From claude at bic.mni.mcgill.ca Mon Dec 1 16:53:25 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Mon, 1 Dec 2008 16:53:25 -0500 (EST) Subject: [MINC-users] mnc2nii dumps core References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Hi Yoshi, I looked at your problem with mnc2nii with a colleague. I have two suggestions for you. 1 - update your minc tools and redo the operation "mincreshape -dimrange time=2,1" to extract the time point with the latest minc, then do the conversion. 2 - still use the old version, but specify "mincreshape -dimrange time=2" (no 2,1). Then redo the conversion with mnc2nii. Option (2) might work but I'm not sure. Option (1) seems to work here for us. This was likely a bug in minc when copying the header. mnc2nii alone will not work if its input has been extracted with the old version of mincreshape. Please try this and let me know if it works. Yours, Claude From ikonomidou at ieee.org Tue Dec 2 17:29:02 2008 From: ikonomidou at ieee.org (Vasiliki N. Ikonomidou) Date: Tue, 02 Dec 2008 17:29:02 -0500 Subject: [MINC-users] Minctracc problem Message-ID: <4935B6AE.5090608@ieee.org> Hi everybody, I am trying to register a T2-weighted image to an IR-SPGR one, using the following command for calculating the transform: minctracc -est_center -est_translations -lsq7 -mi t2.mnc spgr.mnc t2_2_spgr.xfm -clobber This worked out fine for most of my datasets, but for four of them, after getting the message WARNING: source volume not UNSIGNED_BYTE, will do conversion now. Converting: ............................................ (which takes forever) it gives the message Not implemented yet in cache_volume_range_has_changed() WARNING: target volume not UNSIGNED_BYTE, will do conversion now. and then minctracc quits without creating the .xfm file. mri_info gives both source and target volumes to be SHORT(4). minctracc works if I change the cost criterion, but the results are off. Any suggestions as to what I might be doing wrong? Thank you, Vicky From claude at bic.mni.mcgill.ca Tue Dec 2 17:42:44 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 2 Dec 2008 17:42:44 -0500 (EST) Subject: [MINC-users] Minctracc problem Message-ID: <200812022242.mB2Mgiqw4989543@yorick.bic.mni.mcgill.ca> Hi, Some wild suggestion... Set this environment variable in your shell: VOLUME_CACHE_THRESHOLD=-1 If you are using an old version of minc2 (2.0.13 or before), then internal compression was painfully slow. minctracc -version minccalc -version will tell me the version of your minc installation. Often, we use scripts for registration, which is a sequence of calls to minctracc following an hierarchical approach with large to small steps. Also, I would suggest -lsq6 for same subject scans since a scaling may change the size of the head. I believe you want to do only rotations and translations here. If you still have problems, you can contact me (with the inputs). Yours, Claude > Hi everybody, > > I am trying to register a T2-weighted image to an IR-SPGR one, using the > following command for calculating the transform: > minctracc -est_center -est_translations -lsq7 -mi t2.mnc spgr.mnc > t2_2_spgr.xfm -clobber > This worked out fine for most of my datasets, but for four of them, > after getting the message > > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > Converting: ............................................ (which > takes forever) > > it gives the message > > Not implemented yet in cache_volume_range_has_changed() > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > > and then minctracc quits without creating the .xfm file. > mri_info gives both source and target volumes to be SHORT(4). minctracc > works if I change the cost criterion, but the results are off. > > Any suggestions as to what I might be doing wrong? > > Thank you, > > Vicky > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Tue Dec 2 17:44:54 2008 From: vladimir.fonov at gmail.com (Vladimir Fonov) Date: Tue, 02 Dec 2008 17:44:54 -0500 Subject: [MINC-users] Minctracc problem In-Reply-To: <4935B6AE.5090608@ieee.org> References: <4935B6AE.5090608@ieee.org> Message-ID: <4935BA66.70002@gmail.com> Hello, Vasiliki N. Ikonomidou wrote: > I am trying to register a T2-weighted image to an IR-SPGR one, using the > following command for calculating the transform: > minctracc -est_center -est_translations -lsq7 -mi t2.mnc spgr.mnc > t2_2_spgr.xfm -clobber > This worked out fine for most of my datasets, but for four of them, > after getting the message > > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > Converting: ............................................ (which > takes forever) This looks like a bug in the minctracc, which version are you using ? (run minctracc -version). > it gives the message > > Not implemented yet in cache_volume_range_has_changed() > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > > and then minctracc quits without creating the .xfm file. > mri_info gives both source and target volumes to be SHORT(4). minctracc > works if I change the cost criterion, but the results are off. > > Any suggestions as to what I might be doing wrong? You can try converting problematic images into byte first, and see if minctracc will work: mincreshape -unsigned -byte t2.mnc t2_byte.mnc mincreshape -unsigned -byte spgr.mnc spgr_byte.mnc minctracc -est_center -est_translations -lsq7 -mi t2_byte.mnc spgr_byte.mnc t2_2_spgr.xfm -clobber -- Best regards, Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com From claude at bic.mni.mcgill.ca Tue Dec 2 17:55:44 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 2 Dec 2008 17:55:44 -0500 (EST) Subject: [MINC-users] Minctracc problem References: <4935B6AE.5090608@ieee.org> Message-ID: <200812022255.mB2MtisZ5053788@yorick.bic.mni.mcgill.ca> Hi, Another suggestion: When you installed mni_autoreg, you should have with it a perl script named mritoself that came with it (check subdirectory perl/). Try the following: mritoself -clobber -nothreshold -mi -lsq6 t2.mnc spgr.mnc t2_2_spgr.xfm This should work on a recent version of minctracc and minc. bye Claude > Hello, > > Vasiliki N. Ikonomidou wrote: > > I am trying to register a T2-weighted image to an IR-SPGR one, using the > > following command for calculating the transform: > > minctracc -est_center -est_translations -lsq7 -mi t2.mnc spgr.mnc > > t2_2_spgr.xfm -clobber > > This worked out fine for most of my datasets, but for four of them, > > after getting the message > > > > WARNING: source volume not UNSIGNED_BYTE, will do conversion now. > > Converting: ............................................ (which > > takes forever) > This looks like a bug in the minctracc, which version are you using ? > (run minctracc -version). > > > > it gives the message > > > > Not implemented yet in cache_volume_range_has_changed() > > WARNING: target volume not UNSIGNED_BYTE, will do conversion now. > > > > and then minctracc quits without creating the .xfm file. > > mri_info gives both source and target volumes to be SHORT(4). minctracc > > works if I change the cost criterion, but the results are off. > > > > Any suggestions as to what I might be doing wrong? > You can try converting problematic images into byte first, and see if > minctracc will work: > > mincreshape -unsigned -byte t2.mnc t2_byte.mnc > mincreshape -unsigned -byte spgr.mnc spgr_byte.mnc > minctracc -est_center -est_translations -lsq7 -mi t2_byte.mnc > spgr_byte.mnc t2_2_spgr.xfm -clobber > > -- > Best regards, > Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From ikonomidou at ieee.org Tue Dec 2 18:05:21 2008 From: ikonomidou at ieee.org (Vasiliki N. Ikonomidou) Date: Tue, 02 Dec 2008 18:05:21 -0500 Subject: [MINC-users] Minctracc problem In-Reply-To: <4935BA66.70002@gmail.com> References: <4935B6AE.5090608@ieee.org> <4935BA66.70002@gmail.com> Message-ID: <4935BF31.20403@ieee.org> Thank you very much, changing to byte outside of minctracc solved the problem I had. The version that is installed on my machine is the one that comes with the Freesurfer 4.1.0 distribution, for minctracc it gives The program <...> was built from: Package MNI AutoReg, version 0.98r, compiled by nicks at fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:25:48 so I guess it's a fairly old one... Again, thanks a lot, Vicky Vladimir Fonov wrote: > Hello, > > Vasiliki N. Ikonomidou wrote: > >> I am trying to register a T2-weighted image to an IR-SPGR one, using the >> following command for calculating the transform: >> minctracc -est_center -est_translations -lsq7 -mi t2.mnc spgr.mnc >> t2_2_spgr.xfm -clobber >> This worked out fine for most of my datasets, but for four of them, >> after getting the message >> >> WARNING: source volume not UNSIGNED_BYTE, will do conversion now. >> Converting: ............................................ (which >> takes forever) >> > This looks like a bug in the minctracc, which version are you using ? > (run minctracc -version). > > > >> it gives the message >> >> Not implemented yet in cache_volume_range_has_changed() >> WARNING: target volume not UNSIGNED_BYTE, will do conversion now. >> >> and then minctracc quits without creating the .xfm file. >> mri_info gives both source and target volumes to be SHORT(4). minctracc >> works if I change the cost criterion, but the results are off. >> >> Any suggestions as to what I might be doing wrong? >> > You can try converting problematic images into byte first, and see if > minctracc will work: > > mincreshape -unsigned -byte t2.mnc t2_byte.mnc > mincreshape -unsigned -byte spgr.mnc spgr_byte.mnc > minctracc -est_center -est_translations -lsq7 -mi t2_byte.mnc > spgr_byte.mnc t2_2_spgr.xfm -clobber > > From kumakura at bic.mni.mcgill.ca Wed Dec 3 20:05:10 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Wed, 3 Dec 2008 20:05:10 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Message-ID: Hello Claude, Thanks a lot for your suggestions. Since my collaborator in Tokyo has the mnc file that underwnet "mincreshape -dimrange time=2,1", I will get it from him and try your suggestins. (I just have the mnc file that I tested for mnc2nii and left in BIC's scratch space.) I will surely let you know if it works. Best regards, Yoshi On Mon, 1 Dec 2008, Claude LEPAGE wrote: > Hi Yoshi, > > I looked at your problem with mnc2nii with a colleague. I have two suggestions > for you. > > 1 - update your minc tools and redo the operation "mincreshape -dimrange time=2,1" > to extract the time point with the latest minc, then do the conversion. > > 2 - still use the old version, but specify "mincreshape -dimrange time=2" (no > 2,1). Then redo the conversion with mnc2nii. > > Option (2) might work but I'm not sure. Option (1) seems to work here for us. > This was likely a bug in minc when copying the header. mnc2nii alone will not > work if its input has been extracted with the old version of mincreshape. > > Please try this and let me know if it works. > > Yours, > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Wed Dec 3 20:08:32 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 4 Dec 2008 12:08:32 +1100 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Message-ID: > Since my collaborator in Tokyo has the mnc file that underwnet > "mincreshape -dimrange time=2,1", I will get it from him and try your suggestins. (I just have the mnc file that I > tested for mnc2nii and left in BIC's scratch space.) I will surely let you > know if it works. As a quick test you should be able to do this and just cut the time dimension out for now: $ mincreshape -dimrange time=0,0 in.mnc out.mnc -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From kumakura at bic.mni.mcgill.ca Thu Dec 4 01:13:05 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Thu, 4 Dec 2008 01:13:05 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Message-ID: Hi Cluade and Andrew, Option (2) works! I've learned that "-dimrange time=2,1" followed by mincaverage to remove time dimension is redundant. Thank you, Yoshi On Mon, 1 Dec 2008, Claude LEPAGE wrote: > Hi Yoshi, > > I looked at your problem with mnc2nii with a colleague. I have two suggestions > for you. > > 1 - update your minc tools and redo the operation "mincreshape -dimrange time=2,1" > to extract the time point with the latest minc, then do the conversion. > > 2 - still use the old version, but specify "mincreshape -dimrange time=2" (no > 2,1). Then redo the conversion with mnc2nii. > > Option (2) might work but I'm not sure. Option (1) seems to work here for us. > This was likely a bug in minc when copying the header. mnc2nii alone will not > work if its input has been extracted with the old version of mincreshape. > > Please try this and let me know if it works. > > Yours, > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Tue Dec 9 14:44:31 2008 From: vladimir.fonov at gmail.com (Vladimir Fonov) Date: Tue, 09 Dec 2008 14:44:31 -0500 Subject: [MINC-users] minctracc - different results on 32 vs 64 