID: On 03/06/05, Simon Fristed Eskildsen wrote: > Package MNI N3 > > Command: nu_correct native/t1_native.mnc.gz temp/t1_nuc.mnc -clobber > -keeptmp > > Error message: > Files /usr/tmp/nu_correct_28314//t1_nuc_field.mnc and > native/t1_native.mnc.gz have different coordinate spacings (zspace) > nu_evaluate: crashed while running mincmath (termination status=256) > nu_correct: crashed while running nu_evaluate (termination status=256) > > Same output on mincinfo: > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 160 1 -30.4761 > yspace 256 -0.9375 148.799 > xspace 256 -0.9375 119.531 > > Same direction cosines: > mincheader /usr/tmp/nu_correct_28314//t1_nuc_field.mnc | grep > direction_cosine > zspace:direction_cosines = 0., 0., 1. ; > yspace:direction_cosines = -0., 1., -0. ; > xspace:direction_cosines = 1., -0., -0. ; > > Maybe the -0 entries in the cosines are causing the problem? > This is the first time I have encountered this problem. The input minc > file have been converted from dicom using dcm2mnc (minc-1.4, netcdf -3.5.1) > > Any ideas? Another thing to remember is that mincinfo only reports starts and steps with a limited number of decimal places (and thus can round results). To check if the two files are indeed identical with repect to step sizes use something like this: mincinfo -attvalue zspace:start in.mnc mincinfo -attvalue zspace:start two.mnc The simple fix to this is as louis suggested, simply run mincmath with the -nocheck_dimensions argument. -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Sat Jun 4 22:29:04 2005 From: minc-users@bic.mni.mcgill.ca (Seifeddine Ferchichi) Date: Sat Jun 4 21:29:04 2005 Subject: [MINC-users] submissions Message-ID: <002001c5696d$e3d05440$6800a8c0@AD.DMI.USherbrooke.Ca> This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C5694C.58804740 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable ------=_NextPart_000_001B_01C5694C.58804740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
------=_NextPart_000_001B_01C5694C.58804740-- From minc-users@bic.mni.mcgill.ca Mon Jun 6 09:03:05 2005 From: minc-users@bic.mni.mcgill.ca (Daniel Schwarz) Date: Mon Jun 6 08:03:05 2005 Subject: [MINC-users] icbm probabilistic atlas Message-ID: <42A43B49.1040305@feec.vutbr.cz> Dear minc-users, I need to get icbm452_atlas_probability_white.hdr, icbm452_atlas_probability_gray.hdr and icbm452_atlas_probability_csf.hdr aligned with icbm_avg_152_t1_tal_lin.mnc I used ana2mnc to get the atlases into mnc format. Is there a simple way how to crop/pad the images to get them aligned with icbm_avg_152....? file: /usr/local/mni/lib/model/icbm_avg_152_t1_tal_lin.mnc image: signed__ short 0 to 4095 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 181 1 -72 yspace 217 1 -126 xspace 181 1 -90 file: gray.mnc image: signed__ short 0 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 148 1 -74 yspace 188 1 -94 xspace 149 -1 74.5 Thank you in advance for your replies. Daniel Schwarz From minc-users@bic.mni.mcgill.ca Tue Jun 7 07:00:04 2005 From: minc-users@bic.mni.mcgill.ca (Fornito, Alexander) Date: Tue Jun 7 06:00:04 2005 Subject: [MINC-users] MNI tools in Freesurfer Message-ID: <98A56869DA8D624C9869D012AE807A3D0225E4AA@whmail.ssg.org.au> Hi, We seem to have got it working now, thanks! However, when Freesurfer calls nu_correct, I get the following message: nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_14595/ nu/nu0.mnc nu/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done ...and so on, for quite some time, before moving on to other processes. Is the Not implemented yet in cache_volume_range_has_changed() message indicative of some kind of error? Thanks for your help, Alex -----Original Message----- From: Andrew Janke [mailto:a.janke@gmail.com] Sent: Thu 6/2/2005 7:15 PM To: minc-users@bic.mni.mcgill.ca Cc: Subject: Re: [MINC-users] MNI tools in Freesurfer Wierd, I had thought all the packages from now on were using static libraries. Anyhow, I presume you got the .deb packages from packages.bic.mni.mcgill.ca/deb? If so, then I'd still like to know why they are using shared libraries but the fix is to simply add: /usr/local/mni/lib to your LD_LIBRARY_PATH andrew On 01/06/05, Fornito, Alexander wrote: > Hi all, > I've been having trouble with the MNI tools packaged together with Freesurfer. We are running a linux kernel 2.4.26 debian 3.0 (woody). > We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables. > When I run Freesurfer's segmentation algorithm, I get the following error messages: > > segment_subject 190 > cp: cannot stat > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' > : No such file or directory > /data/flanders/work/alex/freesurfer/subjects/190/scripts > /data/flanders/work/ale > x/freesurfer/subjects > registering 190 > mri_convert orig orig/orig.mnc > reading from orig... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to orig/orig.mnc... > mincinfo: error while loading shared libraries: libvolume_io.so.0: > cannot open shared object file: No such file or directory > Error executing mincinfo on orig/orig.mnc > Error: could not open file > "/data/flanders/work/alex/freesurfer/subjects/190/mr > i/transforms/talairach.xfm". > System message: No such file or directory > mri_add_xform_to_header: could not read xform file > '/data/flanders/work/alex/fre > esurfer/subjects/190/mri/transforms/talairach.xfm' > > On their own some of the MNI tools work (eg., Display), whereas others don't (eg., mritotal, which returns with the mincinfo: error while loading shared libraries: libvolume_io.so.0 message). > Any help would be greatly appreciated!!! > Thanks, > Alex > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Wed Jun 8 11:43:04 2005 From: minc-users@bic.mni.mcgill.ca (xingfeng lee) Date: Wed Jun 8 