From Michel.Audette at medizin.uni-leipzig.de Thu Jun 1 11:16:51 2006 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 1 Jun 2006 17:16:51 +0200 Subject: [MINC-users] dcm2mnc with Philips scan Message-ID: <160E3DD4FB702C4CB860C65186686E69AC3955@MRZS152229.medizin.uni-leipzig.de> Hi everyone, there seems to have been trouble with the BIC website, so my Google search for my problem met with silence when I tried to click the link to a prior thread. My current problem is trying to convert Philips dicoms files to minc. I see the following: maudette at icaw164201:~/research/source/hip> dcm2mnc becken-boehme-dicom/dicom/Std165/Ser632/* becken-boehme-mnc Checking file types... File becken-boehme-dicom/dicom/Std165/Ser632/Img15660 appears to be DICOM (CD/Export). Parsing 106 files |<--WARNING: Can't find Philips slice count | WARNING: Can't find Philips slice index WARNING: Can't find Philips private creator ID. WARNING: Can't find Philips slice count ... -> WARNING: Can't find Philips private creator ID. WARNING: calculated slice width (2.0000000000) disagrees with file's slice width (-2.0000000000) nccreate: filename "becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc": netCDF file exists && NC_NOCLOBBER (from micreate): Unable to create file 'becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc' Error creating MINC file becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc. Done processing files. Can anyone offer any guidance? Best regards, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Philipp-Rosenthal-Strasse 55 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From Michel.Audette at medizin.uni-leipzig.de Thu Jun 1 11:26:18 2006 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 1 Jun 2006 17:26:18 +0200 Subject: [MINC-users] dcm2mnc with Philips scan Message-ID: <160E3DD4FB702C4CB860C65186686E69AC3958@MRZS152229.medizin.uni-leipzig.de> Hello again, please disregard the previous message. Looks like the process complains a lot, but somehow produces a minc file. I just noticed that the 2nd time I ran it, it complained of a lack of clobber option, which told me that there was a minc file after all... Best regards, Michel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel Sent: Thu 6/1/2006 5:16 PM To: MINC-users at bic.mni.mcgill.ca Subject: [MINC-users] dcm2mnc with Philips scan Hi everyone, there seems to have been trouble with the BIC website, so my Google search for my problem met with silence when I tried to click the link to a prior thread. My current problem is trying to convert Philips dicoms files to minc. I see the following: maudette at icaw164201:~/research/source/hip> dcm2mnc becken-boehme-dicom/dicom/Std165/Ser632/* becken-boehme-mnc Checking file types... File becken-boehme-dicom/dicom/Std165/Ser632/Img15660 appears to be DICOM (CD/Export). Parsing 106 files |<--WARNING: Can't find Philips slice count | WARNING: Can't find Philips slice index WARNING: Can't find Philips private creator ID. WARNING: Can't find Philips slice count ... -> WARNING: Can't find Philips private creator ID. WARNING: calculated slice width (2.0000000000) disagrees with file's slice width (-2.0000000000) nccreate: filename "becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc": netCDF file exists && NC_NOCLOBBER (from micreate): Unable to create file 'becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc' Error creating MINC file becken-boehme-mnc/becken_boehme_igor_studie_20051122_094405/becken_boehme_igor_studie_20051122_094405_7440.mnc. Done processing files. Can anyone offer any guidance? Best regards, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Philipp-Rosenthal-Strasse 55 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From schwarz at cba.muni.cz Thu Jun 1 11:40:13 2006 From: schwarz at cba.muni.cz (Daniel Schwarz) Date: Thu, 1 Jun 2006 17:40:13 +0200 Subject: [MINC-users] Mritotal - how many parameters? Message-ID: <200606011540.k51FeKLu019617@tirith.ics.muni.cz> Dear minc-users, I have a question which might be too elemental. However I will be happy for any comments: I am going to ask my colleagues-physicians to segment manually several features from a set of brain images. I would like them to do it in the MNI space with Display. Before that, I will do correction for INU artifact with N3 and transformation into the MNI space with the use of ICBM152 template and Mritotal. How many parameters of the transform should I use? If I perform 7-parameter transform (the same scaling factor for x,y,z), I will not have to worry about changing the proportions of the images and computations of the featrue volumes will be very easy. Are there any advantages when using 9-parameter transform? Is it better to use 9-parameter transform and then recompute the feature volumes according to the various scaling factors? Thank you in advance Daniel Schwarz From a.janke at gmail.com Fri Jun 2 00:01:00 2006 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 2 Jun 2006 00:01:00 -0400 Subject: [MINC-users] Mritotal - how many parameters? In-Reply-To: <200606011540.k51FeKLu019617@tirith.ics.muni.cz> References: <200606011540.k51FeKLu019617@tirith.ics.muni.cz> Message-ID: Hi Daniel, A 9 parameter transform is the mritotal default, and a nine parameter fit will generally provide a good linear fit. A 6 or 7 parameter version will often not cut the mustard. As for calculating sizes, this will be no problem, either back-transform the traced structures to the native images (invert the xfms when using mincresample) or simply scale the volumes you obtain in MNI-space by the inverse of the three scale parameters that xfm2param outputs for scale. a On 6/1/06, Daniel Schwarz wrote: > Dear minc-users, > > I have a question which might be too elemental. However I will be happy for > any comments: > > I am going to ask my colleagues-physicians to segment manually several > features from a set of brain images. I would like them to do it in the MNI > space with Display. Before that, I will do correction for INU artifact with > N3 and transformation into the MNI space with the use of ICBM152 template > and Mritotal. How many parameters of the transform should I use? If I > perform 7-parameter transform (the same scaling factor for x,y,z), I will > not have to worry about changing the proportions of the images and > computations of the featrue volumes will be very easy. Are there any > advantages when using 9-parameter transform? Is it better to use 9-parameter > transform and then recompute the feature volumes according to the various > scaling factors? > > Thank you in advance > > Daniel Schwarz > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Sun Jun 4 03:08:06 2006 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 4 Jun 2006 03:08:06 -0400 Subject: [MINC-users] Problem Buliding MNI Models In-Reply-To: <9c80f12d0605180839q20dd972fve6c16461cb392e96@mail.gmail.com> References: <9c80f12d0605111036g56b5558i6b3b239bade6a326@mail.gmail.com> <9c80f12d0605180839q20dd972fve6c16461cb392e96@mail.gmail.com> Message-ID: Hi again Gil, Sorry about the late reply with this, but I just realised that you were using MINC 2.0.10. There are a few "issues" in that release with respect to compression. I woud still suggest that if you are using MINC in a runtime environment to stick with minc 1.x (1.4 at this stage). MINC 2.0 is progressing slowly towards stability but there are still a few lingering issues. a On 5/18/06, Gil Citro wrote: > Actually no, I compiled MINC 2.0.10 myself from the source. I also > compiled NetCDF 3.6.1 from source, because NetCDF 3.5.0 would not > compile on my system. Any suggestions for how to make NetCDF find > gzip? Thanks again. > > Gil > > On 5/17/06, Andrew Janke wrote: > > > > > Looks like netcdf cannot find the gzip runtime libraries (to > > uncompress the input file). If this minc install came from a binary > > package this would be suprising as they are supposed to be compiled > > static. > > > > On 5/11/06, Gil Citro wrote: > > > I'm having trouble building and installing > > > > > > mni-models_average305-lin-1.0 > > > mni-models_colin27-lin-1.0 > > > mni-models_icbm152-lin-1.0 > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Wed Jun 7 03:41:03 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 7 Jun 2006 03:41:03 -0400 Subject: [MINC-users] OSX Intel and MINC Message-ID: Hi all, I have had a first go at some packages for OSX Tiger Intel machines. http://packages.bic.mni.mcgill.ca/osx-10.4-intel/ I'd be very interested to hear usage reports, there were some strange issues with erroring on some files in this build that I haven't managed to track down yet so I am wondering if it just a software quirk on the machine I used to build these. Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From fadeneric at mail.nih.gov Tue Jun 6 08:57:22 2006 From: fadeneric at mail.nih.gov (Faden, Eric (NIH/NIMH) [F]) Date: Tue, 6 Jun 2006 08:57:22 -0400 Subject: [MINC-users] minctracc source_mask option with a transform? Message-ID: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FC86@NIHCESMLBX3.nih.gov> If you input a source_mask with a transform when is it applied? i.e. I am running something like minctracc -source_mask brain.mnc -transform foo.xfm .... .... The source image is still in the same space as the mask is, but when will the mask get applied to the image? Before or after the transform? if after does the mask get transformed also? -Eric From a.janke at gmail.com Wed Jun 7 08:15:00 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 7 Jun 2006 08:15:00 -0400 Subject: [MINC-users] minctracc source_mask option with a transform? In-Reply-To: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FC86@NIHCESMLBX3.nih.gov> References: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FC86@NIHCESMLBX3.nih.gov> Message-ID: Hi Eric, Both source and model masks are never applied directly as such, but used to determine which voxels are included when calculating the objective function. In your case the source mask is used in the space before the current transformation. a On 6/6/06, Faden, Eric (NIH/NIMH) [F] wrote: > If you input a source_mask with a transform when is it applied? i.e. I am running something like > > minctracc -source_mask brain.mnc -transform foo.xfm .... .... > > The source image is still in the same space as the mask is, but when will the mask get applied to the image? Before or after the transform? if after does the mask get transformed also? > > -Eric > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From petra.schweinhardt at mail.mcgill.ca Wed Jun 7 13:09:51 2006 From: petra.schweinhardt at mail.mcgill.ca (petra.schweinhardt@mail.mcgill.ca) Date: Wed, 07 Jun 2006 13:09:51 -0400 Subject: [MINC-users] minc to ANALYZE / nifti Message-ID: <20060607130951.n5hreb6934socgoc@webmail.mcgill.ca> Can anybody point me to a script converting minc format to either ANALYZE or nifti? Cheers, petra From sylvain at bic.mni.mcgill.ca Thu Jun 8 09:21:25 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Thu, 8 Jun 2006 09:21:25 -0400 Subject: [MINC-users] minc to ANALYZE / nifti In-Reply-To: <20060607130951.n5hreb6934socgoc@webmail.mcgill.ca> Message-ID: Hi, Use mnc2nii and nii2mnc. On Wed, 7 Jun 2006 petra.schweinhardt at mail.mcgill.ca wrote: > Can anybody point me to a script converting minc format to either > ANALYZE or nifti? > > Cheers, > > petra > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From tpb1 at ualberta.ca Fri Jun 9 17:09:35 2006 From: tpb1 at ualberta.ca (tpb1@ualberta.ca) Date: Fri, 09 Jun 2006 15:09:35 -0600 Subject: [MINC-users] Re-orienting slice angle Message-ID: <20060609150935.byct7oqqokwwc4gc@webmail.ualberta.ca> I just read Teipel/Pruessner/et al's J. Neurol 2005 paper on volumetry in AD, and I can't figure out how he re-oriented his slices using Display. In his methods section he says "[Display] allows simultaneous visualization and segmentation of volumes in coronal, saggital and horizontal orientations. Additionally, the user can define angles for viewing of images that are presented in a fourth window. This allows the user to view coronal slices simultaneously along the AC-PC line and the line perpendicular to the long axis of the HC." I have been using Display for a while, and I've never seen this "fourth window" where the user can define different angles. I use the Linux version of Display; do I need additional packages in order to get this fourth window? (I've used the 3D rendering window, but I haven't been able to use it to define different viewing angles in the tracing window). Thanks, Thomas From kanadbasu2005 at yahoo.co.in Mon Jun 12 01:26:24 2006 From: kanadbasu2005 at yahoo.co.in (Kanad Basu) Date: Mon, 12 Jun 2006 06:26:24 +0100 (BST) Subject: [MINC-users] help please Message-ID: <20060612052624.92815.qmail@web7905.mail.in.yahoo.com> Sir, I have 2-d brain image slices from MRIcro. I want to construct a 3d image of the brain with them. I have Matlab 6.1 installed in my windows xp machine. I would be grateful if you'll canhelp me out with it. Thanking you, Kanad Basu. Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/ From petra.schweinhardt at mail.mcgill.ca Fri Jun 16 11:39:47 2006 From: petra.schweinhardt at mail.mcgill.ca (petra.schweinhardt@mail.mcgill.ca) Date: Fri, 16 Jun 2006 11:39:47 -0400 Subject: [MINC-users] mnc2nii In-Reply-To: References: Message-ID: <20060616113947.n15sklotwcw4ksk8@webmail.mcgill.ca> Ok, for some reason it seems that my email did not get (fully) sent. So once more: using mnc2nii, the intensity information of the image doesn't seem to get transformed correctly, irrespective which datatype is specified. How does one preserve the intensity? Cheers, petra > > > > > Today's Topics: > > > > 1. minc to ANALYZE / nifti (petra.schweinhardt at mail.mcgill.ca) > > 2. Re: minc to ANALYZE / nifti (Sylvain MILOT) > > > > > > > > > Message: 2 > > Date: Thu, 8 Jun 2006 09:21:25 -0400 > > From: Sylvain MILOT > > Subject: Re: [MINC-users] minc to ANALYZE / nifti > > To: MINC users mailing list > > Message-ID: > > > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > > > Hi, > > > > Use mnc2nii and nii2mnc. > > > > On Wed, 7 Jun 2006 petra.schweinhardt at mail.mcgill.ca wrote: > > > >> Can anybody point me to a script converting minc format to either > >> ANALYZE or nifti? > >> > >> Cheers, > >> > >> petra > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > > From bert at bic.mni.mcgill.ca Fri Jun 16 12:14:26 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 16 Jun 2006 12:14:26 -0400 Subject: [MINC-users] mnc2nii In-Reply-To: <20060616113947.n15sklotwcw4ksk8@webmail.mcgill.ca> Message-ID: Hi Petra, Can you be a bit more specific? What tool are you using to validate the NII file? In most of my testing I can successfully convert a MINC file to NII: mnc2nii -short in.mnc out.nii Then back to MINC: nii2mnc -short out.nii out.mnc and see that the statistical properties of the resulting image are unchanged (within the limits of the voxel precision). It is possible, of course, that I've gotten something wrong with respect to the NII format such that some tools are not reading the intensities as I intended. -bert On Fri, 16 Jun 2006 petra.schweinhardt at mail.mcgill.ca wrote: > Ok, for some reason it seems that my email did not get (fully) sent. So > once more: using mnc2nii, the intensity information of the image > doesn't seem to get transformed correctly, irrespective which datatype > is specified. How does one preserve the intensity? > > Cheers, > petra > > > > > > > > > > Today's Topics: > > > > > > 1. minc to ANALYZE / nifti (petra.schweinhardt at mail.mcgill.ca) > > > 2. Re: minc to ANALYZE / nifti (Sylvain MILOT) > > > > > > > > > > > > > Message: 2 > > > Date: Thu, 8 Jun 2006 09:21:25 -0400 > > > From: Sylvain MILOT > > > Subject: Re: [MINC-users] minc to ANALYZE / nifti > > > To: MINC users mailing list > > > Message-ID: > > > > > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > > > > > > Hi, > > > > > > Use mnc2nii and nii2mnc. > > > > > > On Wed, 7 Jun 2006 petra.schweinhardt at mail.mcgill.ca wrote: > > > > > >> Can anybody point me to a script converting minc format to either > > >> ANALYZE or nifti? > > >> > > >> Cheers, > > >> > > >> petra > > >> _______________________________________________ > > >> MINC-users at bic.mni.mcgill.ca > > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > >> > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From petra.schweinhardt at mail.mcgill.ca Mon Jun 19 14:59:35 2006 From: petra.schweinhardt at mail.mcgill.ca (petra.schweinhardt@mail.mcgill.ca) Date: Mon, 19 Jun 2006 14:59:35 -0400 Subject: [MINC-users] MINC-users Digest, Vol 11, Issue 9 In-Reply-To: References: Message-ID: <20060619145935.9n3gb9ilck48gkgk@webmail.mcgill.ca> Dear Bert, you are right, mnc2nii -short does the trick - I must have overlooked it before - sorry for this! Thanks, petra BTW: I check the files using avwstats. > Today's Topics: > > 1. Re: mnc2nii (Robert VINCENT) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 16 Jun 2006 12:14:26 -0400 > From: Robert VINCENT > Subject: Re: [MINC-users] mnc2nii > To: MINC users mailing list > Message-ID: > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Petra, > > Can you be a bit more specific? What tool are you using to validate the > NII file? > > In most of my testing I can successfully convert a MINC file to NII: > > mnc2nii -short in.mnc out.nii > > Then back to MINC: > > nii2mnc -short out.nii out.mnc > > and see that the statistical properties of the resulting image are > unchanged (within the limits of the voxel precision). It is possible, of > course, that I've gotten something wrong with respect to the NII format > such that some tools are not reading the intensities as I intended. > > -bert > > From ed.gronenschild at mi.unimaas.nl Thu Jun 22 09:40:44 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Thu, 22 Jun 2006 15:40:44 +0200 Subject: [MINC-users] Problems with linking libraries using Xcode Message-ID: <483F9229-DB11-4E07-9995-1C5D1106D198@mi.unimaas.nl> Hi, I'm building my own image processing application with Apple's Xcode 2.3 on a Mac with OS X 10.4.6. I'm linking against the libraries libbicpl.a, libminc.a, libnetcdf.a and libvolume_io.a, all from the minc-1.4 package for OSX 10.3. In Xcode I've set OS X 10.3.9 as cross-develop target SDK. The application runs fine in debug mode, but as soon as I switch to release mode (the application will be used by others) I get linking errors, the same for each of the minc libraries. For instance for libbicpl.a: "table of contents for archive: /...../libbicpl.a is out of date; rerun ranlib(1) (can't load from it)" and finally "/usr/bin/gcc-4.0 failed with exit code 1" Does anybody know what to do? Regards, Ed From jason at bic.mni.mcgill.ca Thu Jun 22 11:31:51 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 22 Jun 2006 11:31:51 -0400 Subject: [MINC-users] Problems with linking libraries using Xcode In-Reply-To: <483F9229-DB11-4E07-9995-1C5D1106D198@mi.unimaas.nl> References: <483F9229-DB11-4E07-9995-1C5D1106D198@mi.unimaas.nl> Message-ID: Have you tried rerunning ranlib on each of the .a files? (I've never used Xcode for minc stuff, but that appears to be what the error message suggests) Jason On 22-Jun-06, at 9:40 AM, Ed Gronenschild wrote: > Hi, > > I'm building my own image processing application with Apple's > Xcode 2.3 on a Mac with OS X 10.4.6. I'm linking against the libraries > libbicpl.a, libminc.a, libnetcdf.a and libvolume_io.a, all from the > minc-1.4 package for OSX 10.3. In Xcode I've set OS X 10.3.9 > as cross-develop target SDK. > The application runs fine in debug mode, but as soon as I switch > to release mode (the application will be used by others) I get > linking errors, the same for each of the minc libraries. For instance > for libbicpl.a: > > "table of contents for archive: /...../libbicpl.a is out of date; > rerun ranlib(1) > (can't load from it)" > > and finally > > "/usr/bin/gcc-4.0 failed with exit code 1" > > Does anybody know what to do? > > Regards, > > Ed > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From fadeneric at mail.nih.gov Thu Jun 22 16:30:31 2006 From: fadeneric at mail.nih.gov (Faden, Eric (NIH/NIMH) [F]) Date: Thu, 22 Jun 2006 16:30:31 -0400 Subject: [MINC-users] Automated Trimming Message-ID: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FCD7@NIHCESMLBX3.nih.gov> I am working on a script to generate brainmasks for a set of macaque scans we have, but since the scans have different amounts of neck in them my script is having some issues. I was wondering if there is a quick way using minccalc or something to draw a circular mask and cut everything outside of it? or if anyone has a trick for creating a very gross mask I could use to remove the neck? -Eric From spmlxf at yahoo.com Fri Jun 23 10:47:07 2006 From: spmlxf at yahoo.com (xingfeng lee) Date: Fri, 23 Jun 2006 07:47:07 -0700 (PDT) Subject: [MINC-users] fmr_preprocess Message-ID: <20060623144707.84302.qmail@web50115.mail.yahoo.com> Dear MINC experts: Could you help? I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc bash: /bin/fmr_preprocess: Permission denied Could you give some advises? If it need install, where should i download it, and how to install it? Thank you very much and have a nice weekend. all the best, Li --------------------------------- Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. From a.janke at gmail.com Sun Jun 25 17:33:31 2006 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 25 Jun 2006 23:33:31 +0200 Subject: [MINC-users] fmr_preprocess In-Reply-To: <20060623144707.84302.qmail@web50115.mail.yahoo.com> References: <20060623144707.84302.qmail@web50115.mail.yahoo.com> Message-ID: Hi Li, I suspect you will have to set the execute bit for the file. ie: $ chmod +x fmr_preprocess a On 6/23/06, xingfeng lee wrote: > Dear MINC experts: > > Could you help? > I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc > bash: /bin/fmr_preprocess: Permission denied > Could you give some advises? > > If it need install, where should i download it, and how to install it? > > Thank you very much and have a nice weekend. > all the best, > Li > > > --------------------------------- > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Sun Jun 25 19:50:50 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 01:50:50 +0200 Subject: [MINC-users] Automated Trimming In-Reply-To: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FCD7@NIHCESMLBX3.nih.gov> References: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FCD7@NIHCESMLBX3.nih.gov> Message-ID: If you happen to know the centre of the head (via a COG/COM calculation) I guess you could use 'make_phantom' that is part of mni-autoreg. >From there it would be a simple mask calculation using either mincmath or minccalc. a On 6/22/06, Faden, Eric (NIH/NIMH) [F] wrote: > I am working on a script to generate brainmasks for a set of macaque scans we have, but since the scans have different amounts of neck in them my script is having some issues. I was wondering if there is a quick way using minccalc or something to draw a circular mask and cut everything outside of it? or if anyone has a trick for creating a very gross mask I could use to remove the neck? > > -Eric > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From spmlxf at yahoo.com Sun Jun 25 21:09:53 2006 From: spmlxf at yahoo.com (xingfeng lee) Date: Sun, 25 Jun 2006 18:09:53 -0700 (PDT) Subject: [MINC-users] fmr_preprocess In-Reply-To: Message-ID: <20060626010953.25500.qmail@web50102.mail.yahoo.com> Hi Andrew, Thank you very much, the new problem is: [root at ambrose Test]# fmr_preprocess Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi /usr/lib/perl5/5.8.6 .) at /bin/fmr_preprocess line 40. BEGIN failed--compilation aborted at /bin/fmr_preprocess line 40. All the best, Li Andrew Janke wrote: Hi Li, I suspect you will have to set the execute bit for the file. ie: $ chmod +x fmr_preprocess a On 6/23/06, xingfeng lee wrote: > Dear MINC experts: > > Could you help? > I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc > bash: /bin/fmr_preprocess: Permission denied > Could you give some advises? > > If it need install, where should i download it, and how to install it? > > Thank you very much and have a nice weekend. > all the best, > Li > > > --------------------------------- > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users Andrew Janke wrote: Hi Li, I suspect you will have to set the execute bit for the file. ie: $ chmod +x fmr_preprocess a On 6/23/06, xingfeng lee wrote: > Dear MINC experts: > > Could you help? > I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc > bash: /bin/fmr_preprocess: Permission denied > Could you give some advises? > > If it need install, where should i download it, and how to install it? > > Thank you very much and have a nice weekend. > all the best, > Li > > > --------------------------------- > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users --------------------------------- Sneak preview the all-new Yahoo.com. It's not radically different. Just radically better. From a.janke at gmail.com Sun Jun 25 22:21:10 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 04:21:10 +0200 Subject: [MINC-users] MINC OSX Monolithic packages Message-ID: Hi, In response to some requests for a monolithic MINC installer for OSX, I have created a test mpkg for PPC OSX Tiger based upon minc 1.4.x http://packages.bic.mni.mcgill.ca/osx-10.4/minc-1.4-20060620.mpkg.tar.gz For those with such beasts you are welcome to try this, as always I will be interested to know how it works for you. I suspect I may have missed a few things but if this works then we can slowly add more and more smaller packages to it. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Sun Jun 25 22:47:04 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 04:47:04 +0200 Subject: [MINC-users] Re-orienting slice angle In-Reply-To: <20060609150935.byct7oqqokwwc4gc@webmail.ualberta.ca> References: <20060609150935.byct7oqqokwwc4gc@webmail.ualberta.ca> Message-ID: Hi again Thomas, Display is no the best regarding documentation so here goes. First place the cross hairs in the 3D view on a place that you want in your oblique view. then.. 1. Press 's' for Slive View 2. Press 'r' to make sure things are visible 3. Press 'e' (Pick slice Angle). Then click somewhere else in the image that you want in your oblique view. after a few hacks at this (#3 only) you will get the hang of it. a On 6/9/06, tpb1 at ualberta.ca wrote: > I just read Teipel/Pruessner/et al's J. Neurol 2005 paper on volumetry > in AD, and I can't figure out how he re-oriented his slices using > Display. In his methods section he says "[Display] allows simultaneous > visualization and segmentation of volumes in coronal, saggital and > horizontal orientations. Additionally, the user can define angles for > viewing of images that are presented in a fourth window. This allows > the user to view coronal slices simultaneously along the AC-PC line and > the line perpendicular to the long axis of the HC." I have been using > Display for a while, and I've never seen this "fourth window" where the > user can define different angles. I use the Linux version of Display; > do I need additional packages in order to get this fourth window? > (I've used the 3D rendering window, but I haven't been able to use it > to define different viewing angles in the tracing window). > > Thanks, > Thomas > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Sun Jun 25 23:22:08 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 05:22:08 +0200 Subject: [MINC-users] Display problems using Display In-Reply-To: <1149015029.447c93f52ead3@www.courrier.umontreal.ca> References: <1149015029.447c93f52ead3@www.courrier.umontreal.ca> Message-ID: Hi Jean, This sounds to me like a GLUT problem. Try installing a later release of GLUT on your redhat(ish) machine and see how things work. a On 5/30/06, Jean-Philippe Mailhot wrote: > > > Hi all, > > I installed Display on Linux Fedora Core 5 but I have some difficulties when I > try to increase the size of the slice window where there are the 3 orthogonal > views of slices. In fact, the size of the window increase but not the 3 slices > in that window ! > > Can anybody help me? > thanks, > > > > Jean-Philippe Mailhot > BRAMS (Brain,Music and Sound) > LNMCA,Universit? de Montr?al > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From sorench at gmail.com Mon Jun 26 01:08:43 2006 From: sorench at gmail.com (Soren Christensen) Date: Mon, 26 Jun 2006 15:08:43 +1000 Subject: [MINC-users] compilation on fedora Message-ID: Dear MINc users, I was wondering if anybody had experience with compiling the MINC tools under Fedora 5. I previously posted a problem with the CLK_TCK macro that could not be found by the linker. I found a solution to that on: http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_19.html In case other people experience the same problem. However, now I am stuck with compilation of Display (MINC, NETCDF and BICPL seem to work). The error below arises when running make (for Display). Could anyone see where the problem is - I guess it has something to do with GLUT but i am not excatly sure how to narrow it down further. Thanks and best regards Soren ..... gcc -g -O2 -o Display dummy.o main/main.o main/display.o main/event_loop.o main/graphics.o main/three_d.o main/transforms.o atlas/atlas.o input_files/input_files.o input_files/volume_file.o callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o callbacks/surf_segmenting.o callbacks/surface_curves.o callbacks/surface_extract.o callbacks/view_ops.o callbacks/volume_ops.o callbacks/volume_transform_ops.o current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o edit_surface/segment.o images/images.o markers/markers.o surface_extraction/boundary_extraction.o surface_extraction/data_structs.o surface_extraction/init_surface.o surface_extraction/extract.o surface_extraction/surface.o surface_extraction/surface_events.o voxel_scan/scan_objects.o events/change_markers.o events/clip_plane.o events/film_loop.o events/magnify.o events/mouse.o events/mouse_trans.o events/pick_object.o events/pick_view.o events/rotate_slice.o events/spaceball.o events/virt_sb.o events/window_man.o events/utilities.o immediate_mode/draw_immed.o intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o menu/input_menu.o menu/selected.o menu/text.o cursor_contours/contours.o segmenting/cut_neighbours.o segmenting/painting.o segmenting/segmenting.o segmenting/segment_polygons.o slice_window/colour_bar.o slice_window/colour_coding.o slice_window/crop.o slice_window/draw_slice.o slice_window/histogram.o slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o slice_window/slice_3d.o slice_window/slice_events.o slice_window/undo.o slice_window/view.o surface_curves/closest_line.o surface_curves/events.o surface_curves/edge_distance.o tubes/convert_lines.o structures/action_table.o structures/fit_view.o structures/lights.o structures/render.o structures/view.o structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl -lvolume_io -lminc -lnetcdf -lm slice_window/crop.o: In function `crop_and_load_volume': /root/download/Display-1.4.1/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp' Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: undefined reference to `glutBitmap8By13' Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: undefined reference to `glutIdleFunc' Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: undefined reference to `glutGet' Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:913: undefined reference to `glutGet' Graphics/libbicgl.a(glut_windows.o): In function `WS_get_screen_size':....... From a.janke at gmail.com Mon Jun 26 01:47:18 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 01:47:18 -0400 Subject: [MINC-users] fmr_preprocess In-Reply-To: <20060626010953.25500.qmail@web50102.mail.yahoo.com> References: <20060626010953.25500.qmail@web50102.mail.yahoo.com> Message-ID: Li, You will have to download and install Getopt::Tabular from www.cpan.org a On 6/25/06, xingfeng lee wrote: > Hi Andrew, > Thank you very much, the new problem is: > > [root at ambrose Test]# fmr_preprocess > Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi /usr/lib/perl5/5.8.6 .) at /bin/fmr_preprocess line 40. > BEGIN failed--compilation aborted at /bin/fmr_preprocess line 40. > > > All the best, > Li > > > > Andrew Janke wrote: Hi Li, > > I suspect you will have to set the execute bit for the file. ie: > > $ chmod +x fmr_preprocess > > > a > > On 6/23/06, xingfeng lee wrote: > > Dear MINC experts: > > > > Could you help? > > I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc > > bash: /bin/fmr_preprocess: Permission denied > > Could you give some advises? > > > > If it need install, where should i download it, and how to install it? > > > > Thank you very much and have a nice weekend. > > all the best, > > Li > > > > > > --------------------------------- > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > Andrew Janke wrote: Hi Li, > > I suspect you will have to set the execute bit for the file. ie: > > $ chmod +x fmr_preprocess > > > a > > On 6/23/06, xingfeng lee wrote: > > Dear MINC experts: > > > > Could you help? > > I came cross a problem when i did fmri data realignment. I copied the function : fmr_preprocess from my computer at McGill to the bin directory of my computer in China, but it did not work. I remember that this function does not need to install, just copy this function to the bin directory. The error message was: > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess qiu_yan_li_20060611_130900_3_mri.mnc > > bash: /bin/fmr_preprocess: Permission denied > > Could you give some advises? > > > > If it need install, where should i download it, and how to install it? > > > > Thank you very much and have a nice weekend. > > all the best, > > Li > > > > > > --------------------------------- > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with Yahoo! Messenger with Voice. > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > --------------------------------- > Sneak preview the all-new Yahoo.com. It's not radically different. Just radically better. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Jun 26 01:49:01 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 01:49:01 -0400 Subject: [MINC-users] compilation on fedora In-Reply-To: References: Message-ID: Hi Soren, Amusingly enough I came across this same problem with a machine or two in Stockholm just last week... In my case the solution was to get and compile a version of GLUT as opposed to using the system version. I canna remember the version that I used though.. :( Suffice to say, no RPM that I could find (via rpmfind/etc) seemed to work. a On 6/26/06, Soren Christensen wrote: > Dear MINc users, > I was wondering if anybody had experience with compiling the MINC > tools under Fedora 5. > I previously posted a problem with the CLK_TCK macro that could not be > found by the linker. I found a solution to that on: > http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_19.html > In case other people experience the same problem. > However, now I am stuck with compilation of Display (MINC, NETCDF and > BICPL seem to work). > The error below arises when running make (for Display). > Could anyone see where the problem is - I guess it has something to do > with GLUT but i am not excatly sure how to narrow it down further. > > Thanks and best regards > Soren > > ..... > gcc -g -O2 -o Display dummy.o main/main.o main/display.o > main/event_loop.o main/graphics.o main/three_d.o main/transforms.o > atlas/atlas.o input_files/input_files.o input_files/volume_file.o > callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o > callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o > callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o > callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o > callbacks/surf_segmenting.o callbacks/surface_curves.o > callbacks/surface_extract.o callbacks/view_ops.o > callbacks/volume_ops.o callbacks/volume_transform_ops.o > current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o > edit_surface/segment.o images/images.o markers/markers.o > surface_extraction/boundary_extraction.o > surface_extraction/data_structs.o surface_extraction/init_surface.o > surface_extraction/extract.o surface_extraction/surface.o > surface_extraction/surface_events.o voxel_scan/scan_objects.o > events/change_markers.o events/clip_plane.o events/film_loop.o > events/magnify.o events/mouse.o events/mouse_trans.o > events/pick_object.o events/pick_view.o events/rotate_slice.o > events/spaceball.o events/virt_sb.o events/window_man.o > events/utilities.o immediate_mode/draw_immed.o > intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o > cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o > menu/input_menu.o menu/selected.o menu/text.o > cursor_contours/contours.o segmenting/cut_neighbours.o > segmenting/painting.o segmenting/segmenting.o > segmenting/segment_polygons.o slice_window/colour_bar.o > slice_window/colour_coding.o slice_window/crop.o > slice_window/draw_slice.o slice_window/histogram.o > slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o > slice_window/slice_3d.o slice_window/slice_events.o > slice_window/undo.o slice_window/view.o surface_curves/closest_line.o > surface_curves/events.o surface_curves/edge_distance.o > tubes/convert_lines.o structures/action_table.o structures/fit_view.o > structures/lights.o structures/render.o structures/view.o > structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl > -lvolume_io -lminc -lnetcdf -lm > slice_window/crop.o: In function `crop_and_load_volume': > /root/download/Display-1.4.1/slice_window/crop.c:165: warning: the use > of `tmpnam' is dangerous, better use `mkstemp' > Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: > undefined reference to `glutBitmap8By13' > Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: > undefined reference to `glutIdleFunc' > Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: > undefined reference to `glutGet' > Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:913: > undefined reference to `glutGet' > Graphics/libbicgl.a(glut_windows.o): In function `WS_get_screen_size':....... > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From forrest.bao at gmail.com Mon Jun 26 03:09:08 2006 From: forrest.bao at gmail.com (Sheng Bao) Date: Mon, 26 Jun 2006 15:09:08 +0800 Subject: [MINC-users] fmr_preprocess In-Reply-To: References: <20060626010953.25500.qmail@web50102.mail.yahoo.com> Message-ID: <889df5f00606260009v6bba2298ja07aad00686ee251@mail.gmail.com> hi, guys, actually these days I am help Xingfeng Lee to install software he needed to run his program. I have downloaded the Getopt::Tabular from CPAN. But I encountered the following problem when I did exactly as what the instruction said [root at ambrose Getopt-Tabular-0.3]# perl Makefile.PL Config.pm did not return a true value at /usr/lib/perl5/5.8.6/ExtUtils/MakeMaker.pm line 9. BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.6/ExtUtils/MakeMaker.pm line 9. Compilation failed in require at Makefile.PL line 1. BEGIN failed--compilation aborted at Makefile.PL line 1. Coz Dr.Li came to Nanjing Jingling Hospital to cooperate a research with a friend of mine, I installed the Fedora Core 4 system, the Matlab and other tools(such as display, regiser, minc, etc.). Here in China, only quite a few people know how to use Linux operating system and I have never used Perl programming language before. Before I help Dr.Li, my friend has asked many other people to prepare the workstation. But they failed. So I was involved in this issue just these days. I do need some intructions to help Dr. Li finish his experiment. Cheers, Sheng On 6/26/06, Andrew Janke wrote: > > Li, > > You will have to download and install Getopt::Tabular from www.cpan.org > > > a > > On 6/25/06, xingfeng lee wrote: > > Hi Andrew, > > Thank you very much, the new problem is: > > > > [root at ambrose Test]# fmr_preprocess > > Can't locate Getopt/Tabular.pm in @INC (@INC contains: > /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 > /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 > /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi > /usr/lib/perl5/5.8.6 .) at /bin/fmr_preprocess line 40. > > BEGIN failed--compilation aborted at /bin/fmr_preprocess line 40. > > > > > > All the best, > > Li > > > > > > > > Andrew Janke wrote: Hi Li, > > > > I suspect you will have to set the execute bit for the file. ie: > > > > $ chmod +x fmr_preprocess > > > > > > a > > > > On 6/23/06, xingfeng lee wrote: > > > Dear MINC experts: > > > > > > Could you help? > > > I came cross a problem when i did fmri data realignment. I copied the > function : fmr_preprocess from my computer at McGill to the bin directory of > my computer in China, but it did not work. I remember that this function > does not need to install, just copy this function to the bin directory. The > error message was: > > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess > qiu_yan_li_20060611_130900_3_mri.mnc > > > bash: /bin/fmr_preprocess: Permission denied > > > Could you give some advises? > > > > > > If it need install, where should i download it, and how to install > it? > > > > > > Thank you very much and have a nice weekend. > > > all the best, > > > Li > > > > > > > > > --------------------------------- > > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with > Yahoo! Messenger with Voice. > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > > Canada->Montreal Cell: +1 (514) 924 > 2012 > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > Andrew Janke wrote: Hi Li, > > > > I suspect you will have to set the execute bit for the file. ie: > > > > $ chmod +x fmr_preprocess > > > > > > a > > > > On 6/23/06, xingfeng lee wrote: > > > Dear MINC experts: > > > > > > Could you help? > > > I came cross a problem when i did fmri data realignment. I copied the > function : fmr_preprocess from my computer at McGill to the bin directory of > my computer in China, but it did not work. I remember that this function > does not need to install, just copy this function to the bin directory. The > error message was: > > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess > qiu_yan_li_20060611_130900_3_mri.mnc > > > bash: /bin/fmr_preprocess: Permission denied > > > Could you give some advises? > > > > > > If it need install, where should i download it, and how to install > it? > > > > > > Thank you very much and have a nice weekend. > > > all the best, > > > Li > > > > > > > > > --------------------------------- > > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with > Yahoo! Messenger with Voice. > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > > Canada->Montreal Cell: +1 (514) 924 > 2012 > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > --------------------------------- > > Sneak preview the all-new Yahoo.com. It's not radically different. Just > radically better. > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- EE is no more about circuits than CS is about computers. Home Page: http://grandlab.cer.net/~bao Blog: http://blog.360.yahoo.com/forrestbao http://spaces.msn.com/forrestbao MSN: bsh1984 at hotmail.com (IM only) Gmail: forrest.bao at gmail.com (Email also) Yahoo! ID: forrestbao at yahoo.com.cn (Email also) AIM: forrestbao Skype: forrestbao From louis.collins at mcgill.ca Mon Jun 26 08:46:13 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Mon, 26 Jun 2006 08:46:13 -0400 Subject: [MINC-users] Automated Trimming In-Reply-To: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FCD7@NIHCESMLBX3.nih.gov> References: <323E7EA8AF5B4F42BBEE78D8B88816FB0175FCD7@NIHCESMLBX3.nih.gov> Message-ID: <5a273f706c505623e9d7cd4967b32fd7@mcgill.ca> Eric, Stephen Frey (MNI) and I are working on a 'mritotal' package for monkey brains with a standard model, coordinate system, and brain mask. Should be ready in 2-3 weeks if you want to wait. -Louis On Jun 22, 2006, at 4:30 PM, Faden, Eric (NIH/NIMH) [F] wrote: > I am working on a script to generate brainmasks for a set of macaque > scans we have, but since the scans have different amounts of neck in > them my script is having some issues. I was wondering if there is a > quick way using minccalc or something to draw a circular mask and cut > everything outside of it? or if anyone has a trick for creating a > very gross mask I could use to remove the neck? > > -Eric > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From acaroli at fatebenefratelli.it Mon Jun 26 09:24:41 2006 From: acaroli at fatebenefratelli.it (Anna Caroli) Date: Mon, 26 Jun 2006 15:24:41 +0200 Subject: [MINC-users] change origin Message-ID: <200606261324.k5QDOhXg004565@mail.bic.mni.mcgill.ca> Dear MINC users, does anybody know how to change the origin in a .mnc file? My file looks like this: > mincinfo myfile.mnc file: myfile.mnc image: signed__ short 0 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 91 2 -91 yspace 109 2 -109 xspace 91 -2 91 and, opening the file with Display or register, I can see that the origin is in 45, 54, 45. I would like to change the origin in order to have it in 46, 64, 37. Can anybody help me? Thanks a lot for your help! Anna Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni di Dio FBF The National Center for Research and Care of Alzheimer's Disease via Pilastroni 4, 25125 - Brescia, Italy Tel: +39 030 3501 361, Fax: +39 02 700 435 727 www.centroAlzheimer.it From a.janke at gmail.com Mon Jun 26 09:31:16 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 