bit Message-ID: <493ECA9F.6090803@gmail.com> Hello, we came a cross an interesting behavior of minctracc - it produces slightly different results depending on the architecture. I run mritotal on 9 subjects and the differences between 32 and 64 bit version runs are up to 0.3 degree in determining rotations, 0.1 mm in terms of shifts and up to 0.01 in scale. -- Best regards, Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com From claude at bic.mni.mcgill.ca Tue Dec 9 15:14:54 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 9 Dec 2008 15:14:54 -0500 (EST) Subject: [MINC-users] minctracc - different results on 32 vs 64 bit Message-ID: <200812092014.mB9KEsCN5468130@yorick.bic.mni.mcgill.ca> Hi Vlad, > we came a cross an interesting behavior of minctracc - it produces > slightly different results depending on the architecture. > > I run mritotal on 9 subjects and the differences between 32 and 64 bit > version runs are up to 0.3 degree in determining rotations, 0.1 mm in > terms of shifts and up to 0.01 in scale. I know this. I once told Louis about it. It is due to rounding errors when determining the degrees of freedom. If you run minctracc with -debug, you will see that the lattice size in x, y, z may be off by 1 in 32 vs 64 bits, thus causing different number of sampling points and registration. Of course, you can go and dig into the source code if you want to fix it, but to be fair, I don't know which one of the two results, 32 or 64 bits, is the correct one. Claude From jween at klaru-baycrest.on.ca Wed Dec 10 22:30:19 2008 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 10 Dec 2008 22:30:19 -0500 Subject: [MINC-users] Skull stripping In-Reply-To: References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Message-ID: <64D6F74A-A1FF-43FE-8309-B87B0E952602@klaru-baycrest.on.ca> Hi Sorry for a newbee question, but no luck Google-ing this: Does anyone have a link or howto on skull stripping MRIs in .mnc format? Bouncing back and forth between mnc, nifti and analyze etc often gets coordinate spaces confused, particularly with batch processing in pipelines. Any help would be much appreciated! Cheers Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. From claude at bic.mni.mcgill.ca Wed Dec 10 23:07:31 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Wed, 10 Dec 2008 23:07:31 -0500 (EST) Subject: [MINC-users] Skull stripping References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> Message-ID: <200812110407.mBB47VV55594015@yorick.bic.mni.mcgill.ca> Hello, > Sorry for a newbee question, but no luck Google-ing this: Does anyone > have a link or howto on skull stripping MRIs in .mnc format? Bouncing > back and forth between mnc, nifti and analyze etc often gets > coordinate spaces confused, particularly with batch processing in > pipelines. Any help would be much appreciated! Of course, there is a tool. It is basically FSL bet with a minc interface and a few other modifications. It is available on demand, thus I don't think I want to post the link here. I will verify tomorrow and send you the link in a private communication. Remember that this tool is based on FSL bet, so you will have to acknowledge Stephen Smith's paper in your work. Agree? Yours, Claude From jween at klaru-baycrest.on.ca Thu Dec 11 08:49:43 2008 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Thu, 11 Dec 2008 08:49:43 -0500 Subject: [MINC-users] Skull stripping In-Reply-To: <200812110407.mBB47VV55594015@yorick.bic.mni.mcgill.ca> References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> <200812012153.mB1LrP4G5060337@yorick.bic.mni.mcgill.ca> <200812110407.mBB47VV55594015@yorick.bic.mni.mcgill.ca> Message-ID: Claude I just noticed that you are on the CIVET team and work with Alan Evans. It may interest you to know that Alan and I have met as Stephen Strother and I are working with him to implement the MNI framework here at Rotman/KLARU. My understanding is that the database is up and running, but I don't know the status of the processing tools in BIC/mnc here. I'm trying to get a pipeline set up to do lesion analysis (stroke), VBM and VLSM. So any suggestions you could make regarding the getting the BIC/mnc tools or CIVET framework going here would be greatly appreciated! (Another interesting factoid: I've been messing with MNI tools