10:43:04 2005 Subject: [MINC-users] emma and matlab7 Message-ID: <20050608144228.39716.qmail@web50106.mail.yahoo.com> Hello All, it seems to me that the new matlab 7(Release 14) does not work well with EMMA (Linux version). The program work well with matlab6p5 but when i run the same program in matlab7, i met the following error: ??? Maximum recursion limit of 100 reached. Use set(0,'RecursionLimit',N) to change the limit. Be aware that exceeding your available stack space can crash MATLAB and/or your computer. Error in ==> unix at 16 Error in ==> testTimeSeries at 26 newHandle = newimage(outName,[0 nSlice imageHeight imageWidth],... I set the RecursionLimit, but Matlab crashed, Does anyone meet the same problem? regards __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From minc-users@bic.mni.mcgill.ca Wed Jun 8 14:00:05 2005 From: minc-users@bic.mni.mcgill.ca (Dylan David Wagner) Date: Wed Jun 8 13:00:05 2005 Subject: [MINC-users] mincsample mask problems In-Reply-To: References: Message-ID: <42A723DA.3050605@bic.mni.mcgill.ca> Hi, I've finally gotten around to using the -mask feature in mincsample to extract all voxel values and coords within a mask. ie: mincsample -mask average12_hippo.mnc -coords s1_multi_tal_t.mnc Which would, if I understand the program, give me the voxel values and coordinates of all voxels in my tstat file that lie inside the hippocampus mask I painted. However I get the following error: Files average12_hippo.mnc and s1_multi_tal_t.mnc have different sizes of dimensions. My mask file has a voxel size of 1x1x1 and the fmri file has 2x2x2. So I resample the mask to 2x2x2 but that didn't help. The mask was painted on the anatomical mri (for obvious reasons). so while both files are in tal space and now have the same voxel size I expect other "dimensions" will remain different. Is there anyway around this (short of distorting mask to fit the tstat file's dimensions?). Until then it's back to the old way of using minctotag. Which doesn't accept masks :( (So instead one has to multiply the fmri file by the mask and add a constant of say 100. And then get minctotag (modified to output real values and not just integers, thanks Jason!) to grab all voxels above 1, this way it ignores the 0 voxel values that result from the mask multiplication yet it doesn't reject the any negative voxel values in the t-stat file (cause they're bumped up by 100). Time consuming to say the least, especially as I have to bump them back down by 100 in SPSS to get the original values. If anyone knows of other tricks, I'm all ears). PS: if anyone cares, mincsample compiles for cygwin right out of the box! Unlike other apps that I've been unable to compile in cygwin. Best, DDW -- Dylan David Wagner Neuropsychology and Cognitive Neuroscience Unit Montreal Neurological Institute Tel: (514) 398-4400 (x089722) Email: dylan.wagner@mail.mcgill.ca Lab website: http://www.mni.mcgill.ca/cog/jonesgotman/ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From minc-users@bic.mni.mcgill.ca Wed Jun 8 14:22:06 2005 From: minc-users@bic.mni.mcgill.ca (Dylan David Wagner) Date: Wed Jun 8 13:22:06 2005 Subject: [MINC-users] mincsample mask problems In-Reply-To: <42A723DA.3050605@bic.mni.mcgill.ca> References: <42A723DA.3050605@bic.mni.mcgill.ca> Message-ID: <42A72920.9040901@bic.mni.mcgill.ca> Spoke too soon, ignore my previous question, I forgot to mincresample with the -like switch. Everything works great now. Thanks for the updated mincsample Andrew! It's a real time saver. Best, -- Dylan David Wagner Neuropsychology and Cognitive Neuroscience Unit Montreal Neurological Institute Tel: (514) 398-4400 (x089722) Email: dylan.wagner@mail.mcgill.ca Lab website: http://www.mni.mcgill.ca/cog/jonesgotman/ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From minc-users@bic.mni.mcgill.ca Thu Jun 9 05:42:04 2005 From: minc-users@bic.mni.mcgill.ca (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Thu Jun 9 04:42:04 2005 Subject: [MINC-users] netcdf 3.5.0 and fedora core 3 Message-ID: Hi, I was thinking that this issue might be of interest to other newbies. I have tried to compile NetCDF 3.5.0 on Fedora 3 core, but the c++ compiler is unable to compile the test program during config. I tried with NetCDF 3.6.0 from Unidatas site and there were no problems. The config log says: .... configure:1225: checking C++ compiler "c++" configure:1243: c++ -o conftest -DNDEBUG conftest.C 1>&5 In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c ++/3.4.3/backward/iostream.h:31, from configure:1235: /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/back ward_warning.h:32:2: warning: #warning This file includes at least one deprecate d or antiquated header. Please consider using one of the 32 headers found in sec tion 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated h eader . To disable this warning use -Wno-deprecated. In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c ++/3.4.3/cstdlib:52, .... 