From minc-users@bic.mni.mcgill.ca Wed Oct 1 11:30:06 2003 From: minc-users@bic.mni.mcgill.ca (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Wed, 1 Oct 2003 12:30:06 +0200 Subject: [MINC-users] motion correcting EPI perfusion scans Message-ID: <7C29E4E1BCCD57438CA5C882106B0478783F5A@hugin.svf.au.dk> This is a multi-part message in MIME format. ------_=_NextPart_001_01C38806.FB748930 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am trying to motion correct dynamic EPI mri studies (bolus passage) = using mritoself, but with only partial success. Does anyone on the list = have any hints regarding which options to use to enhance the result? I was also wondering if anyone might have some general comments on = motion correcting bolus passage EPI studies such as general feasability, = which timepoint to register to and alternative appoaches. Thanks! 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> >   > > Thank you > > Shapoor > From minc-users@bic.mni.mcgill.ca Thu Oct 2 00:47:27 2003 From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween) Date: Wed, 1 Oct 2003 16:47:27 -0700 Subject: [MINC-users] Shapoor from Dr. Bushnell's lab In-Reply-To: <000f01c3869a$951fca40$c22bd884@medserv.mcgill.ca> Message-ID: <9D09BD25-F469-11D7-A4C2-000A958A4286@som.llu.edu> --Apple-Mail-4-845501532 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed This can be a real headache. Rick Hoge at MGH has written a utility to=20= send DICOM and translate to minc, as well as a stand-alone command line=20= converter. This works OK if all you need to do is translate T1 or=20 MPRAGE DICOMS to minc and you know exactly what's in your DICOM series.=20= The problem comes when the scanner or PACS system lumps sequences=20 together, such as first and second T2 echos, DWI/ADC and fMRI=20 sequences. I know of no utility that will parse mosaiced fMRI DICOM to=20= minc at all. The easiest way is to get *.img files off the scanner and=20= convert those. If anyone knows of a good way to do this I'd love to hear about it. Rick's email is: rhoge@nmr.mgh.harvard.edu. Jon On Monday, September 29, 2003, at 08:01 AM, Shapoor wrote: > Hi, > > =A0 > > I have files that are in dicom format, I was wondering how can I=20 > transfer them into minc format? > > =A0 > > Thank you > > Shapoor > > Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University --Apple-Mail-4-845501532 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=ISO-8859-1 This can be a real headache. Rick Hoge at MGH has written a utility to send DICOM and translate to minc, as well as a stand-alone command line converter. This works OK if all you need to do is translate T1 or MPRAGE DICOMS to minc and you know exactly what's in your DICOM series. The problem comes when the scanner or PACS system lumps sequences together, such as first and second T2 echos, DWI/ADC and fMRI sequences. I know of no utility that will parse mosaiced fMRI DICOM to minc at all. The easiest way is to get *.img files off the scanner and convert those. If anyone knows of a good way to do this I'd love to hear about it. Rick's email is: Lucida Granderhoge@nmr.mgh.harvard.edu. Jon On Monday, September 29, 2003, at 08:01 AM, Shapoor wrote: = ArialHi, Arial=A0 ArialI have files that are in dicom format, I was wondering how can I transfer them into minc = format? Arial=A0 ArialThank = you ArialShapoor Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University --Apple-Mail-4-845501532-- From minc-users@bic.mni.mcgill.ca Thu Oct 2 00:55:23 2003 From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween) Date: Wed, 1 Oct 2003 16:55:23 -0700 Subject: [MINC-users] Shapoor from Dr. Bushnell's lab In-Reply-To: Message-ID: --Apple-Mail-6-845978064 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed This will work if you have *.dcm files for a single series in a folder=20= and the *.dcm files are named in the appropriate sequential order. Many=20= indexing databases (such as the Oldenburg CTN) assigns random names to=20= files, so they are concatenated correctly by dicom_to_minc. Using the=20 mklinks2 utility can help with the filename problem (as outlined on the=20= (x)medcon website) but then, if you have a "smart" PACS that saves=20 space by concatenating different sequences into a single DICOM series,=20= dicom_to_minc will not parse these correctly. Jon On Wednesday, October 1, 2003, at 04:20 PM, Jason Lerch wrote: > Hello Shapoor, > > try: > > dicom_to_minc > > Cheers, > > Jason > > On Monday, September 29, 2003, at 11:01 AM, Shapoor wrote: > >> Hi, >> >> =A0 >> >> I have files that are in dicom format, I was wondering how can I=20 >> transfer them into minc format? >> >> =A0 >> >> Thank you >> >> Shapoor >> > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University --Apple-Mail-6-845978064 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=ISO-8859-1 This will work if you have *.dcm files for a single series in a folder and the *.dcm files are named in the appropriate sequential order. Many indexing databases (such as the Oldenburg CTN) assigns random names to files, so they are concatenated correctly by dicom_to_minc. Using the mklinks2 utility can help with the filename problem (as outlined on the (x)medcon website) but then, if you have a "smart" PACS that saves space by concatenating different sequences into a single DICOM series, dicom_to_minc will not parse these correctly. Jon On Wednesday, October 1, 2003, at 04:20 PM, Jason Lerch wrote: Hello Shapoor, try: dicom_to_minc Cheers, Jason On Monday, September 29, 2003, at 11:01 AM, Shapoor wrote: Hi, =A0 I have files that are in dicom format, I was wondering how can I transfer them into minc format? =A0 Thank you Shapoor _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University --Apple-Mail-6-845978064-- From minc-users@bic.mni.mcgill.ca Thu Oct 2 12:22:13 2003 From: minc-users@bic.mni.mcgill.ca (Jonathan Harlap) Date: Thu, 02 Oct 2003 07:22:13 -0400 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: References: Message-ID: <1065093732.2955.17.camel@zaphod> actually, dicom_to_minc will handle being told to convert more than one series-worth of data at a time, the caveat being that it may split the single series into a number of mincs (which can then be concatenated with mincconcat (or concat_mri, which is just a wrapper to simplify mincconcat usage). alternately, you can make sure to pass dicom_to_minc the files in the order they belong - this significantly helps it generate the proper set of files... i have a tool `get_dicom_info` which currently lives (at the bic) at ~jharlap/bin/get_dicom_info which is basically the dicom version of Mincinfo (capital M - deals with multiple mincs). in conjuction with my modified dicom_to_minc (changed only to add the -stdin option such that it can accept a list of dicom filenames via STDIN rather than on the command line), you can have much better control over what files are passed to get_dicom_info and in what order. for example, given a tree full of dicom files /path/to/dicom (which may contain subdirs full of dicom, and so on): `find /path/to/dicom -type f -name \*.dcm \ | ~jharlap/bin/get_dicom_info -stdin -studyuid -series -echo -image -file \ | sort -n -k1 -k2 -k3 -k4 | cut -f 5 \ | ~jharlap/bin/my_dicom_to_minc /path/to/put/mincs -stdin -notape` what all that does is, simply, find all the dicom files, get the study instance uid, series number, echo number, and image number (and filename) for each of those files, sort the list on studyuid & series & echo & image, and then pass the filenames in that new order to my_dicom_to_minc, which should generate mincs in /path/to/put/mincs. i haven't tried this on fMRI data, although i don't see any reason why it wouldn't work... i would love to hear if/how it works for fMRI - or if people at the bic want these two tools in /usr/local/mni/bin rather than in my space ;) jon