since my early days as a resident in the early '90s... They just don't seem to go away!) Cheers Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 10-Dec-08, at 11:07 PM, Claude LEPAGE wrote: > Hello, > >> Sorry for a newbee question, but no luck Google-ing this: Does anyone >> have a link or howto on skull stripping MRIs in .mnc format? Bouncing >> back and forth between mnc, nifti and analyze etc often gets >> coordinate spaces confused, particularly with batch processing in >> pipelines. Any help would be much appreciated! > > Of course, there is a tool. It is basically FSL bet with a minc > interface and a few other modifications. It is available on demand, > thus I don't think I want to post the link here. I will verify > tomorrow and send you the link in a private communication. Remember > that this tool is based on FSL bet, so you will have to acknowledge > Stephen Smith's paper in your work. Agree? > > Yours, > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From louis.collins at mcgill.ca Thu Dec 11 16:53:43 2008 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Thu, 11 Dec 2008 16:53:43 -0500 Subject: [MINC-users] minctracc - different results on 32 vs 64 bit In-Reply-To: <493ECA9F.6090803@gmail.com> References: <493ECA9F.6090803@gmail.com> Message-ID: An interesting confirmation: I've just run automated HC segmentation with MAC (64b) and Linux (32b) implementations of the pipeline using non-linear registration of minctracc. I find that on average over 20 subjects, on both left and right HC, there is a 2% average magnitude difference in label volume between the 32bit and 64bit pipelines. (and there is a 0.5% bias in the magnitude). However, the correlation between the 32bit and 64bit HC volumes is 0.990 - so the results are similar, but not the same. A potential 'gotcha' to worry about. -Louis On Dec 9, 2008, at 2:44 PM, Vladimir Fonov wrote: > Hello, > > we came a cross an interesting behavior of minctracc - it produces > slightly different results depending on the architecture. > > I run mritotal on 9 subjects and the differences between 32 and 64 bit > version runs are up to 0.3 degree in determining rotations, 0.1 mm in > terms of shifts and up to 0.01 in scale. > > -- > Best regards, > Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From k.diaz99 at gmail.com Sat Dec 20 12:02:06 2008 From: k.diaz99 at gmail.com (Camilo Diaz) Date: Sat, 20 Dec 2008 12:02:06 -0500 Subject: [MINC-users] mnc2nii Message-ID: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> Hello List: Here's the deal: Im trying to use on of the images from brainweb for a VBM (SPM5) experiment, so i tried to use the mnc2nii, but..... , well, i tried to build it, but, i didn't know it needs so many librarys ( HDF5, NETCDF..... ), so , it is taking me a while to get the mnc2nii.exe. Does anyone have this mnc2nii.exe already that i can use ? or, Does anyone know a way to make this convertion ( mnc to nii ) more easily? Thank you Camilo -- Kmilo From a.janke at gmail.com Sun Dec 21 18:20:10 2008 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 22 Dec 2008 10:20:10 +1100 Subject: [MINC-users] mnc2nii In-Reply-To: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> References: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> Message-ID: Hi Camilo, > Im trying to use on of the images from brainweb for a VBM (SPM5) experiment, > so i tried to use the mnc2nii, but..... , well, i tried to build it, but, i > didn't know it needs so many librarys ( HDF5, NETCDF..... ), so , it is > taking me a while to get the mnc2nii.exe. I am guessing from the .exe extension above that you are trying a native build on windows? or using cygwin? There are some win32 builds here: http://packages.bic.mni.mcgill.ca/win32 -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From k.diaz99 at gmail.com Mon Dec 22 10:24:57 2008 From: k.diaz99 at gmail.com (Camilo Diaz) Date: Mon, 22 Dec 2008 10:24:57 -0500 Subject: [MINC-users] mnc2nii In-Reply-To: References: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> Message-ID: <75a372b20812220724x2f1e2f9ewb73553cb203bb023@mail.gmail.com> Hello Andrew: I installed the minc 2.11 and minc 2.15 that are in the link you sent me, but i couldn't find the minc2niff.exe that is te one that i need. Do you have the min2niff.exe or a