1) Should i expect problems from using a never netCDF version (than the one listed at http://www.bic.mni.mcgill.ca/software/distribution/) 2) What is the cause of the problem? Is it a deprecated header in NetCDF 3.5.0 relative to the default c++ compiler in Fedora? Thanks! Soren From minc-users@bic.mni.mcgill.ca Thu Jun 9 11:40:04 2005 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Jun 9 10:40:04 2005 Subject: [MINC-users] netcdf 3.5.0 and fedora core 3 In-Reply-To: Message-ID: Hi Søren, Regarding the first issue, I have not experienced any problems using MINC with netCDF 3.6.0-p1, the most recent release. As for the second issue, the "configure" script for netcdf-3.5.0 tests for the presence of iostream.h, which is considered deprecated in recent versions of GNU C++. If you set the CXX environment variable to an empty string, the script will skip the tests of the C++ compiler and the C++ interface will not be built. Since MINC does not need the C++ interface to netCDF, this should not pose a problem. Hope this helps, -bert On Wed, 8 Jun 2005, Søren Christensen wrote: > Hi, > I was thinking that this issue might be of interest to other newbies. > I have tried to compile NetCDF 3.5.0 on Fedora 3 core, but the c++ compiler is unable to compile the test program during config. > I tried with NetCDF 3.6.0 from Unidatas site and there were no problems. > > The config log says: > .... > configure:1225: checking C++ compiler "c++" > configure:1243: c++ -o conftest -DNDEBUG conftest.C 1>&5 > In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c ++/3.4.3/backward/iostream.h:31, > from configure:1235: > /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/back ward_warning.h:32:2: warning: #warning This file includes at least one deprecate d or antiquated header. Please consider using one of the 32 headers found in sec tion 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated h eader . To disable this warning use -Wno-deprecated. > In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c ++/3.4.3/cstdlib:52, > .... > > > 1) Should i expect problems from using a never netCDF version (than the one listed at http://www.bic.mni.mcgill.ca/software/distribution/) > > 2) What is the cause of the problem? Is it a deprecated header in NetCDF 3.5.0 relative to the default c++ compiler in Fedora? > > Thanks! > Soren > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Thu Jun 9 22:11:04 2005 From: minc-users@bic.mni.mcgill.ca (Steve M. Robbins) Date: Thu Jun 9 21:11:04 2005 Subject: [MINC-users] netcdf 3.5.0 and fedora core 3 In-Reply-To: References: Message-ID: <20050610010953.GB11782@nyongwa.montreal.qc.ca> On Wed, Jun 08, 2005 at 07:17:26PM +0200, Søren Christensen wrote: > Hi, > I was thinking that this issue might be of interest to other newbies. > I have tried to compile NetCDF 3.5.0 on Fedora 3 core, but the c++ compiler is unable to compile the test program during config. > I tried with NetCDF 3.6.0 from Unidatas site and there were no problems. > > The config log says: > .... > configure:1225: checking C++ compiler "c++" > configure:1243: c++ -o conftest -DNDEBUG conftest.C 1>&5 > In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c ++/3.4.3/backward/iostream.h:31, > from configure:1235: > /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/back ward_warning.h:32:2: warning: #warning This file includes at least one deprecate d or antiquated header. Please consider using one of the 32 headers found in sec tion 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated h eader . To disable this warning use -Wno-deprecated. But this is just a warning. The compile ought to have worked. Did the configure script actually fail at this point? > 2) What is the cause of the problem? Is it a deprecated header in NetCDF 3.5.0 relative to the default c++ compiler in Fedora? No, it is a deprecated header *USED* by NetCDF. Typically you can ignore such warnings, or fix the code to use instead of , etc. From what you say, upstream has already made these changes, so I'd just use the newer NetCDF. -Steve From minc-users@bic.mni.mcgill.ca Fri Jun 10 02:58:04 2005 From: minc-users@bic.mni.mcgill.ca (Michel Audette) Date: Fri Jun 10 01:58:04 2005 Subject: [MINC-users] combining component labelling with size-thresholding Message-ID: <004001c56d95$85e26a90$3a751d96@surgsim2> Hi folks, I would like to use the mincmorph -successive "G" option together with mincstats to perform a component labeling of binary data that I have, and to retain only the contiguous blobs whose size is greater than some threshold T_A. Is there a simple way to do this with the two commands, or do I have to write a script that looks at a histogram file produced by mincstats? Thanks for your kind help. Cheers, Michel Michel Audette, Ph.D., Research Fellow, Surgical Simulation, Surgical Assist Technology Group, AIST, Namiki 1-2, Tsukuba, Japan, 305-8564. -------------------------------------------------------- "If you think you can do it, you're right. If you think you can't do it, you're still right." - Henry Ford From minc-users@bic.mni.mcgill.ca Tue Jun 14 05:29:05 2005 From: minc-users@bic.mni.mcgill.ca (Colin HAWCO) Date: Tue Jun 14 04:29:05 2005 Subject: [MINC-users] Re: [BIC-users] Matlab 7.0.4,Matlab6.5, and EMMA (emma-0.9.7) In-Reply-To: <1118285383.42a7ae4741499@webmail.mcgill.ca> Message-ID: In some matlab versions, the following error will occure and can be ignored. I run fmrilm and many other functions that call emma from matlab 7 routinely now and have had no troubles. The error you can ignor is: warning: Warning: File not found or permission denied > In miwriteimages at 96 In putimages at 112 In testMatlab7 at 54 The only sad thing is that I can't seem to turn this warning off (warning off doesn't work), and so the printing of the warning to the screen many tines ovr seems to slow down my file processing, since print commands seem generally slow. Personaly, I think everyone should just stick with matlab 6.5 I regret upgrading now. It's been nothing but trouble, and many of the new features are not, in my opinion, improvements. On Wed, 8 Jun 2005 xli96@po-box.mcgill.ca wrote: > > > Hello all, > > It seems Matlab 7.0.4 does not work well with EMMA. Does anyone meet the same > problem? > In windows XP: > The EMMA programs work well using Matlab 6.5. However, when I used new version > Matlab 7.0.4 and EMMA(0.9.7) to read and write MINC files, I got the following > warning: > Warning: File not found or permission denied > > In miwriteimages at 96 > In putimages at 112 > In testMatlab7 at 54 > > In Fedora Core