On Wed, 2003-10-01 at 19:55, Jon Erik Ween wrote: > This will work if you have *.dcm files for asingle series in a folder > and the *.dcm filesare named in the appropriate sequential order. Many > indexing databases(such as the Oldenburg CTN) assigns random names to > files, so they areconcatenated correctly by dicom_to_minc. Using the > mklinks2 utilitycan help with the filename problem (as outlined on the > (x)medconwebsite) but then, if you have a "smart" PACS that saves > space byconcatenating different sequences into a single DICOM > series,dicom_to_minc will not parse these correctly. > > Jon > > On Wednesday, October 1, 2003, at 04:20 PM, Jason Lerch wrote: > > Hello Shapoor, > > try: > > dicom_to_minc > > Cheers, > > Jason > > On Monday, September 29, 2003, at 11:01 AM, Shapoor wrote: > > Hi, > > > > I have files that are in dicom format, I was wondering > how can Itransfer them into minc format? > > > > Thank you > > Shapoor > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > Jon Erik Ween, MD, MS > Assistant Professor > Cognitive and Cerebrovascular Neurology > Director, Stroke Program > Loma Linda University From minc-users@bic.mni.mcgill.ca Thu Oct 2 19:42:54 2003 From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween) Date: Thu, 2 Oct 2003 11:42:54 -0700 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: <1065093732.2955.17.camel@zaphod> Message-ID: <3C0136EE-F508-11D7-A4C2-000A958A4286@som.llu.edu> Jon Would you mind sharing get_dicom_info and my_dicom_to_minc? So far, all I've gotten out of my DICOM database is mush (and a lot of strange axis flipping and scaling problems). Thanks Jon On Thursday, October 2, 2003, at 04:22 AM, Jonathan Harlap wrote: > ~jharlap Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University From minc-users@bic.mni.mcgill.ca Fri Oct 3 13:46:03 2003 From: minc-users@bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri, 03 Oct 2003 08:46:03 -0400 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) References: <3C0136EE-F508-11D7-A4C2-000A958A4286@som.llu.edu> Message-ID: <3F7D6F8B.1060000@bic.mni.mcgill.ca> Of course - I've posted both files at www.bic.mni.mcgill.ca/~jharlap/dicom/ Good luck! :) Jon Jon Erik Ween wrote: > Jon > > Would you mind sharing get_dicom_info and my_dicom_to_minc? So far, all > I've gotten out of my DICOM database is mush (and a lot of strange axis > flipping and scaling problems). > > Thanks > > Jon > > On Thursday, October 2, 2003, at 04:22 AM, Jonathan Harlap wrote: > >> ~jharlap > > Jon Erik Ween, MD, MS > Assistant Professor > Cognitive and Cerebrovascular Neurology > Director, Stroke Program > Loma Linda University > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Oct 3 16:02:44 2003 From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween) Date: Fri, 3 Oct 2003 08:02:44 -0700 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: <3F7D6F8B.1060000@bic.mni.mcgill.ca> Message-ID: Thanks!! BTW, dicom_to_minc does not parse mosaiced DICOM files. I don't suppose the modified version will either. It works well for straight structural data, and I got it to work for concatenated DICOM files (I was missing a component ;-> ) I thought I saw a tool Peter Neelin wrote for Mosaiced files off Siemens machines, but the links I've found so far seem to be dead. If anyone knows where these live now it would be nice to know where they are. http://www.idoimaging.com/index.shtml is a good index over free imaging tools with fairly up-to-date links. Jon On Friday, October 3, 2003, at 05:46 AM, Jonathan HARLAP wrote: > Of course - I've posted both files at > www.bic.mni.mcgill.ca/~jharlap/dicom/ > > Good luck! :) > > Jon > > > Jon Erik Ween wrote: >> Jon >> Would you mind sharing get_dicom_info and my_dicom_to_minc? So far, >> all I've gotten out of my DICOM database is mush (and a lot of >> strange axis flipping and scaling problems). >> Thanks >> Jon >> On Thursday, October 2, 2003, at 