09:31:16 -0400 Subject: [MINC-users] change origin In-Reply-To: <200606261324.k5QDOhXg004565@mail.bic.mni.mcgill.ca> References: <200606261324.k5QDOhXg004565@mail.bic.mni.mcgill.ca> Message-ID: Hi Anna, The simplest way to do this is to change the start value for each dimension. For example if you wish to change the origin of the zspace co-ordinate from 45 to 47 then you need to subtract 2 off the start as such: minc_modify_header -dinsert zspace:start=-93 myfile.mnc a On 6/26/06, Anna Caroli wrote: > Dear MINC users, > does anybody know how to change the origin in a .mnc file? > My file looks like this: > > > mincinfo myfile.mnc > > file: myfile.mnc > image: signed__ short 0 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 91 2 -91 > yspace 109 2 -109 > xspace 91 -2 91 > > and, opening the file with Display or register, I can see that the origin is > in 45, 54, 45. > > I would like to change the origin in order to have it in 46, 64, 37. > > Can anybody help me? > Thanks a lot for your help! > > Anna > > Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni > di Dio FBF > The National Center for Research and Care of Alzheimer's Disease > via Pilastroni 4, 25125 - Brescia, Italy > Tel: +39 030 3501 361, Fax: +39 02 700 435 727 www.centroAlzheimer.it > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Jun 26 09:41:33 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 26 Jun 2006 09:41:33 -0400 Subject: [MINC-users] fmr_preprocess In-Reply-To: <889df5f00606260009v6bba2298ja07aad00686ee251@mail.gmail.com> References: <20060626010953.25500.qmail@web50102.mail.yahoo.com> <889df5f00606260009v6bba2298ja07aad00686ee251@mail.gmail.com> Message-ID: Hi Sheng, The sort of problems you are having are really not MINC related but rather linux related, as such you will be better of to use one of the more generic linux support groups or Fedora groups. My only observation is that Fedora 4 is a somwhat older distribution, whilst a re-install may sound like a rather drastic step to solve a perl problem, it ay be worth it in the long run. We use a debian based system here at the BIC and other places. A more friendly Debian based system is Ubuntu. a On 6/26/06, Sheng Bao wrote: > hi, guys, actually these days I am help Xingfeng Lee to install software he > needed to run his program. > I have downloaded the Getopt::Tabular from CPAN. > But I encountered the following problem when I did exactly as what the > instruction said > > [root at ambrose Getopt-Tabular-0.3]# perl Makefile.PL > Config.pm did not return a true value at > /usr/lib/perl5/5.8.6/ExtUtils/MakeMaker.pm line 9. > BEGIN failed--compilation aborted at > /usr/lib/perl5/5.8.6/ExtUtils/MakeMaker.pm line 9. > Compilation failed in require at Makefile.PL line 1. > BEGIN failed--compilation aborted at Makefile.PL line 1. > > Coz Dr.Li came to Nanjing Jingling Hospital to cooperate a research with a > friend of mine, I installed the Fedora Core 4 system, the Matlab and other > tools(such as display, regiser, minc, etc.). Here in China, only quite a few > people know how to use Linux operating system and I have never used Perl > programming language before. Before I help Dr.Li, my friend has asked many > other people to prepare the workstation. But they failed. So I was involved > in this issue just these days. I do need some intructions to help Dr. Li > finish his experiment. > > Cheers, > Sheng > > On 6/26/06, Andrew Janke wrote: > > > > Li, > > > > You will have to download and install Getopt::Tabular from www.cpan.org > > > > > > a > > > > On 6/25/06, xingfeng lee wrote: > > > Hi Andrew, > > > Thank you very much, the new problem is: > > > > > > [root at ambrose Test]# fmr_preprocess > > > Can't locate Getopt/Tabular.pm in @INC (@INC contains: > > /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 > > /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 > > /usr/lib/perl5/site_perl > > /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 > > /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > > /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi > > /usr/lib/perl5/5.8.6 .) at /bin/fmr_preprocess line 40. > > > BEGIN failed--compilation aborted at /bin/fmr_preprocess line 40. > > > > > > > > > All the best, > > > Li > > > > > > > > > > > > Andrew Janke wrote: Hi Li, > > > > > > I suspect you will have to set the execute bit for the file. ie: > > > > > > $ chmod +x fmr_preprocess > > > > > > > > > a > > > > > > On 6/23/06, xingfeng lee wrote: > > > > Dear MINC experts: > > > > > > > > Could you help? > > > > I came cross a problem when i did fmri data realignment. I copied the > > function : fmr_preprocess from my computer at McGill to the bin directory of > > my computer in China, but it did not work. I remember that this function > > does not need to install, just copy this function to the bin directory. The > > error message was: > > > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess > > qiu_yan_li_20060611_130900_3_mri.mnc > > > > bash: /bin/fmr_preprocess: Permission denied > > > > Could you give some advises? > > > > > > > > If it need install, where should i download it, and how to install > > it? > > > > > > > > Thank you very much and have a nice weekend. > > > > all the best, > > > > Li > > > > > > > > > > > > --------------------------------- > > > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with > > Yahoo! Messenger with Voice. > > > > _______________________________________________ > > > > MINC-users at bic.mni.mcgill.ca > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > > > > -- > > > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > > > Canada->Montreal Cell: +1 (514) 924 > > 2012 > > > > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > > > Andrew Janke wrote: Hi Li, > > > > > > I suspect you will have to set the execute bit for the file. ie: > > > > > > $ chmod +x fmr_preprocess > > > > > > > > > a > > > > > > On 6/23/06, xingfeng lee wrote: > > > > Dear MINC experts: > > > > > > > > Could you help? > > > > I came cross a problem when i did fmri data realignment. I copied the > > function : fmr_preprocess from my computer at McGill to the bin directory of > > my computer in China, but it did not work. I remember that this function > > does not need to install, just copy this function to the bin directory. The > > error message was: > > > > [root at ambrose qiu_yan_li_20060611_130900]# fmr_preprocess > > qiu_yan_li_20060611_130900_3_mri.mnc > > > > bash: /bin/fmr_preprocess: Permission denied > > > > Could you give some advises? > > > > > > > > If it need install, where should i download it, and how to install > > it? > > > > > > > > Thank you very much and have a nice weekend. > > > > all the best, > > > > Li > > > > > > > > > > > > --------------------------------- > > > > Ring'em or ping'em. Make PC-to-phone calls as low as 1?/min with > > Yahoo! Messenger with Voice. > > > > _______________________________________________ > > > > MINC-users at bic.mni.mcgill.ca > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > > > > -- > > > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > > > Canada->Montreal Cell: +1 (514) 924 > > 2012 > > > > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > > > > --------------------------------- > > > Sneak preview the all-new Yahoo.com. It's not radically different. Just > > radically better. > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > > Canada->Montreal Cell: +1 (514) 924 2012 > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > -- > EE is no more about circuits than CS is about computers. > > Home Page: http://grandlab.cer.net/~bao > Blog: http://blog.360.yahoo.com/forrestbao > http://spaces.msn.com/forrestbao > MSN: bsh1984 at hotmail.com (IM only) > Gmail: forrest.bao at gmail.com (Email also) > Yahoo! ID: forrestbao at yahoo.com.cn (Email also) > AIM: forrestbao > Skype: forrestbao > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From duchesne at ieee.org Mon Jun 26 11:11:45 2006 From: duchesne at ieee.org (Simon Duchesne) Date: Mon, 26 Jun 2006 17:11:45 +0200 Subject: [MINC-users] MINC OSX Monolithic packages In-Reply-To: Message-ID: Andrew Many thanks. Will give it a try. Meanwhile, for the Mac OS X - Display users, a simple question: whenever inputting requested values (e.g. Brush size) through the X-terminal window, my Display hangs up. Has anyone seen that before ? Thanks Simon Simon Duchesne Post-doctoral researcher Chercheur post-doctoral ---------------------------------------------------- Unit?/Projet VISAGES U746 INSERM/INRIA/CNRS/U. de Rennes I IRISA Campus de Beaulieu, 35042 Rennes Cedex, France Ph: +33 (2) 99 84 25 23 / Fax: +33 (2) 99 84 71 71 INSERM Universite de Rennes I, CS 34317, 35043 Rennes Cedex, France Ph: +33 (2) 23 23 45 88 / Fax: +33 (2) 99 84 71 71 ----------------------------------------------------- duchesne at ieee.org From louis.collins at mcgill.ca Mon Jun 26 11:24:02 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Mon, 26 Jun 2006 11:24:02 -0400 Subject: [MINC-users] MINC OSX Monolithic packages In-Reply-To: References: Message-ID: <488cd7478fe331af563e5f4acc6c1854@mcgill.ca> could be a question of 'click-to-focus'. I find that you have to click the mouse in the xterm, type in the value, and then click back into Display. -Louis On Jun 26, 2006, at 11:11 AM, Simon Duchesne wrote: > Andrew > > Many thanks. Will give it a try. > > Meanwhile, for the Mac OS X - Display users, a simple question: > whenever > inputting requested values (e.g. Brush size) through the X-terminal > window, > my Display hangs up. Has anyone seen that before ? > > Thanks > Simon > > > > Simon Duchesne > Post-doctoral researcher > Chercheur post-doctoral > > ---------------------------------------------------- > Unit?