Linux: > Matlab 6.5 and EMMA works well too, but after I uninstalled Matlab 6.5 and > installed Matlab 7.0.4, I can not write MINC files using the same EMMA although > it read MINC files very well , the error massages as follows: > > Command: micreateimage matlab7.0.4.352.mnc -parent > /home/xingfeng2/matlab/emma/mri.mnc -size 0 140 92 83 -type short -valid_range > 0 4095 -orientation sagittal > Output:  > ??? Error using ==> newimage > Error running micreateimage to create file matlab7.0.4.352.mnc > > Error in ==> testMatlab7 at 44 > new_handle = newimage(outFile,[0 ns imageHeight imageWidth],deblank(likeFile)). > > Does anyone meet the same problem in Windows and Linux (work with Matlab 7.0.4 > and EMMA), and how can I solve the problem? > > > Thank you very much! > > _______________________________________________ > BIC-users mailing list > BIC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/bic-users > From minc-users@bic.mni.mcgill.ca Tue Jun 14 05:29:55 2005 From: minc-users@bic.mni.mcgill.ca (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Tue Jun 14 04:29:55 2005 Subject: SV: [MINC-users] netcdf 3.5.0 and fedora core 3 Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C56D1B.B8367987 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Bert, Yes, that is reasurring to hear; unexplained errors are always a pest! = I haven't had problems with Register and Display using NetCDF 3.6.0 = either. Thanks for the explanation! =20 Soren=20 ________________________________ Fra: minc-users-admin@bic.mni.mcgill.ca p=E5 vegne af Robert VINCENT Sendt: to 09-06-2005 16:40 Til: minc-users@bic.mni.mcgill.ca Emne: Re: [MINC-users] netcdf 3.5.0 and fedora core 3 Hi S=F8ren, Regarding the first issue, I have not experienced any problems using = MINC with netCDF 3.6.0-p1, the most recent release. As for the second issue, the "configure" script for netcdf-3.5.0 tests = for the presence of iostream.h, which is considered deprecated in recent versions of GNU C++. If you set the CXX environment variable to an = empty string, the script will skip the tests of the C++ compiler and the C++ interface will not be built. Since MINC does not need the C++ interface = to netCDF, this should not pose a problem. Hope this helps, -bert On Wed, 8 Jun 2005, S=F8ren Christensen wrote: > Hi, > I was thinking that this issue might be of interest to other newbies. > I have tried to compile NetCDF 3.5.0 on Fedora 3 core, but the c++ = compiler is unable to compile the test program during config. > I tried with NetCDF 3.6.0 from Unidatas site and there were no = problems. > > The config log says: > .... > configure:1225: checking C++ compiler "c++" > configure:1243: c++ -o conftest -DNDEBUG conftest.C 1>&5 > In file included from = /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c = ++/3.4.3/backward/iostream.h:31, > from configure:1235: > = /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backwa= rd/back ward_warning.h:32:2: warning: #warning This file includes at = least one deprecate d or antiquated header. Please consider using one of = the 32 headers found in sec tion 17.4.1.2 of the C++ standard. Examples = include substituting the header for the header for C++ = includes, or instead of the deprecated h eader . = To disable this warning use -Wno-deprecated. > In file included from = /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c = ++/3.4.3/cstdlib:52, > .... > > > 1) Should i expect problems from using a never netCDF version (than = the one listed at http://www.bic.mni.mcgill.ca/software/distribution/) > > 2) What is the cause of the problem? Is it a deprecated header in = NetCDF 3.5.0 relative to the default c++ compiler in Fedora? > > Thanks! > Soren > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users ------_=_NextPart_001_01C56D1B.B8367987 Content-Type: application/ms-tnef; name="winmail.dat" Content-Transfer-Encoding: base64 eJ8+IhwRAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEAMAAAAFNWOiBbTUlOQy11c2Vyc10g bmV0Y2RmIDMuNS4wIGFuZCBmZWRvcmEgY29yZSAzAOkOAQWAAwAOAAAA1QcGAAkAEwAuADAABABg AQEggAMADgAAANUHBgAJABMAMgAbAAQATwEBCYABACEAAABEODRGOUZEQjhCMUY5NzRCQjM4MzZC OTMxQzYzQ0MxQQBrBwEDkAYAxBUAADcAAAADADYAAAAAAEAAOQAdQRg2G23FAR4APQABAAAABQAA AFNWOiAAAAAAAgFHAAEAAAApAAAAYz1ESzthPSA7cD1TVkY7bD1VUkQtMDUwNjA5MTc1MDI3Wi0x 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The config could actually procede but as i remember it, the make exited with an error - but due to some missing fortran functionality. However with netCDF 3.6.0 p1 there were no problems and i used that in stead. Best regards Soren From Andrew Janke Tue Jun 14 05:40:05 2005 From: Andrew Janke (Andrew Janke) Date: Tue Jun 14 04:40:05 2005 Subject: [MINC-users] combining component labelling with size-thresholding In-Reply-To: <004001c56d95$85e26a90$3a751d96@surgsim2> References: <004001c56d95$85e26a90$3a751d96@surgsim2> Message-ID: On 10/06/05, Michel Audette wrote: > > I would like to use the mincmorph -successive "G" option together with > mincstats to perform a component labeling of binary data that I have, and to > retain only the contiguous blobs whose size is greater than some threshold > T_A. Is there a simple way to do this with the two commands, or do I have to > write a script that looks at a histogram file produced by mincstats? Michel, Sorry about the delay in replying, I'm in Nottingham and a bit out of touch with the world. In a way the answer is yes. In that the output of the group option numbers the groups in decending order of size. Thus the group with the value of 1 is the largest. So you can very easily specify to keep the largest 10 groups (using K[0:10]). however this isn't quite what you want given that I suspect you want to filter based upon absolute group size. I have wanted