04:22 AM, Jonathan Harlap wrote: >>> ~jharlap >> Jon Erik Ween, MD, MS >> Assistant Professor >> Cognitive and Cerebrovascular Neurology >> Director, Stroke Program >> Loma Linda University >> _______________________________________________ >> MINC-users@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University From minc-users@bic.mni.mcgill.ca Sat Oct 4 01:32:12 2003 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Fri, 3 Oct 2003 20:32:12 -0400 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: Message-ID: On Fri, 3 Oct 2003, Jon Erik Ween wrote: > I thought I saw a tool Peter Neelin wrote for Mosaiced files off > Siemens machines, but the links I've found so far seem to be dead. If > anyone knows where these live now it would be nice to know where they > are. I wrote a dicom client that would read mosaic'ed Siemens Vision internal format files, separate them out into normal DICOM images and do DICOM C-STORE's to a server. That code was based on Siemens headers obtained under NDA, so it cannot be freely distributed. But if you have a Siemens NDA, then you may be able to arrange something with the appropriate person at the BIC (MNI). Note that that code only works with the Vision, but it may have been adapted for use with the Sonata. I am not sure how images are currently being converted and extracted from mosaic structure at the BIC. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Sat Oct 4 01:51:23 2003 From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween) Date: Fri, 3 Oct 2003 17:51:23 -0700 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: Message-ID: Thanks Peter, I found a description of the routine and noticed it was for .img and not .dcm files! I don't know what our NDA status is with Siemens. So far no luck in getting mosaiced DICOM files parsed correctly. Jon On Friday, October 3, 2003, at 05:32 PM, Peter NEELIN wrote: > On Fri, 3 Oct 2003, Jon Erik Ween wrote: > >> I thought I saw a tool Peter Neelin wrote for Mosaiced files off >> Siemens machines, but the links I've found so far seem to be dead. If >> anyone knows where these live now it would be nice to know where they >> are. > > I wrote a dicom client that would read mosaic'ed Siemens Vision > internal > format files, separate them out into normal DICOM images and do DICOM > C-STORE's to a server. That code was based on Siemens headers obtained > under NDA, so it cannot be freely distributed. But if you have a > Siemens > NDA, then you may be able to arrange something with the appropriate > person > at the BIC (MNI). > > Note that that code only works with the Vision, but it may have been > adapted for use with the Sonata. I am not sure how images are currently > being converted and extracted from mosaic structure at the BIC. > > Peter > ---- > Peter Neelin (neelin@bic.mni.mcgill.ca) > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > Jon Erik Ween, MD, MS Assistant Professor Cognitive and Cerebrovascular Neurology Director, Stroke Program Loma Linda University From minc-users@bic.mni.mcgill.ca Thu Oct 9 19:13:46 2003 From: minc-users@bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Thu, 9 Oct 2003 14:13:46 -0400 Subject: [MINC-users] how to insert frame time info Message-ID: Hello minc users, I have a minc 4D PET data, which seems to have no frame time information in it. Actually, postf gets frozen reading it, but split frames look OK with register. mincinfo tells it has 30 frames properly as included in dimension part of its header, but I can find no frame time and width info there. How can I precisely insert frame time info to this 4D data using mincedit? Is there any other way to do this? I have worked on some other 4D PET data with no frame info in its header before, but those files didn't give me any trouble. This is why I suspect something to do out of minc's header. Thank you in advance. Best regards, Yoshi Kumakura From minc-users@bic.mni.mcgill.ca Thu Oct 9 