/Projet VISAGES U746 > INSERM/INRIA/CNRS/U. de Rennes I > > IRISA > Campus de Beaulieu, 35042 Rennes Cedex, France > Ph: +33 (2) 99 84 25 23 / Fax: +33 (2) 99 84 71 71 > > INSERM > Universite de Rennes I, CS 34317, 35043 Rennes Cedex, France > Ph: +33 (2) 23 23 45 88 / Fax: +33 (2) 99 84 71 71 > ----------------------------------------------------- > duchesne at ieee.org > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From duchesne at ieee.org Mon Jun 26 12:11:53 2006 From: duchesne at ieee.org (Simon Duchesne) Date: Mon, 26 Jun 2006 18:11:53 +0200 Subject: [MINC-users] MINC OSX Monolithic packages In-Reply-To: <488cd7478fe331af563e5f4acc6c1854@mcgill.ca> Message-ID: Louis It's even simpler than that (goes to show my level of eegnoorance). I was calling Display and sending it straight to bg > Display input.mnc & And, well, that just doesn't do it. It needs to be fg BTW, Andrew, I'm using your new package on my PowerBook laptop w/ Tiger 10.4.6 - it installed without a glitch. Everything seems to be there. Thanks again for all your work. Next target, Intel-Macs ? Simon On 26/06/06 17:24, "D. Louis Collins" wrote: > could be a question of 'click-to-focus'. I find that you have to click > the mouse in the xterm, type in the value, and then click back into > Display. > > -Louis > > > On Jun 26, 2006, at 11:11 AM, Simon Duchesne wrote: > >> Andrew >> >> Many thanks. Will give it a try. >> >> Meanwhile, for the Mac OS X - Display users, a simple question: >> whenever >> inputting requested values (e.g. Brush size) through the X-terminal >> window, >> my Display hangs up. Has anyone seen that before ? >> >> Thanks >> Simon >> From forrest.bao at gmail.com Mon Jun 26 21:15:32 2006 From: forrest.bao at gmail.com (Sheng Bao) Date: Tue, 27 Jun 2006 09:15:32 +0800 Subject: [MINC-users] fmr_preprocess In-Reply-To: References: <20060626010953.25500.qmail@web50102.mail.yahoo.com> <889df5f00606260009v6bba2298ja07aad00686ee251@mail.gmail.com> Message-ID: <889df5f00606261815x1f9b0709xc41ed6098181c88e@mail.gmail.com> Hi Andrew, So you mean the distribution you are using is Ubuntu? You can run all software ,including fmr_preprocess, successfully on Ubuntu? what is it version? the latest one Dapper(6.10)? Actually, I use FC5 and Ubuntu 6.10 on my laptop. If it is, I will try to test on my laptop first and then install it onto the workstation that Dr.Liwill use. The funny things is when I asked Dr.Lee, he said "we use FC4". On 6/26/06, Andrew Janke wrote: > > Hi Sheng, > > The sort of problems you are having are really not MINC related but > rather linux related, as such you will be better of to use one of the > more generic linux support groups or Fedora groups. > > My only observation is that Fedora 4 is a somwhat older distribution, > whilst a re-install may sound like a rather drastic step to solve a > perl problem, it ay be worth it in the long run. We use a debian based > system here at the BIC and other places. A more friendly Debian based > system is Ubuntu. > -- EE is no more about circuits than CS is about computers. Home Page: http://grandlab.cer.net/~bao Blog: http://blog.360.yahoo.com/forrestbao http://spaces.msn.com/forrestbao MSN: bsh1984 at hotmail.com (IM only) Gmail: forrest.bao at gmail.com (Email also) Yahoo! ID: forrestbao at yahoo.com.cn (Email also) AIM: forrestbao Skype: forrestbao From ed.gronenschild at mi.unimaas.nl Tue Jun 27 06:07:15 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Tue, 27 Jun 2006 12:07:15 +0200 Subject: [MINC-users] Problems with linking libraries using Xcode In-Reply-To: References: Message-ID: Hi Jason, I tried ranlib and that resulted in a successful building of my application. Thanks for the tip. Ed On 22 Jun 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote: > Message: 2 > Date: Thu, 22 Jun 2006 11:31:51 -0400 > From: Jason Lerch > Subject: Re: [MINC-users] Problems with linking libraries using Xcode > To: MINC users mailing list > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Have you tried rerunning ranlib on each of the .a files? > > (I've never used Xcode for minc stuff, but that appears to be what > the error message suggests) > > Jason > > On 22-Jun-06, at 9:40 AM, Ed Gronenschild wrote: > >> Hi, >> >> I'm building my own image processing application with Apple's >> Xcode 2.3 on a Mac with OS X 10.4.6. I'm linking against the >> libraries >> libbicpl.a, libminc.a, libnetcdf.a and libvolume_io.a, all from the >> minc-1.4 package for OSX 10.3. In Xcode I've set OS X 10.3.9 >> as cross-develop target SDK. >> The application runs fine in debug mode, but as soon as I switch >> to release mode (the application will be used by others) I get >> linking errors, the same for each of the minc libraries. For >> instance >> for libbicpl.a: >> >> "table of contents for archive: /...../libbicpl.a is out of date; >> rerun ranlib(1) >> (can't load from it)" >> >> and finally >> >> "/usr/bin/gcc-4.0 failed with exit code 1" >> >> Does anybody know what to do? >> >> Regards, >> >> Ed >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From sorench at gmail.com Wed Jun 28 00:15:08 2006 From: sorench at gmail.com (Soren Christensen) Date: Wed, 28 Jun 2006 14:15:08 +1000 Subject: [MINC-users] compilation on fedora In-Reply-To: References: Message-ID: Hi Andrew, I tried to compile Mesa but it causes some trouble that the X libraries are relocated in Fedora 5. However, I tried to run the command where make fails (below), but adding -lglut as an option - that seemed to work. My skills in the Make system are limited to trial and error + googling, so I'd really apreciate if some one could direct me to where I should enter -lglut so that it is put as an option automatically. Also, if someone has an idea why (Display) it is not working out of the box on Fedora 5 I'd like to hear about that. Thanks! Soren gcc -g -O2 -o Display dummy.o main/main.o main/display.o main/event_loop.o main/graphics.o main/three_d.o main/transforms.o atlas/atlas.o input_files/input_files.o input_files/volume_file.o callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o callbacks/surf_segmenting.o callbacks/surface_curves.o callbacks/surface_extract.o callbacks/view_ops.o callbacks/volume_ops.o callbacks/volume_transform_ops.o current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o edit_surface/segment.o images/images.o markers/markers.o surface_extraction/boundary_extraction.o surface_extraction/data_structs.o surface_extraction/init_surface.o surface_extraction/extract.o surface_extraction/surface.o surface_extraction/surface_events.o voxel_scan/scan_objects.o events/change_markers.o events/clip_plane.o events/film_loop.o events/magnify.o events/mouse.o events/mouse_trans.o events/pick_object.o events/pick_view.o events/rotate_slice.o events/spaceball.o events/virt_sb.o events/window_man.o events/utilities.o immediate_mode/draw_immed.o intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o menu/input_menu.o menu/selected.o menu/text.o cursor_contours/contours.o segmenting/cut_neighbours.o segmenting/painting.o segmenting/segmenting.o segmenting/segment_polygons.o slice_window/colour_bar.o slice_window/colour_coding.o slice_window/crop.o slice_window/draw_slice.o slice_window/histogram.o slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o slice_window/slice_3d.o slice_window/slice_events.o slice_window/undo.o slice_window/view.o surface_curves/closest_line.o surface_curves/events.o surface_curves/edge_distance.o tubes/convert_lines.o structures/action_table.o structures/fit_view.o structures/lights.o structures/render.o structures/view.o structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl -lvolume_io -lminc -lnetcdf -lm Gives: slice_window/crop.o: In function `crop_and_load_volume': /root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp' Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': /root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: undefined reference to `glutBitmap8By13' Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': /root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: undefined reference to `glutIdleFunc' Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': /root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: undefined reference to `glutGet' Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': But adding -lglut to that line will give slice_window/crop.o: In function `crop_and_load_volume': /root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp' Which i assume is an insignificant warning. On 6/26/06, Andrew Janke wrote: > Hi Soren, > > Amusingly enough I came across this same problem with a machine or two > in Stockholm just last week... In my case the solution was to get and > compile a version of GLUT as opposed to using the system version. I > canna remember the version that I used though.. :( Suffice to say, no > RPM that I could find (via rpmfind/etc) seemed to work. > > > a > > On 6/26/06, Soren Christensen wrote: > > Dear MINc users, > > I was wondering if anybody had experience with compiling the MINC > > tools under Fedora 5. > > I previously posted a problem with the CLK_TCK macro that could not be > > found by the linker. I found a solution to that on: > > http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_19.html > > In case other people experience the same problem. > > However, now I am stuck with compilation of Display (MINC, NETCDF and > > BICPL seem to work). > > The error below arises when running make (for Display). > > Could anyone see where the problem is - I guess it has something to do > > with GLUT but i am not excatly sure how to narrow it down further. > > > > Thanks and best regards > > Soren > > > > ..... > > gcc -g -O2 -o Display dummy.o main/main.o main/display.o > > main/event_loop.o main/graphics.o main/three_d.o main/transforms.o > > atlas/atlas.o input_files/input_files.o input_files/volume_file.o > > callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o > > callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o > > callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o > > callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o > > callbacks/surf_segmenting.o callbacks/surface_curves.o > > callbacks/surface_extract.o callbacks/view_ops.o > > callbacks/volume_ops.o callbacks/volume_transform_ops.o > > current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o > > edit_surface/segment.o images/images.o markers/markers.o > > surface_extraction/boundary_extraction.o > > surface_extraction/data_structs.o surface_extraction/init_surface.o > > surface_extraction/extract.o surface_extraction/surface.o > > surface_extraction/surface_events.o voxel_scan/scan_objects.o > > events/change_markers.o events/clip_plane.o events/film_loop.o > > events/magnify.o events/mouse.o events/mouse_trans.o > > events/pick_object.o events/pick_view.o events/rotate_slice.o > > events/spaceball.o events/virt_sb.o events/window_man.o > > events/utilities.o immediate_mode/draw_immed.o > > intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o > > cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o > > menu/input_menu.o menu/selected.o menu/text.o > > cursor_contours/contours.o segmenting/cut_neighbours.o > > segmenting/painting.o segmenting/segmenting.o > > segmenting/segment_polygons.o slice_window/colour_bar.o > > slice_window/colour_coding.o slice_window/crop.o > > slice_window/draw_slice.o slice_window/histogram.o > > slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o > > slice_window/slice_3d.o slice_window/slice_events.o > > slice_window/undo.o slice_window/view.o surface_curves/closest_line.o > > surface_curves/events.o surface_curves/edge_distance.o > > tubes/convert_lines.o structures/action_table.o structures/fit_view.o > > structures/lights.o structures/render.o structures/view.o > > structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl > > -lvolume_io -lminc -lnetcdf -lm > > slice_window/crop.o: In function `crop_and_load_volume': > > /root/download/Display-1.4.1/slice_window/crop.c:165: warning: the use > > of `tmpnam' is dangerous, better use `mkstemp' > > Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': > > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: > > undefined reference to `glutBitmap8By13' > > Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': > > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: > > undefined reference to `glutIdleFunc' > > Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': > > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: > > undefined reference to `glutGet' > > Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': > > /root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:913: > > undefined reference to `glutGet' > > Graphics/libbicgl.a(glut_windows.o): In function `WS_get_screen_size':....... > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canada->Montreal Cell: +1 (514) 924 2012 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From se at hst.aau.dk Wed Jun 28 07:07:10 2006 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Wed, 28 Jun 2006 13:07:10 +0200 