to do this for a while but I couldn't think of a non-ambiguous way to add it to the list of options (given that I would have to store state from a previous operation). So in the meantime you will just have to filter the output of mincstats -histogram. -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From Andrew Janke Tue Jun 14 05:45:05 2005 From: Andrew Janke (Andrew Janke) Date: Tue Jun 14 04:45:05 2005 Subject: [MINC-users] icbm probabilistic atlas In-Reply-To: <42A43B49.1040305@feec.vutbr.cz> References: <42A43B49.1040305@feec.vutbr.cz> Message-ID: On 06/06/05, Daniel Schwarz wrote: > > I need to get > > icbm452_atlas_probability_white.hdr, > icbm452_atlas_probability_gray.hdr and > icbm452_atlas_probability_csf.hdr > > aligned with > > icbm_avg_152_t1_tal_lin.mnc > > I used ana2mnc to get the atlases into mnc format. Is there a simple way > how to crop/pad the images to get them aligned with icbm_avg_152....? Daniel, I am unfamiliar with this atlas, but: presuming the icbm452 images are indeed aligned in ICBM space (I suspect that they are) and presuming they orginate from SPM somewhere. Then you are best of to convert using spm2mnc or nii2mnc. ana2mnc ignores a few of things that SPM does with the ANALYZE header. nii2mnc is a new converter written by Bert Vincent for NifTi-1 data that is now included in minc 1.4. If this all fails then you are going to have to perform a registration between the models using mritotal/mritoself. Can you provide a copy of this model or a source to download it? -- Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Tue Jun 14 10:58:03 2005 From: minc-users@bic.mni.mcgill.ca (minc-users@bic.mni.mcgill.ca) Date: Tue Jun 14 09:58:03 2005 Subject: [MINC-users] Subsampling in mritoself In-Reply-To: <200506071601.j57G19YG9633197@shadow.bic.mni.mcgill.ca> Message-ID: Hello, Does anyone know for certain if subsampling is a default option in 'mritoself'?? There is a section on Preprocessing options in the mritoself man page, but it is unclear. The perl source seems to indicate that 'no subsampling' is the default, but again I am not 100% sure. The deactivation of subsampling in 'mritotal' is one way to improve accuracy (at the expense of memory). So I am investigating whether or not this would be a possibility for 'mritoself' as well. Thank you very much! Ernest Lo NeuroRX Research Montreal, Canada From minc-users@bic.mni.mcgill.ca Thu Jun 16 07:04:04 2005 From: minc-users@bic.mni.mcgill.ca (Oliver Winz) Date: Thu Jun 16 06:04:04 2005 Subject: [MINC-users] different image origin Message-ID: <42B14E67.1000604@fz-juelich.de> Hello all, i have a problem with the tool "ecattominc". There are no problems at the conversion step but when i want to realign using register i can't see the overlay image because of the huge different in the image origin. --> PET: > mincinfo SC1CN022M1_42b_b45_5-avgTime.mnc file: SC1CN022M1_42b_b45_5-avgTime.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 63 -2.425 -445.58 yspace 128 2.00331 -127.21 xspace 128 2.00331 -127.21 --> MRT: > mincinfo 7945_20050127_130638_2_mri.mnc file: 7945_20050127_130638_2_mri.mnc image: unsigned short 0 to 4095 image dimensions: xspace zspace yspace dimension name length step start -------------- ------ ---- ----- xspace 160 1 -85.8789 zspace 256 -1 120.659 yspace 256 -1 154.073 How can i reshape the both images to the same origin (e.g. 0 0 0)? Thank you very much! Oliver -- Oliver Winz, M.Sc. AG Molekulares Neuroimaging Institut für Medizin (IME) Forschungszentrum Jülich D-52425 Jülich Tel.: (02461) 61-6493 Internet: http://www.fz-juelich.de/ime/mni Ort: Gebäude 15.9, Raum 3010 From minc-users@bic.mni.mcgill.ca Thu Jun 16 08:23:04 2005 From: minc-users@bic.mni.mcgill.ca (Kuan H. Kho) Date: Thu Jun 16 07:23:04 2005 Subject: [MINC-users] different image origin In-Reply-To: <42B14E67.1000604@fz-juelich.de> References: <42B14E67.1000604@fz-juelich.de> Message-ID: Hi Oliver, I don't use ecattominc, but if you simply want to change the origin of both images you could use minc_modify_header and change the startposition of each space. Best, Kuan --- Kuan H. Kho, MD Depts. of Psychiatry & Neurosurgery, G03.124 University Medical Center Utrecht Heidelberglaan 100 P.O.Box 85500 3508 GA Utrecht The Netherlands P +31-30-2507969/2507953 F +31-30-2542100 E k.h.kho_'at'_azu.nl >Hello all, > >i have a problem with the tool "ecattominc". >There are no problems at the conversion step but when i want to >realign using register i can't see the overlay image because of the >huge different in the image origin. >--> PET: >> mincinfo SC1CN022M1_42b_b45_5-avgTime.mnc >file: SC1CN022M1_42b_b45_5-avgTime.mnc >image: signed__ short -32768 to 32767 >image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 63 -2.425 -445.58 > yspace 128 2.00331 -127.21 > xspace 128 2.00331 -127.21 > >--> MRT: >> mincinfo 7945_20050127_130638_2_mri.mnc >file: 7945_20050127_130638_2_mri.mnc >image: unsigned short 0 to 4095 >image dimensions: xspace zspace yspace > dimension name length step start > -------------- ------ ---- ----- > xspace 160 1 -85.8789 > zspace 256 -1 120.659 > yspace 256 -1 154.073 > >How can i reshape the both images to the same origin (e.g. 0 0 0)? > >Thank you very much! > >Oliver From minc-users@bic.mni.mcgill.ca Thu Jun 16 12:15:04 2005 From: minc-users@bic.mni.mcgill.ca (Sean McBride) Date: Thu Jun 16 11:15:04 2005 Subject: [MINC-users] MINC integration with VTK? Message-ID: <20050616151445.32316@smtp10.qc.aibn.com> Hello, Does anyone know of any MINC support for VTK? For example, VTK supports DICOM via the vtkDICOMImageReader class. Is there something similar for MINC? As far as I can tell, VTK proper does not support it. I found something called vtkMINCReader but it is in Python and I'm looking for a C/C++ solution. (Forgive me if this is a FAQ, but I could not find the answer elsewhere.) Thanks! -- ____________________________________________________________ Sean McBride, B. Eng sean@rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montréal, Québec, Canada From Peter Neelin Thu Jun 16 22:18:04 2005 From: Peter Neelin (Peter Neelin) Date: Thu Jun 16 21:18:04 2005 Subject: [MINC-users] different image origin In-Reply-To: <42B14E67.1000604@fz-juelich.de> References: <42B14E67.1000604@fz-juelich.de> Message-ID: On 6/16/05, Oliver Winz wrote: > i have a problem with the tool "ecattominc". > There are no problems at the conversion step but when i want to realign > using register i can't see the overlay image because of the huge > different in the image origin. Yes. If I recall correctly, the scanner puts the the origin around the middle of the body, so the head has a large offset. If you are aligning volumes with register, then they do not need to be overlaid in the third column. Simply select a number of equivalent points on the PET and MRI images (make sure that they do not all lie in or close to a plane). Once you have selected at least four, the MRI and PET should align approximately and the merged images become useful. For a good registration you should select about 15 points. If you are using a tracer that does not distribute well throughout the brain, then you may need to do the registration first with a transmission scan. Note that if you just translate the PET data so that both MRI and PET appear overlaid, they will not be properly aligned. So you should not worry about the large displacement of the PET - it just helps prevent you from reading to much into the unregistered merged images. Do a registration first (which does not require the merged images), and then you can think about looking at the merged PET and MRI. Peter -- Peter Neelin (peter.neelin@gmail.com) From minc-users@bic.mni.mcgill.ca Sun Jun 19 23:43:04 2005 From: minc-users@bic.mni.mcgill.ca (Fornito, Alexander) Date: Sun Jun 19 22:43:04 2005 Subject: [MINC-users] Thickness analysis Message-ID: <98A56869DA8D624C9869D012AE807A3D0225E4E8@whmail.ssg.org.au> Hi, I've been reading your papers on thickness analysis (MacDonald, et al, 2000, NeuroImage, 12; Lerch and Evans, 2005, NeuroImage 24) and I was seeking some clarification on the nature of the surface that is generated. The MacDonald paper states that the final surfaces created contain 81, 920 triangles. The Lerch and Evans paper states that the number of 'nodes' generated is 40, 962, which is about half that quoted by MaDonald et al. My questions: By 'nodes' do you refer to vertices? Is 40, 962 the number of vertices per hemisphere, whereas 81, 920 the total number for both hemispheres? If so, my next question is, wouldn't the number of vertices be greater than the number of triangles? Lastly, is the T link algorithm for calculating thickness available for download, and can it be applied to calculate thickness of surfaces using other methods (eg., freesurfer)? Thanks for your help, Alex From minc-users@bic.mni.mcgill.ca Mon Jun 20 00:35:03 2005 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Sun Jun 19 23:35:03 2005 Subject: [MINC-users] Thickness analysis In-Reply-To: <98A56869DA8D624C9869D012AE807A3D0225E4E8@whmail.ssg.org.au> References: <98A56869DA8D624C9869D012AE807A3D0225E4E8@whmail.ssg.org.au> Message-ID: <53325a2191867bc827dea631156fb4f6@bic.mni.mcgill.ca> On Jun 19, 2005, at 10:43 PM, Fornito, Alexander wrote: > > Hi, > I've been reading your papers on thickness analysis (MacDonald, et al, > 2000, NeuroImage, 12; Lerch and Evans, 2005, NeuroImage 24) and I was > seeking some clarification on the nature of the surface that is > generated. The MacDonald paper states that the final surfaces created > contain 81, 920 triangles. The Lerch and Evans paper states that the > number of 'nodes' generated is 40, 962, which is about half that > quoted by MaDonald et al. > My questions: > By 'nodes' do you refer to vertices? > Is 40, 962 the number of vertices per hemisphere, whereas 81, 920 the > total number for both hemispheres? > If so, my next question is, wouldn't the number of vertices be greater > than the number of triangles? Nope. Both papers are correct - remember that a single node/vertex belongs to multiple polygons. So we do in fact normally use surfaces consisting of 40,962 vertices and 81,920 polygons. > > Lastly, is the T link algorithm for calculating thickness available > for download, and can it be applied to calculate thickness of surfaces > using other methods (eg., freesurfer)? Not really - the link algorithm is the one (of the six) that is the most dependent on our method of extracting surfaces, and would thus not work with freesurfer. Cheers, Jason > > Thanks for your help, > Alex > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Mon Jun 20 02:35:04 2005 From: minc-users@bic.mni.mcgill.ca (Fornito, Alexander) Date: Mon Jun 20 01:35:04 2005 Subject: [MINC-users] Thickness analysis Message-ID: <98A56869DA8D624C9869D012AE807A3D0225E4EA@whmail.ssg.org.au> This is a multi-part message in MIME format. ------_=_NextPart_001_01C57559.D3D3E192 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 VGhhbmtzLCB0aGF0IGNsZWFyZWQgdGhhdCB1cC4gU28gaXMgdGhhdCA0MCwgOTYyIHZlcnRpY2Vz IHBlciBoZW1pc3BoZXJlLCBvciBhY3Jvc3MgdGhlIGVudGlyZSBicmFpbj8NCg0KCS0tLS0tT3Jp Z2luYWwgTWVzc2FnZS0tLS0tIA0KCUZyb206IEphc29uIExlcmNoIFttYWlsdG86amFzb25AYmlj Lm1uaS5tY2dpbGwuY2FdIA0KCVNlbnQ6IE1vbiA2LzIwLzIwMDUgMTozNCBQTSANCglUbzogbWlu Yy11c2Vyc0BiaWMubW5pLm1jZ2lsbC5jYSANCglDYzogDQoJU3ViamVjdDogUmU6IFtNSU5DLXVz 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<42B67AEC.2090604@feec.vutbr.cz> Thank you Andrew, I'll try it. I have downloaded the tissue probabilistic