22:00:53 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Thu, 9 Oct 2003 17:00:53 -0400 (EDT) Subject: [MINC-users] mincmorph Message-ID: Hi, who knows where I can find the mincmorph that I can install into Mac OS X or the source that I can compile? Thanks! -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Fri Oct 10 15:31:47 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Fri, 10 Oct 2003 10:31:47 -0400 Subject: [MINC-users] mincmorph In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Thu, Oct 09, 2003 at 05:00:53PM -0400 References: Message-ID: <20031010103147.D1351661@shadow.bic.mni.mcgill.ca> On Thu, Oct 09, 2003 at 05:00:53PM -0400, Andre MATOS wrote: > > Hi, > > who knows where I can find the mincmorph that I can install into Mac OS X > or the source that I can compile? Assuming you can log into one of the BIC systems, you can find the source by: cvs -d /software/source checkout minc_dev/mincmorph Otherwise, ask Andrew Janke for it. -S From minc-users@bic.mni.mcgill.ca Tue Oct 14 15:53:57 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 14 Oct 2003 10:53:57 -0400 Subject: dicom_to_minc (was Re: [MINC-users] Shapoor from Dr. Bushnell's lab) In-Reply-To: <1065093732.2955.17.camel@zaphod>; from jharlap@bic.mni.mcgill.ca on Thu, Oct 02, 2003 at 07:22:13AM -0400 References: <1065093732.2955.17.camel@zaphod> Message-ID: <20031014105356.G1672886@shadow.bic.mni.mcgill.ca> On Thu, Oct 02, 2003 at 07:22:13AM -0400, Jonathan Harlap wrote: > Mincinfo (capital M - deals with multiple mincs). For what it's worth: "mincinfo" with small "m" was patched at some point to handle multiple minc files. -S From minc-users@bic.mni.mcgill.ca Fri Oct 3 14:32:31 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Crabb) Date: Fri, 3 Oct 2003 09:32:31 -0400 (EDT) Subject: [MINC-users] Re: dicom_to_minc - and other DICOM and Minc programs. In-Reply-To: <3F7D6F8B.1060000@bic.mni.mcgill.ca> Message-ID: I maintain a database of about 130 free imaging-related programs at www.idoimaging.com - I've added a link to Jon's programs and you can also find a variety of other DICOM and Minc-related software. You can search by input and output format etc, or just plug your way through the list. In addition to Jon's get_dicom_info, I have a link to my Dicom Perl library, which I imaginatively call DICOM.pm. It's on Sourceforge and is a reasonably comprehensive Perl API for DICOM files. If anyone has or knows of other free imaging programs not in my database, I'd appreciate hearing about them so I can help steer people to them. Cheers Andy Crabb On Fri, 3 Oct 2003, Jonathan HARLAP wrote: > Of course - I've posted both files at www.bic.mni.mcgill.ca/~jharlap/dicom/ > > Good luck! :) > > Jon > > > Jon Erik Ween wrote: > > Jon > > > > Would you mind sharing get_dicom_info and my_dicom_to_minc? So far, all > > I've gotten out of my DICOM database is mush (and a lot of strange axis > > flipping and scaling problems). From stevenal@ohsu.edu Thu Oct 16 18:25:08 2003 From: stevenal@ohsu.edu (Alexander Stevens) Date: Thu, 16 Oct 2003 10:25:08 -0700 Subject: [MINC-users] Re: dicom_to_minc - and other DICOM and Minc programs. Message-ID: I will be out of the office from October 15 - 20. I will reply to you when I return. If you need to reach someone in my lab before I return, contact Matt Snodgrass (email: snodgram@ohsu.edu, phone: 503-494-6494). Alex Stevens >>> minc-users 10/03/03 06:32 >>> I maintain a database of about 130 free imaging-related programs at www.idoimaging.com - I've added a link to Jon's programs and you can also find a variety of other DICOM and Minc-related software. You can search by input and output format etc, or just plug your way through the list. In addition to Jon's get_dicom_info, I have a link to my Dicom Perl library, which I imaginatively call DICOM.pm. It's on Sourceforge and is a reasonably comprehensive Perl API for DICOM files. If anyone has or knows of other free