Subject: [MINC-users] compilation on fedora In-Reply-To: References: Message-ID: <44A262DE.8010903@hst.aau.dk> Hi Soren, If configure cannot find the glut lib, the -lglut is not added to the gcc command. So you need to make sure that configure finds the glut lib: checking for OpenGL library... -lGL checking for OpenGL Utility library... -lGLU checking for GLUT library... -lglut The autoconf macro AX_CHECK_GLUT is used to check for glut: dnl Check for GLUT. If GLUT is found, the required compiler and linker dnl flags are included in the output variables "GLUT_CFLAGS" and dnl "GLUT_LIBS", respectively. Since adding -lglut to the gcc manually seems to work, you obviously have glut installed. If it is installed outside /usr/lib try setting the LDFLAGS environment variable. export LDFLAGS=-L/path/to/libglut ...and perhaps the LD_LIBRARY_PATH: export LD_LIBRARY_PATH=-L/path/to/libglut The last one however should not be necessary as the run-time shared library loader finds the glut lib ok. Simon Soren Christensen wrote: >Hi Andrew, > I tried to compile Mesa but it causes some trouble that the X >libraries are relocated in Fedora 5. However, I tried to run the >command where make fails (below), but adding -lglut >as an option - that seemed to work. >My skills in the Make system are limited to trial and error + >googling, so I'd really apreciate if some one could direct me to where >I should enter -lglut so that it is put as an option automatically. >Also, if someone has an idea why (Display) it is not working out of >the box on Fedora 5 I'd like to hear about that. > >Thanks! > >Soren > > > > > > >gcc -g -O2 -o Display dummy.o main/main.o main/display.o >main/event_loop.o main/graphics.o main/three_d.o main/transforms.o >atlas/atlas.o input_files/input_files.o input_files/volume_file.o >callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o >callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o >callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o >callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o >callbacks/surf_segmenting.o callbacks/surface_curves.o >callbacks/surface_extract.o callbacks/view_ops.o >callbacks/volume_ops.o callbacks/volume_transform_ops.o >current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o >edit_surface/segment.o images/images.o markers/markers.o >surface_extraction/boundary_extraction.o >surface_extraction/data_structs.o surface_extraction/init_surface.o >surface_extraction/extract.o surface_extraction/surface.o >surface_extraction/surface_events.o voxel_scan/scan_objects.o >events/change_markers.o events/clip_plane.o events/film_loop.o >events/magnify.o events/mouse.o events/mouse_trans.o >events/pick_object.o events/pick_view.o events/rotate_slice.o >events/spaceball.o events/virt_sb.o events/window_man.o >events/utilities.o immediate_mode/draw_immed.o >intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o >cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o >menu/input_menu.o menu/selected.o menu/text.o >cursor_contours/contours.o segmenting/cut_neighbours.o >segmenting/painting.o segmenting/segmenting.o >segmenting/segment_polygons.o slice_window/colour_bar.o >slice_window/colour_coding.o slice_window/crop.o >slice_window/draw_slice.o slice_window/histogram.o >slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o >slice_window/slice_3d.o slice_window/slice_events.o >slice_window/undo.o slice_window/view.o surface_curves/closest_line.o >surface_curves/events.o surface_curves/edge_distance.o >tubes/convert_lines.o structures/action_table.o structures/fit_view.o >structures/lights.o structures/render.o structures/view.o >structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl >-lvolume_io -lminc -lnetcdf -lm > >Gives: >slice_window/crop.o: In function `crop_and_load_volume': >/root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: >the use of `tmpnam' is dangerous, better use `mkstemp' >Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: >undefined reference to `glutBitmap8By13' >Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: >undefined reference to `glutIdleFunc' >Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: >undefined reference to `glutGet' >Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': > > >But adding -lglut to that line will give >slice_window/crop.o: In function `crop_and_load_volume': >/root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: >the use of `tmpnam' is dangerous, better use `mkstemp' > >Which i assume is an insignificant warning. > > > > >On 6/26/06, Andrew Janke wrote: > > >>Hi Soren, >> >>Amusingly enough I came across this same problem with a machine or two >>in Stockholm just last week... In my case the solution was to get and >>compile a version of GLUT as opposed to using the system version. I >>canna remember the version that I used though.. :( Suffice to say, no >>RPM that I could find (via rpmfind/etc) seemed to work. >> >> >>a >> >>On 6/26/06, Soren Christensen wrote: >> >> >>>Dear MINc users, >>> I was wondering if anybody had experience with compiling the MINC >>>tools under Fedora 5. >>>I previously posted a problem with the CLK_TCK macro that could not be >>>found by the linker. I found a solution to that on: >>>http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_19.html >>>In case other people experience the same problem. >>>However, now I am stuck with compilation of Display (MINC, NETCDF and >>>BICPL seem to work). >>>The error below arises when running make (for Display). >>>Could anyone see where the problem is - I guess it has something to do >>>with GLUT but i am not excatly sure how to narrow it down further. >>> >>>Thanks and best regards >>>Soren >>> >>>..... >>>gcc -g -O2 -o Display dummy.o main/main.o main/display.o >>>main/event_loop.o main/graphics.o main/three_d.o main/transforms.o >>>atlas/atlas.o input_files/input_files.o input_files/volume_file.o >>>callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o >>>callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o >>>callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o >>>callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o >>>callbacks/surf_segmenting.o callbacks/surface_curves.o >>>callbacks/surface_extract.o callbacks/view_ops.o >>>callbacks/volume_ops.o callbacks/volume_transform_ops.o >>>current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o >>>edit_surface/segment.o images/images.o markers/markers.o >>>surface_extraction/boundary_extraction.o >>>surface_extraction/data_structs.o surface_extraction/init_surface.o >>>surface_extraction/extract.o surface_extraction/surface.o >>>surface_extraction/surface_events.o voxel_scan/scan_objects.o >>>events/change_markers.o events/clip_plane.o events/film_loop.o >>>events/magnify.o events/mouse.o events/mouse_trans.o >>>events/pick_object.o events/pick_view.o events/rotate_slice.o >>>events/spaceball.o events/virt_sb.o events/window_man.o >>>events/utilities.o immediate_mode/draw_immed.o >>>intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o >>>cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o >>>menu/input_menu.o menu/selected.o menu/text.o >>>cursor_contours/contours.o segmenting/cut_neighbours.o >>>segmenting/painting.o segmenting/segmenting.o >>>segmenting/segment_polygons.o slice_window/colour_bar.o >>>slice_window/colour_coding.o slice_window/crop.o >>>slice_window/draw_slice.o slice_window/histogram.o >>>slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o >>>slice_window/slice_3d.o slice_window/slice_events.o >>>slice_window/undo.o slice_window/view.o surface_curves/closest_line.o >>>surface_curves/events.o surface_curves/edge_distance.o >>>tubes/convert_lines.o structures/action_table.o structures/fit_view.o >>>structures/lights.o structures/render.o structures/view.o >>>structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl >>>-lvolume_io -lminc -lnetcdf -lm >>>slice_window/crop.o: In function `crop_and_load_volume': >>>/root/download/Display-1.4.1/slice_window/crop.c:165: warning: the use >>>of `tmpnam' is dangerous, better use `mkstemp' >>>Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: >>>undefined reference to `glutBitmap8By13' >>>Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: >>>undefined reference to `glutIdleFunc' >>>Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: >>>undefined reference to `glutGet' >>>Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:913: >>>undefined reference to `glutGet' >>>Graphics/libbicgl.a(glut_windows.o): In function `WS_get_screen_size':....... >>>_______________________________________________ >>>MINC-users at bic.mni.mcgill.ca >>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >>> >>> >>-- >>Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) >>Canada->Montreal Cell: +1 (514) 924 2012 >>_______________________________________________ >>MINC-users at bic.mni.mcgill.ca >>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> >> >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > -- Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) From sorench at gmail.com Wed Jun 28 07:21:48 2006 From: sorench at gmail.com (Soren Christensen) Date: Wed, 28 Jun 2006 21:21:48 +1000 Subject: [MINC-users] compilation on fedora In-Reply-To: <44A262DE.8010903@hst.aau.dk> References: <44A262DE.8010903@hst.aau.dk> Message-ID: Hi Simon, Thanks for the advice. It seems that configure cannot find glut on my Fedora 5 (although it is there). I get a "no" where you get lglut. I manually edited the Makefile after configure and put GLUTLIB=-lglut, that worked. Same thing with register. Not sure why configure cannot establish -lglut. I am working on a little note on how to solve a few additional problems on Fedora 5 in case others a stuck with the same issues. Cheers Soren On 6/28/06, Simon Fristed Eskildsen wrote: > Hi Soren, > If configure cannot find the glut lib, the -lglut is not added to the > gcc command. So you need to make sure that configure finds the glut lib: > checking for OpenGL library... -lGL > checking for OpenGL Utility library... -lGLU > checking for GLUT library... -lglut > > The autoconf macro AX_CHECK_GLUT is used to check for glut: > dnl Check for GLUT. If GLUT is found, the required compiler and linker > dnl flags are included in the output variables "GLUT_CFLAGS" and > dnl "GLUT_LIBS", respectively. > > Since adding -lglut to the gcc manually seems to work, you obviously > have glut installed. If it is installed outside /usr/lib try setting the > LDFLAGS environment variable. > export LDFLAGS=-L/path/to/libglut > ...and perhaps the LD_LIBRARY_PATH: > export LD_LIBRARY_PATH=-L/path/to/libglut > The last one however should not be necessary as the run-time shared > library loader finds the glut lib ok. > > Simon > > Soren Christensen wrote: > > >Hi Andrew, > > I tried to compile Mesa but it causes some trouble that the X > >libraries are relocated in Fedora 5. However, I tried to run the > >command where make fails (below), but adding -lglut > >as an option - that seemed to work. > >My skills in the Make system are limited to trial and error + > >googling, so I'd really apreciate if some one could direct me to where > >I should enter -lglut so that it is put as an option automatically. > >Also, if someone has an idea why (Display) it is not working out of > >the box on Fedora 5 I'd like to hear about that. > > > >Thanks! > > > >Soren > > > > > > > > > > > > > >gcc -g -O2 -o