place were i can find it ? Thank you. Camilo On Sun, Dec 21, 2008 at 6:20 PM, Andrew Janke wrote: > Hi Camilo, > > > Im trying to use on of the images from brainweb for a VBM (SPM5) > experiment, > > so i tried to use the mnc2nii, but..... , well, i tried to build it, > but, i > > didn't know it needs so many librarys ( HDF5, NETCDF..... ), so , it is > > taking me a while to get the mnc2nii.exe. > > I am guessing from the .exe extension above that you are trying a > native build on windows? or using cygwin? There are some win32 builds > here: > > http://packages.bic.mni.mcgill.ca/win32 > > > -- > Andrew Janke - andrew.janke at anu.edu.au > Department of Geriatric Medicine, ANU > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Kmilo From a.janke at gmail.com Mon Dec 22 16:04:16 2008 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 23 Dec 2008 07:04:16 +1000 Subject: [MINC-users] mnc2nii In-Reply-To: <75a372b20812220724x2f1e2f9ewb73553cb203bb023@mail.gmail.com> References: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> <75a372b20812220724x2f1e2f9ewb73553cb203bb023@mail.gmail.com> Message-ID: On Tue, Dec 23, 2008 at 1:24 AM, Camilo Diaz wrote: > I installed the minc 2.11 and minc 2.15 that are in the link you sent me, > but i couldn't find the minc2niff.exe that is te one that i need. > Do you have the min2niff.exe or a place were i can find it ? Hi, You should be looking for mnc2nii.exe I am not sure where the installer puts these but Leila will know as she made it. a From baghdadi at phenogenomics.ca Mon Dec 22 16:14:47 2008 From: baghdadi at phenogenomics.ca (Leila Baghdadi) Date: Mon, 22 Dec 2008 16:14:47 -0500 Subject: [MINC-users] mnc2nii In-Reply-To: References: <75a372b20812200902l4f006467s674fa1c816f356f6@mail.gmail.com> Message-ID: <1229980487.7477.5.camel@mouse30.phenogenomics.ca> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20081222/3639a68b/attachment.txt From k.diaz99 at gmail.com Mon Dec 22 17:00:12 2008 From: k.diaz99 at gmail.com (Camilo Diaz) Date: Mon, 22 Dec 2008 17:00:12 -0500 Subject: [MINC-users] mnc2nii In-Reply-To: <1229980487.7477.5.camel@mouse30.phenogenomics.ca> References: <1229980487.7477.5.camel@mouse30.phenogenomics.ca> Message-ID: <75a372b20812221400q5a33919bpb05853d4eaaf4e96@mail.gmail.com> Ok Thank you so much for your help On Mon, Dec 22, 2008 at 4:14 PM, Leila Baghdadi wrote: > Hi guys > > sorry about this but the only conversion program that I have included in > my windows installer is vff2mnc and that's because we needed it here. > I did try adding the rest of the conversion programs but some of them > gave me a lot of trouble, > for instance the dicom stuff, I could not find a matching windows header > for all the sockets and all and so I gave up. > > I am not sure about mnc2nii, I can check that out and see if I can port > it to windows. > > This is all because I try to reduce my involvement with windows to the > minimum possible! > > Leila > > p.s will let you know soon if I can port mnc2nii > > > On Tue, 2008-12-23 at 07:04 +1000, Andrew Janke wrote: > > On Tue, Dec 23, 2008 at 1:24 AM, Camilo Diaz wrote: > > > I installed the minc 2.11 and minc 2.15 that are in the link you sent > me, > > > but i couldn't find the minc2niff.exe that is te one that i need. > > > Do you have the min2niff.exe or a place were i can find it ? > > > > Hi, You should be looking for mnc2nii.exe I am not sure where the > > installer puts these but Leila will know as she made it. > > > > > > a > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Kmilo From paulclyon at gmail.com Tue Dec 23 16:11:33 2008 From: paulclyon at gmail.com (Paul Lyon) Date: Tue, 23 Dec 2008 21:11:33 +0000 Subject: [MINC-users] Accessing 4D image data in MINC / Normalisation Message-ID: <4bd8ecf80812231311o5892dc82kc2b4e705cf93ab75@mail.gmail.com> Dear MINC User Community I have been developing a piece of software to analyse neuro PET images under MINC 1.5 and it is nearly complete other than one outstanding problem that I have. The PET images that I am using are converted from MINC and have a 4th (time) dimension and are converted from ECAT using ecattominc. I need to manipulate data across the temporal aspect and so I would like to load in the entire 4D image into memory space at once. The problem is I do not know how to access