imaging programs not in my database, I'd appreciate hearing about them so I can help steer people to them. Cheers Andy Crabb On Fri, 3 Oct 2003, Jonathan HARLAP wrote: > Of course - I've posted both files at www.bic.mni.mcgill.ca/~jharlap/dicom/ > > Good luck! :) > > Jon > > > Jon Erik Ween wrote: > > Jon > > > > Would you mind sharing get_dicom_info and my_dicom_to_minc? So far, all > > I've gotten out of my DICOM database is mush (and a lot of strange axis > > flipping and scaling problems). _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Thu Oct 23 21:33:00 2003 From: minc-users@bic.mni.mcgill.ca (Roy Yves) Date: Thu, 23 Oct 2003 16:33:00 -0400 Subject: [MINC-users] Problems installing MINC from source... Message-ID: Hi, I am installing MINC into my Linux RedHat 9, however, I run into problems not very far in the process.... the configure script. I installed, apparently successfully, netcdf (using RPM), then proceeded to install MINC from source (since RPM form MINC hung...): % rpm -i netcdf-3.5.0-linux-2.4-intel.rpm % rpm -q netcdf netcdf-3.5.0-0 The installed packages: % rpm -ql netcdf /usr/local/mni/bin /usr/local/mni/bin/ncdump /usr/local/mni/bin/ncgen /usr/local/mni/include /usr/local/mni/include/netcdf.h /usr/local/mni/lib /usr/local/mni/lib/libnetcdf.a /usr/local/mni/man /usr/local/mni/man/man1 /usr/local/mni/man/man1/ncdump.1 /usr/local/mni/man/man1/ncgen.1 /usr/local/mni/man/man3 /usr/local/mni/man/man3/netcdf.3 Things seem fine there. Then I proceed to minc installation from source: minc-1.1-1.tar.gz which I got from: http://www.bic.mni.mcgill.ca/software/distribution/ After uncompressing and extracting the files, I change to the directory minc-1.1-1, run the configure script ('./configure') which has errors: If I look at the output of ./configure I find the last two lines saying: checking for library netcdf... no configure: error: cannot find required library netcdf Well, I check the environment variable LDFLAGS and CPPFLAGS: % echo $LDFLAGS -L/usr/local/mni/lib % echo $CPPFLAGS -I/usr/local/mni/include Which seems OK since the header and library needed are in: % ls /usr/local/mni/lib/ libminc.a libnetcdf.a libvolume_io.a % ls /usr/local/mni/include/ minc.h netcdf.h time_stamp.h volume_io.h nd_loop.h ParseArgv.h volume_io voxel_loop.h config.log also contains the following lines: ... configure:17387: checking for library netcdf configure:17409: gcc -o conftest -g -O2 -L/usr/local/mni/include -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 configure:17391:20: netcdf.h: No such file or directory configure:17412: $? = 1 configure: failed program was: #line 17390 "configure" #include "confdefs.h" #include #ifdef F77_DUMMY_MAIN # ifdef __cplusplus extern "C" # endif int F77_DUMMY_MAIN() { return 1; } #endif int main () { int i = ncopen("",0); ; return 0; } configure:17427: result: no configure:17430: error: cannot find required library netcdf If you have any idea what I missed, please let me know. Thanks yves roy From minc-users@bic.mni.mcgill.ca Thu Oct 23 21:46:12 2003 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu, 23 Oct 2003 16:46:12 -0400 Subject: [MINC-users] Problems installing MINC from source... In-Reply-To: Message-ID: Yves, If you copied this in literally, somehow the flag: -L/usr/local/mni/include is present on the failing gcc command line. It's a -L instead of a -I, and so the compiler could not find netcdf.h. Could it be that the CPPFLAGS value was set incorrectly when you ran ./configure? -bert On Thu, 23 Oct 2003, Roy Yves wrote: > Hi, > > I am installing MINC into my Linux RedHat 9, however, I run into problems not very far in the process.... the configure script. I installed, apparently successfully, netcdf (using RPM), then proceeded to install MINC from source (since RPM form MINC hung...): > > % rpm -i netcdf-3.5.0-linux-2.4-intel.rpm > % rpm -q netcdf > netcdf-3.5.0-0 > > The installed packages: > > % rpm -ql netcdf > /usr/local/mni/bin > /usr/local/mni/bin/ncdump > /usr/local/mni/bin/ncgen > /usr/local/mni/include > /usr/local/mni/include/netcdf.h > /usr/local/mni/lib > /usr/local/mni/lib/libnetcdf.a > /usr/local/mni/man > /usr/local/mni/man/man1 > /usr/local/mni/man/man1/ncdump.1 > /usr/local/mni/man/man1/ncgen.1 > /usr/local/mni/man/man3 > /usr/local/mni/man/man3/netcdf.3 > > Things seem fine there. Then I proceed to minc installation from source: > > minc-1.1-1.tar.gz > > which I got from: > > http://www.bic.mni.mcgill.ca/software/distribution/ > > After uncompressing and extracting the files, I change to the directory minc-1.1-1, run the configure script ('./configure') which has errors: > > If I look at the output of ./configure I find the last two lines saying: > > checking for library netcdf... no > configure: error: cannot find required library netcdf > > Well, I check the environment variable LDFLAGS and CPPFLAGS: > > % echo $LDFLAGS > -L/usr/local/mni/lib > % echo $CPPFLAGS > -I/usr/local/mni/include > > Which seems OK since the header and library needed are in: > > % ls /usr/local/mni/lib/ > libminc.a libnetcdf.a libvolume_io.a > > % ls /usr/local/mni/include/ > minc.h netcdf.h time_stamp.h volume_io.h > nd_loop.h ParseArgv.h volume_io voxel_loop.h > > config.log also contains the following lines: > ... > configure:17387: checking for library netcdf > configure:17409: gcc -o conftest -g -O2 -L/usr/local/mni/include -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 > configure:17391:20: netcdf.h: No such file or directory > configure:17412: $? = 1 > configure: failed program was: > #line 17390 "configure" > #include "confdefs.h" > #include > #ifdef F77_DUMMY_MAIN > # ifdef __cplusplus > extern "C" > # endif > int F77_DUMMY_MAIN() { return 1; } > #endif > int > main () > { > int i = ncopen("",0); > ; > return 0; > } > configure:17427: result: no > configure:17430: error: cannot find required library netcdf > > If you have any idea what I missed, please let me know. > > Thanks > yves roy > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Fri Oct 24 17:35:06 2003 From: minc-users@bic.mni.mcgill.ca (Roy Yves) Date: Fri, 24 Oct 2003 12:35:06 -0400 Subject: [MINC-users] RE: Problem installing MINC from source Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C39A4C.C85E683D Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Bert, sorry I pasted from an old config.log file... but even with the correct = flag the reported error is the same in config.log: configure:17387: checking for library netcdf configure:17409: gcc -o conftest -g -O2 -I/usr/local/mni/include = -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 /usr/local/mni/lib/libnetcdf.a(string.o)(.text+0x62): In function = `NC_check_name': : undefined reference to `__ctype_b' collect2: ld returned 1 exit status configure:17412: $? 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In-Reply-To: Message-ID: you also can install the source of netCDF and minc and compile both, as I did in my RedHat 9 at home: 1st) NETCDF - set environment: file -> .bash_profile export CPPFLAGS='-Df2cFortran -DNDEBUG' export CC=/usr/bin/cc export CFLAGS=-O export FC=g77 export FFLAGS=-O export CXX=/usr/bin/c++ - get and compile netcdf: wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-beta.tar.gz tar -xvzf netcdf-beta.tar.gz cd netcdf-3.5.1-beta13/src ./configure --disable-shared --prefix=/usr/local/mni make make test mkdir /usr/local/mni make install 2) MINC wget ftp://ftp.bic.mni.mcgill.ca/pub/minc/minc-1.1-tar.gz tar -xvzf minc-1.1.tar.gz cd minc-1.1 ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni make make install ranlib /usr/local/mni/lib/libminc.a /usr/local/mni/lib/libvolume_io.a Andre Matos amatos@mrs.mni.mcgill.ca On Thu, 23 Oct 2003, Roy Yves wrote: > Hi, > > I am installing MINC into my Linux RedHat 9, however, I run into problems not very far in the process.... the configure script. I installed, apparently