Display dummy.o main/main.o main/display.o > >main/event_loop.o main/graphics.o main/three_d.o main/transforms.o > >atlas/atlas.o input_files/input_files.o input_files/volume_file.o > >callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o > >callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o > >callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o > >callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o > >callbacks/surf_segmenting.o callbacks/surface_curves.o > >callbacks/surface_extract.o callbacks/view_ops.o > >callbacks/volume_ops.o callbacks/volume_transform_ops.o > >current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o > >edit_surface/segment.o images/images.o markers/markers.o > >surface_extraction/boundary_extraction.o > >surface_extraction/data_structs.o surface_extraction/init_surface.o > >surface_extraction/extract.o surface_extraction/surface.o > >surface_extraction/surface_events.o voxel_scan/scan_objects.o > >events/change_markers.o events/clip_plane.o events/film_loop.o > >events/magnify.o events/mouse.o events/mouse_trans.o > >events/pick_object.o events/pick_view.o events/rotate_slice.o > >events/spaceball.o events/virt_sb.o events/window_man.o > >events/utilities.o immediate_mode/draw_immed.o > >intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o > >cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o > >menu/input_menu.o menu/selected.o menu/text.o > >cursor_contours/contours.o segmenting/cut_neighbours.o > >segmenting/painting.o segmenting/segmenting.o > >segmenting/segment_polygons.o slice_window/colour_bar.o > >slice_window/colour_coding.o slice_window/crop.o > >slice_window/draw_slice.o slice_window/histogram.o > >slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o > >slice_window/slice_3d.o slice_window/slice_events.o > >slice_window/undo.o slice_window/view.o surface_curves/closest_line.o > >surface_curves/events.o surface_curves/edge_distance.o > >tubes/convert_lines.o structures/action_table.o structures/fit_view.o > >structures/lights.o structures/render.o structures/view.o > >structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl > >-lvolume_io -lminc -lnetcdf -lm > > > >Gives: > >slice_window/crop.o: In function `crop_and_load_volume': > >/root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: > >the use of `tmpnam' is dangerous, better use `mkstemp' > >Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': > >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: > >undefined reference to `glutBitmap8By13' > >Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': > >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: > >undefined reference to `glutIdleFunc' > >Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': > >/root/Desktop/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: > >undefined reference to `glutGet' > >Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': > > > > > >But adding -lglut to that line will give > >slice_window/crop.o: In function `crop_and_load_volume': > >/root/Desktop/download/Display-1.4.1/slice_window/crop.c:165: warning: > >the use of `tmpnam' is dangerous, better use `mkstemp' > > > >Which i assume is an insignificant warning. > > > > > > > > > >On 6/26/06, Andrew Janke wrote: > > > > > >>Hi Soren, > >> > >>Amusingly enough I came across this same problem with a machine or two > >>in Stockholm just last week... In my case the solution was to get and > >>compile a version of GLUT as opposed to using the system version. I > >>canna remember the version that I used though.. :( Suffice to say, no > >>RPM that I could find (via rpmfind/etc) seemed to work. > >> > >> > >>a > >> > >>On 6/26/06, Soren Christensen wrote: > >> > >> > >>>Dear MINc users, > >>> I was wondering if anybody had experience with compiling the MINC > >>>tools under Fedora 5. > >>>I previously posted a problem with the CLK_TCK macro that could not be > >>>found by the linker. I found a solution to that on: > >>>http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_19.html > >>>In case other people experience the same problem. > >>>However, now I am stuck with compilation of Display (MINC, NETCDF and > >>>BICPL seem to work). > >>>The error below arises when running make (for Display). > >>>Could anyone see where the problem is - I guess it has something to do > >>>with GLUT but i am not excatly sure how to narrow it down further. > >>> > >>>Thanks and best regards > >>>Soren > >>> > >>>..... > >>>gcc -g -O2 -o Display dummy.o main/main.o main/display.o > >>>main/event_loop.o main/graphics.o main/three_d.o main/transforms.o > >>>atlas/atlas.o input_files/input_files.o input_files/volume_file.o > >>>callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o > >>>callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o > >>>callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o > >>>callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o > >>>callbacks/surf_segmenting.o callbacks/surface_curves.o > >>>callbacks/surface_extract.o callbacks/view_ops.o > >>>callbacks/volume_ops.o callbacks/volume_transform_ops.o > >>>current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o > >>>edit_surface/segment.o images/images.o markers/markers.o > >>>surface_extraction/boundary_extraction.o > >>>surface_extraction/data_structs.o surface_extraction/init_surface.o > >>>surface_extraction/extract.o surface_extraction/surface.o > >>>surface_extraction/surface_events.o voxel_scan/scan_objects.o > >>>events/change_markers.o events/clip_plane.o events/film_loop.o > >>>events/magnify.o events/mouse.o events/mouse_trans.o > >>>events/pick_object.o events/pick_view.o events/rotate_slice.o > >>>events/spaceball.o events/virt_sb.o events/window_man.o > >>>events/utilities.o immediate_mode/draw_immed.o > >>>intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o > >>>cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o > >>>menu/input_menu.o menu/selected.o menu/text.o > >>>cursor_contours/contours.o segmenting/cut_neighbours.o > >>>segmenting/painting.o segmenting/segmenting.o > >>>segmenting/segment_polygons.o slice_window/colour_bar.o > >>>slice_window/colour_coding.o slice_window/crop.o > >>>slice_window/draw_slice.o slice_window/histogram.o > >>>slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o > >>>slice_window/slice_3d.o slice_window/slice_events.o > >>>slice_window/undo.o slice_window/view.o surface_curves/closest_line.o > >>>surface_curves/events.o surface_curves/edge_distance.o > >>>tubes/convert_lines.o structures/action_table.o structures/fit_view.o > >>>structures/lights.o structures/render.o structures/view.o > >>>structures/window.o Graphics/libbicgl.a -lGLU -lGL -lbicpl > >>>-lvolume_io -lminc -lnetcdf -lm > >>>slice_window/crop.o: In function `crop_and_load_volume': > >>>/root/download/Display-1.4.1/slice_window/crop.c:165: warning: the use > >>>of `tmpnam' is dangerous, better use `mkstemp' > >>>Graphics/libbicgl.a(glut_windows.o): In function `lookup_font': > >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:692: > >>>undefined reference to `glutBitmap8By13' > >>>Graphics/libbicgl.a(glut_windows.o): In function `WS_add_idle_function': > >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:1151: > >>>undefined reference to `glutIdleFunc' > >>>Graphics/libbicgl.a(glut_windows.o): In function `flip_screen_y': > >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:919: > >>>undefined reference to `glutGet' > >>>Graphics/libbicgl.a(glut_windows.o): In function `flip_window_y': > >>>/root/download/Display-1.4.1/Graphics/GLUT_windows/glut_windows.c:913: > >>>undefined reference to `glutGet' > >>>Graphics/libbicgl.a(glut_windows.o): In function `WS_get_screen_size':....... > >>>_______________________________________________ > >>>MINC-users at bic.mni.mcgill.ca > >>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >>> > >>> > >>> > >>-- > >>Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > >>Canada->Montreal Cell: +1 (514) 924 2012 > >>_______________________________________________ > >>MINC-users at bic.mni.mcgill.ca > >>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > >> > >> > >_______________________________________________ > >MINC-users at bic.mni.mcgill.ca > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > -- > Simon Fristed Eskildsen, M.Sc.EE., Ph.D. Student > Denmark->Aalborg->HST->MI (se at hst.aau.dk || +45 9635 9823) > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Jun 29 09:16:59 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 29 Jun 2006 09:16:59 -0400 Subject: [MINC-users] minc 2.0.11 Message-ID: Hi all, Thanks to Leili we have a 2.0.11 release of MINC. This point release fixes a number of bugs relating to conversion between 1.x and 2.x files amongst other things. Details are below. Source release here: http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.11.tar.gz Windows Binary installer: http://packages.bic.mni.mcgill.ca/win32/minc-2.0.11.exe NEWS: New in Release 2.0.11 --------------------- * Many small fixes * fix to mincresample * Small fix to mincconvert * -like flag added to rawtominc * Added additional tests for minc2 files. ChangeLog: 2006-06-26 Leila Baghdadi * libsrc2/test/testminctools.sh - added script to test various minc tools on a minc2 file. * libsrc2/test/Makfile.am - modified to execute a script which will call various minc tool starting with mincconvert to test whether they work correctly on a minc2.0 file 2006-05-31 Jonathan Harlap * Makefile.am - modified to build and install image_filters/extract and image_filters/byte_swap if the ACR NEMA tools are intstalled, as they are required by dicom_to_minc.pl 2006-05-18 Bert Vincent * progs/various... added config.h to source files that need it for proper operation with MINC 2.0 2006-04-19 Claude Lepage * fix duplicate instances of solve_linear_system and scaled_maximal_pivoting_gaussian_elimination in volume_io/Geometry/gaussian.c and libsrc.2. Make static. This is to avoid linker problems with minc2. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canada->Montreal Cell: +1 (514) 924 2012 From spmlxf at yahoo.com Thu Jun 29 10:49:04 2006 From: spmlxf at yahoo.com (xingfeng lee) Date: Thu, 29 Jun 2006 07:49:04 -0700 (PDT) Subject: [MINC-users] help mincblur Message-ID: <20060629144904.85940.qmail@web50113.mail.yahoo.com> Dear MINC experts, Could you help to find mincblur? I had tried to install mincblur function from MINC package, but mincblur does not work. My OS is Fedora 5. Where can i find mincblur? Thank you for your help. All the best, Li --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. From jharlap at bic.mni.mcgill.ca Thu Jun 29 10:55:40 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Thu, 29 Jun 2006 10:55:40 -0400 Subject: [MINC-users] help mincblur In-Reply-To: <20060629144904.85940.qmail@web50113.mail.yahoo.com> References: <20060629144904.85940.qmail@web50113.mail.yahoo.com> Message-ID: <44A3E9EC.9010108@bic.mni.mcgill.ca> Hi Li, mincblur comes with mni-autoreg, which you can get from http://packages.bic.mni.mcgill.ca/ Cheers, Jon xingfeng lee wrote: > Dear MINC experts, > > Could you help to find mincblur? I had tried to install mincblur function from MINC package, but mincblur does not work. My OS is Fedora 5. Where can i find mincblur? > > Thank you for your help. > > All the best, > Li > > > --------------------------------- > Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users