the image data voxels for a time, t. As a result I am working around by extracting frame by frame, writing to temporary file, and reading back in again. This is inefficient and worse still is causing me all sorts of bother with normalisation such that my voxel values become scewed. Please can someone tell me how to access / index 4D image voxel data directly in MINC 1.5. At present I am using the following code to assign an index 4D array of image data called voxel[][][][] by first pulling out a frame then a slice of that frame and making new assignments: signed short int* image; ... image = malloc(vol4d->nrows * vol4d->ncols * sizeof(*image)); for (t=0; tnframes; t++) { /* Extract the frame and perform the copy */ extractFrame(mincId, icvId, framefile, vol4d, &vol3d, t); openFrame(framefile, NC_NOWRITE, &tempIcvId, &tempMincId, &vol3d); for (i=0; inrows; j++) { for (k=0; kncols; k++) { /* Make the assignment */ index = j*vol4d->ncols+k; vol4d->voxel[t][i][j][k]=image[index]; ... } } } } Where the methods extractFrame(), openFrame() and getSlice() are methods written by myself which save a frame to file, open that frame for reading and read a slice from that file respectively. In the struct for the Volume4d datatype I have: signed short int ****voxel; Surely there must be an easier and cleaner way? Any help with this matter / relevant documentation would be very much appreciated. Also if anyone has any knowledge of the normalisation process which goes on in loading images under MINC 1.5 I would love to discuss with you. I could potentially stick with my current workaround and solve the problem by modifying the normalisation parameters. Dr. Paul Lyon (paulclyon at gmail.com) University of Nottingham, England Working under Dr. Alex Theil, MNI From rupe.brooks at gmail.com Tue Dec 23 20:55:55 2008 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 23 Dec 2008 20:55:55 -0500 Subject: [MINC-users] mnc2nii In-Reply-To: <75a372b20812221400q5a33919bpb05853d4eaaf4e96@mail.gmail.com> References: <1229980487.7477.5.camel@mouse30.phenogenomics.ca> <75a372b20812221400q5a33919bpb05853d4eaaf4e96@mail.gmail.com> Message-ID: Hi, Sorry i didnt get into this conversation sooner, i only follow along from time to time. I have posted minc windows binaries on my web page a while ago. www.rupertbrooks.ca/code.html I see a mnc2nii.exe lurking in there. I have high hopes it works, but i never tested it because i dont have a test case for it. Please let me know if you try it and if it works or not. (Note that I will be away from email for the next few days) Cheers Rupert B. On Mon, Dec 22, 2008 at 5:00 PM, Camilo Diaz wrote: > Ok > > Thank you so much for your help > > On Mon, Dec 22, 2008 at 4:14 PM, Leila Baghdadi > wrote: > >> Hi guys >> >> sorry about this but the only conversion program that I have included in >> my windows installer is vff2mnc and that's because we needed it here. >> I did try adding the rest of the conversion programs but some of them >> gave me a lot of trouble, >> for instance the dicom stuff, I could not find a matching windows header >> for all the sockets and all and so I gave up. >> >> I am not sure about mnc2nii, I can check that out and see if I can port >> it to windows. >> >> This is all because I try to reduce my involvement with windows to the >> minimum possible! >> >> Leila >> >> p.s will let you know soon if I can port mnc2nii >> >> >> On Tue, 2008-12-23 at 07:04 +1000, Andrew Janke wrote: >> > On Tue, Dec 23, 2008 at 1:24 AM, Camilo Diaz wrote: >> > > I installed the minc 2.11 and minc 2.15 that are in the link you sent >> me, >> > > but i couldn't find the minc2niff.exe that is te one that i need. >> > > Do you have the min2niff.exe or a place were i can find it ? >> > >> > Hi, You should be looking for mnc2nii.exe I am not sure where the >> > installer puts these but Leila will know as she made it. >> > >> > >> > a >> > _______________________________________________ >> > MINC-users at bic.mni.mcgill.ca >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > Kmilo > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks, Ph. D. Attach? de recherches | Research Associate Simulation des Mat?riaux D?formables | Simulation of Deformable Materials Institut des mat?riaux industriels | Industrial Materials Institute Conseil national