atlas (after short registration) here: http://www.loni.ucla.edu/Atlases/Atlas_Detail.jsp?atlas_id=7 Daniel Schwarz Andrew Janke napsal(a): >On 06/06/05, Daniel Schwarz wrote: > > >>I need to get >> >>icbm452_atlas_probability_white.hdr, >>icbm452_atlas_probability_gray.hdr and >>icbm452_atlas_probability_csf.hdr >> >>aligned with >> >>icbm_avg_152_t1_tal_lin.mnc >> >>I used ana2mnc to get the atlases into mnc format. Is there a simple way >>how to crop/pad the images to get them aligned with icbm_avg_152....? >> >> > >Daniel, > >I am unfamiliar with this atlas, but: > >presuming the icbm452 images are indeed aligned in ICBM space (I >suspect that they are) and presuming they orginate from SPM somewhere. > Then you are best of to convert using spm2mnc or nii2mnc. ana2mnc >ignores a few of things that SPM does with the ANALYZE header. > >nii2mnc is a new converter written by Bert Vincent for NifTi-1 data >that is now included in minc 1.4. > >If this all fails then you are going to have to perform a registration >between the models using mritotal/mritoself. > >Can you provide a copy of this model or a source to download it? > > > > > From minc-users@bic.mni.mcgill.ca Mon Jun 20 10:17:04 2005 From: minc-users@bic.mni.mcgill.ca (Steve M. Robbins) Date: Mon Jun 20 09:17:04 2005 Subject: [MINC-users] Thickness analysis In-Reply-To: <98A56869DA8D624C9869D012AE807A3D0225E4EA@whmail.ssg.org.au> References: <98A56869DA8D624C9869D012AE807A3D0225E4EA@whmail.ssg.org.au> Message-ID: <20050620131529.GA14704@nyongwa.montreal.qc.ca> On Mon, Jun 20, 2005 at 03:35:11PM +1000, Fornito, Alexander wrote: > Thanks, that cleared that up. So is that 40, 962 vertices per hemisphere, or across the entire brain? Entire brain. -Steve From minc-users@bic.mni.mcgill.ca Fri Jun 24 22:45:03 2005 From: minc-users@bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Fri Jun 24 21:45:03 2005 Subject: [MINC-users] mincedit core dumps! Message-ID: Hi, I am trying to change one attribute of a minc file and upon exitting the editor (xemacs) it fails to write the output and dumps the core. Here's the error! Segmentation fault (core dumped) Error generating new file. Redit the file (y/n)? (def=n): Thanks for any hints! Najma From minc-users@bic.mni.mcgill.ca Mon Jun 27 14:00:04 2005 From: minc-users@bic.mni.mcgill.ca (minc-users@bic.mni.mcgill.ca) Date: Mon Jun 27 13:00:04 2005 Subject: [MINC-users] =?iso-8859-1?Q?R=E9f=2E_=3A_[MINC-users]_mincedit_core_dumps=21?= Message-ID: Hi Najma, Were you able to solve your problem? The same thing appened to me a while ago, and the problem was that some elements of the header contained weird stuff. To be able to do some modifications to the headers I had to erase these weird parts first... Let me know if you still have the problem and I can try to find the commend that I was using for that. Good luck, Amélie _______________________________________________ Groupe d'Imagerie Cérébrale / Brain Imaging Group Douglas Hospital Research Centre tel: (514) 761-6131 ext. 3389 Web site: www.douglas.qc.ca/big "Najmeh Khalili M." cc : (ccc : Amélie Achim/Hopital Douglas/Reg06/SSSS) Envoyé par : Objet : [MINC-users] mincedit core dumps! minc-users-admin@bic.mn i.mcgill.ca 06/24/2005 09:44 PM Veuillez répondre à minc-users Hi, I am trying to change one attribute of a minc file and upon exitting the editor (xemacs) it fails to write the output and dumps the core. Here's the error! Segmentation fault (core dumped) Error generating new file. Redit the file (y/n)? (def=n): Thanks for any hints! Najma _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Mon Jun 27 14:22:03 2005 From: minc-users@bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Mon Jun 27 13:22:03 2005 Subject: [MINC-users] =?iso-8859-1?Q?R=E9f=2E_=3A_[MINC-users]_mincedit_core_dumps=21?= In-Reply-To: Message-ID: Hi Amelie, Yes I figured out how to solve the problem (thanks to Mike, Bert and Andrew). For the record, the short answer is to use minc_modify_header instead of mincedit, as it is a safer alternative to shortening the header file in order to make it mincedittable! Thanks a lot, Naj On Mon, 27 Jun 2005 achame@douglas.mcgill.ca wrote: > > Hi Najma, > > Were you able to solve your problem? The same thing appened to me a while > ago, and the problem was that some elements of the header contained weird > stuff. To be able to do some modifications to the headers I had to erase > these weird parts first... > > Let me know if you still have the problem and I can try to find the commend > that I was using for that. > > Good luck, > > Amélie > _______________________________________________ > Groupe d'Imagerie Cérébrale / Brain Imaging Group > Douglas Hospital Research Centre > tel: (514) 761-6131 ext. 3389 > Web site: www.douglas.qc.ca/big > > > > > > > "Najmeh Khalili M." > a> cc : (ccc : Amélie Achim/Hopital Douglas/Reg06/SSSS) > Envoyé par : Objet : [MINC-users] mincedit core dumps! > minc-users-admin@bic.mn > i.mcgill.ca > > > 06/24/2005 09:44 PM > Veuillez répondre à > minc-users > > > > > > > > Hi, > > I am trying to change one attribute of a minc file and upon exitting the > editor (xemacs) it fails to write the output and dumps the core. > > Here's the error! > Segmentation fault (core dumped) > Error generating new file. Redit the file (y/n)? (def=n): > > Thanks for any hints! > > Najma > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Tue Jun 28 20:31:04 2005 From: minc-users@bic.mni.mcgill.ca (Ian) Date: Tue Jun 28 19:31:04 2005 Subject: [MINC-users] Image Rotation Message-ID: <42C64DED@webmail.ualberta.ca> Hey MINC Users, While this ought to be a simple problem, I've found myself banging my head against my desk a few times this week already... Does anybody know of a tool or means by which to rotate MINC format images (as viewed in 3 planes in Display) in a single plane (i.e. Z-plane rotating 10 degrees clockwise) without spatial distortion and while maintaining the image in its native space (while transferring to standardized space should do the trick, I'd like to leave that as a last case option)? Another option would be to rotate the original DICOM images before I transform them into MINC format, but I've also struck out here as well. Thanks in advance! Ian Ian Harding, BSc.