successfully, netcdf (using RPM), then proceeded to install MINC from source (since RPM form MINC hung...): > > % rpm -i netcdf-3.5.0-linux-2.4-intel.rpm > % rpm -q netcdf > netcdf-3.5.0-0 > > The installed packages: > > % rpm -ql netcdf > /usr/local/mni/bin > /usr/local/mni/bin/ncdump > /usr/local/mni/bin/ncgen > /usr/local/mni/include > /usr/local/mni/include/netcdf.h > /usr/local/mni/lib > /usr/local/mni/lib/libnetcdf.a > /usr/local/mni/man > /usr/local/mni/man/man1 > /usr/local/mni/man/man1/ncdump.1 > /usr/local/mni/man/man1/ncgen.1 > /usr/local/mni/man/man3 > /usr/local/mni/man/man3/netcdf.3 > > Things seem fine there. Then I proceed to minc installation from source: > > minc-1.1-1.tar.gz > > which I got from: > > http://www.bic.mni.mcgill.ca/software/distribution/ > > After uncompressing and extracting the files, I change to the directory minc-1.1-1, run the configure script ('./configure') which has errors: > > If I look at the output of ./configure I find the last two lines saying: > > checking for library netcdf... no > configure: error: cannot find required library netcdf > > Well, I check the environment variable LDFLAGS and CPPFLAGS: > > % echo $LDFLAGS > -L/usr/local/mni/lib > % echo $CPPFLAGS > -I/usr/local/mni/include > > Which seems OK since the header and library needed are in: > > % ls /usr/local/mni/lib/ > libminc.a libnetcdf.a libvolume_io.a > > % ls /usr/local/mni/include/ > minc.h netcdf.h time_stamp.h volume_io.h > nd_loop.h ParseArgv.h volume_io voxel_loop.h > > config.log also contains the following lines: > ... > configure:17387: checking for library netcdf > configure:17409: gcc -o conftest -g -O2 -L/usr/local/mni/include -L/usr/local/mni/lib conftest.c -lnetcdf -lm >&5 > configure:17391:20: netcdf.h: No such file or directory > configure:17412: $? = 1 > configure: failed program was: > #line 17390 "configure" > #include "confdefs.h" > #include > #ifdef F77_DUMMY_MAIN > # ifdef __cplusplus > extern "C" > # endif > int F77_DUMMY_MAIN() { return 1; } > #endif > int > main () > { > int i = ncopen("",0); > ; > return 0; > } > configure:17427: result: no > configure:17430: error: cannot find required library netcdf > > If you have any idea what I missed, please let me know. > > Thanks > yves roy > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Fri Oct 31 23:43:39 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 31 Oct 2003 18:43:39 -0500 Subject: [MINC-users] MINC-workshop, November 19, 2003 Message-ID: <0D625E12-0BFC-11D8-9398-000A95DBBFD8@bic.mni.mcgill.ca> Hello all, We hereby invite everyone to a free workshop on the MINC toolkit and other brain imaging tools developed at the Brain Imaging Centre. It will be held in the afternoon of the 19th of November at the Montreal Neurological Institute, Room W201. This workshop is for anyone who uses - or would like to begin using - the tools developed at the MNI. The talks will be kept general and should serve as an introduction to the analysis techniques available, be they for structural images or fMRI. Each talk will allow time for any questions. For those interested we will also be providing a CD-ROM with the freely available parts of our software toolkit. The current (though subject change) schedule is: 19th November, W201 Killam Lecture Theatre 1.00pm Alan Evans Introduction to the workshop 1.05pm John Sled An Introduction to MINC (1.x) 1.30pm Jason Lerch Pipelines: tools to analyse structural MRI data 2.00pm Louis Collins Registration techniques and issues. 2.30pm Steve Robbins An overview of our command line tools 3.00pm Vitamin C break: Coffee, Cookies, Coke and CD-ROMS 3.30pm Keith Worsley: fMRI analysis and fmristat 4.00pm Andrew Janke Getting your data into MINC and other MINC tools 4.30pm Robert Vincent MINC 2.0: plans for the future Please do not hesitate to write if you have any questions. Hope to see you there! The MINC-workshop organizers. P.S. My apologies for cross-posting to two lists.