(Hon.) Research Assistant, Dr. P. Tibbo Bebensee Schizophrenia Research Unit Department of Psychiatry University of Alberta (780)492 6033 From Peter Neelin Tue Jun 28 21:04:04 2005 From: Peter Neelin (Peter Neelin) Date: Tue Jun 28 20:04:04 2005 Subject: [MINC-users] Image Rotation In-Reply-To: <42C64DED@webmail.ualberta.ca> References: <42C64DED@webmail.ualberta.ca> Message-ID: On 6/28/05, Ian wrote: > Does anybody know of a tool or means by which to rotate MINC format images (as > viewed in 3 planes in Display) in a single plane (i.e. Z-plane rotating 10 > degrees clockwise) without spatial distortion and while maintaining the image > in its native space (while transferring to standardized space should do the > trick, I'd like to leave that as a last case option)? You can use param2xfm to create a .xfm (transform) file, specifying the rotation and centre of rotation. You can then feed this as the transform into mincresample. param2xfm comes as part of the mni_autoreg package which can be downloaded from http://www.bic.mni.mcgill.ca/software/distribution/. Peter -- Peter Neelin (peter.neelin@gmail.com) From Andrew Janke Tue Jun 28 21:55:04 2005 From: Andrew Janke (Andrew Janke) Date: Tue Jun 28 20:55:04 2005 Subject: [MINC-users] Image Rotation In-Reply-To: <42C64DED@webmail.ualberta.ca> References: <42C64DED@webmail.ualberta.ca> Message-ID: ------=_Part_1616_1041822.1120006469277 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Ian,=20 This is something that we all know we should never have to do if the conversion goes right. But we don't live in a perfect world. I too have struck this same problem and wrote the attached script. This should do the trick: volrot -z_rotation 10 in.mnc out.mnc Andrew On 28/06/05, Ian wrote: > Hey MINC Users, >=20 > While this ought to be a simple problem, I've found myself banging my hea= d > against my desk a few times this week already... >=20 > Does anybody know of a tool or means by which to rotate MINC format image= s (as > viewed in 3 planes in Display) in a single plane (i.e. Z-plane rotating 1= 0 > degrees clockwise) without spatial distortion and while maintaining the i= mage > in its native space (while transferring to standardized space should do t= he > trick, I'd like to leave that as a last case option)? >=20 > Another option would be to rotate the original DICOM images before I tran= sform > them into MINC format, but I've also struck out here as well. >=20 > Thanks in advance! >=20 > Ian >=20 > Ian Harding, BSc.(Hon.) > Research Assistant, Dr. P. Tibbo > Bebensee Schizophrenia Research Unit > Department of Psychiatry > University of Alberta > (780)492 6033 >=20 > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >=20 --=20 Andrew Janke (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 ------=_Part_1616_1041822.1120006469277 Content-Type: application/octet-stream; name="volrot" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="volrot" IyEgL3Vzci9iaW4vZW52IHBlcmwKIwojIEFuZHJldyBKYW5rZSAtIHJvdG9yQGNtci51cS5lZHUu YXUKIyBDZW50ZXIgZm9yIE1hZ25ldGljIFJlc29uYW5jZQojIFRoZSBVbml2ZXJzaXR5IG9mIFF1 ZWVuc2xhbmQKIyBodHRwOi8vd3d3LmNtci51cS5lZHUuYXUvfnJvdG9yCiMKIyBDb3B5cmlnaHQg QW5kcmV3IEphbmtlLCBUaGUgVW5pdmVyc2l0eSBvZiBRdWVlbnNsYW5kLgojIFBlcm1pc3Npb24g dG8gdXNlLCBjb3B5LCBtb2RpZnksIGFuZCBkaXN0cmlidXRlIHRoaXMgc29mdHdhcmUgYW5kIGl0 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I tried to build Display 1.3.9 under Mandrake 9.2, gcc 3.3.1, ld 2.14.90 and got this error during "make": ...Graphics/libbicgl.a /usr/lib/libglut.so /usr/lib/libGLU.so /usr/lib/libGL.so -lXext -lpthread -lSM -lICE -lX11 -lXmu -lXi /usr/lib/libbicpl.a -L/home/jason/lib -L/usr/local/mni/lib -L/usr/local/qt3/lib -lppm /usr/local/lib/libvolume_io.a /usr/local/lib/libminc.a -lnetcdf -lm /usr/bin/ld: cannot find -lppm collect2: ld returned 1 exit status... I don't have anything like /home/jason/lib or /usr/local/qt3/lib... Anybody there to translate it to human language? Or tell me, what is '-lppm'? Thank You, Tomas Kasparek From minc-users@bic.mni.mcgill.ca Wed Jun 29 20:52:04 2005 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Wed Jun 29 19:52:04 2005 Subject: [MINC-users] Error - building Display 1.3.9 In-Reply-To: <200506241218.32007@centrum.cz> References: <200506241218.32007@centrum.cz> Message-ID: Greetings, where did you get the source from? And what options did you pass to configure? And ppm is an image library that is part of netpbm - an open source library for which Mandrake surely has packages. Cheers, Jason On Jun 24, 2005, at 6:18 AM, tomas kasparek wrote: > Hi there! > I tried to build Display 1.3.9 under Mandrake 9.2, gcc 3.3.1, ld > 2.14.90 and got this error during "make": > > ...Graphics/libbicgl.a /usr/lib/libglut.so /usr/lib/libGLU.so > /usr/lib/libGL.so -lXext -lpthread -lSM -lICE -lX11 -lXmu -lXi > /usr/lib/libbicpl.a -L/home/jason/lib -L/usr/local/mni/lib > -L/usr/local/qt3/lib -lppm /usr/local/lib/libvolume_io.a > /usr/local/lib/libminc.a -lnetcdf -lm > /usr/bin/ld: cannot find -lppm > collect2: ld returned 1 exit status... > > I don't have anything like /home/jason/lib or /usr/local/qt3/lib... > > Anybody there to translate it to human language? Or tell me, what is > '-lppm'? > > Thank You, > Tomas Kasparek > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users