de recherches Canada | National Research Council Canada 75, de Mortagne, Boucherville, Qu?bec, Canada, J4B 6Y4 Gouvernement du Canada | Government of Canada From rcomeau at mac.com Sat Dec 27 16:28:05 2008 From: rcomeau at mac.com (Roch M. Comeau) Date: Sat, 27 Dec 2008 16:28:05 -0500 Subject: [MINC-users] missing model files for mritotal (on OS X) Message-ID: <41A54DB2-6923-413E-B960-85E3BD500409@mac.com> Hi, I recently installed the latest bic_tools using Alex's 64bit tar file. I also installed Greg's GetOptTabular and tried to use mritotal and got the following erreo: /usr/local/bic/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist /usr/local/bic/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist /usr/local/bic/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist /usr/local/bic/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist /usr/local/bic/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist /usr/local/bic/bin/../share/mni_autoreg/average_305_headmask.mnc does not exist I tried to instal the average_305 based models by downloading the mni_models_average305-lin-1.0 and installing that, unfortunately they don't create/install the missing files. Anyone know what I am missing? Thanks, Roch -- Roch M. Comeau, Ph.D. Rogue Research Inc. 4398 St-Laurent, Suite 206 Montreal, QC, Canada, H2W 1Z5 Phone:(514)284-3888 Fax: (514)284-6750 roch at rogue-research.com www.rogue-research.com From rcomeau at mac.com Sat Dec 27 16:35:52 2008 From: rcomeau at mac.com (Roch M. Comeau) Date: Sat, 27 Dec 2008 16:35:52 -0500 Subject: [MINC-users] missing model files for mritotal (on OS X) In-Reply-To: <41A54DB2-6923-413E-B960-85E3BD500409@mac.com> References: <41A54DB2-6923-413E-B960-85E3BD500409@mac.com> Message-ID: Answer to my own question: Install mni_autoreg_model-1.03 Roch On 27-Dec-08, at 4:28 PM, Roch M. Comeau wrote: > Hi, > > I recently installed the latest bic_tools using Alex's 64bit tar file. > I also installed Greg's GetOptTabular and tried to use mritotal and > got the following erreo: > > /usr/local/bic/bin/../share/mni_autoreg/average_305_16_blur.mnc does > not exist > /usr/local/bic/bin/../share/mni_autoreg/average_305_8_blur.mnc does > not exist > /usr/local/bic/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does > not exist > /usr/local/bic/bin/../share/mni_autoreg/average_305_16_mask.mnc does > not exist > /usr/local/bic/bin/../share/mni_autoreg/average_305_8_mask.mnc does > not exist > /usr/local/bic/bin/../share/mni_autoreg/average_305_headmask.mnc does > not exist > > I tried to instal the average_305 based models by downloading the > mni_models_average305-lin-1.0 and installing that, unfortunately they > don't create/install the missing files. > > Anyone know what I am missing? > > Thanks, > > Roch > > -- > Roch M. Comeau, Ph.D. > Rogue Research Inc. > 4398 St-Laurent, Suite 206 > Montreal, QC, Canada, H2W 1Z5 > Phone:(514)284-3888 > Fax: (514)284-6750 > roch at rogue-research.com > www.rogue-research.com > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Wed Dec 31 06:32:28 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 31 Dec 2008 22:32:28 +1100 Subject: [MINC-users] missing model files for mritotal (on OS X) In-Reply-To: References: <41A54DB2-6923-413E-B960-85E3BD500409@mac.com> Message-ID: On Sun, Dec 28, 2008 at 8:35 AM, Roch M. Comeau wrote: > Answer to my own question: > > Install mni_autoreg_model-1.03 Ah, back from holidays and I see I have been beaten to the punch. Yes the model you are talking about is in that (old) package. Unfortunately we have decided to stick with not changing mritotal so that things dont just break elsewhere when the default model was changed. Ideally you should be using mritotal with an ICBM model like this: mritotal -model icbm_avg_152_t1_tal_lin ... a From a.janke at gmail.com Wed Dec 31 06:40:17 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 31 Dec 2008 22:40:17 +1100 Subject: [MINC-users] Accessing 4D image data in MINC / Normalisation In-Reply-To: <4bd8ecf80812231311o5892dc82kc2b4e705cf93ab75@mail.gmail.com> References: <4bd8ecf80812231311o5892dc82kc2b4e705cf93ab75@mail.gmail.com> Message-ID: Hi Paul, On Wed, Dec 24, 2008 at 8:11 AM, Paul Lyon wrote: > I have been developing a piece of software to analyse neuro PET images > under MINC 1.5 and it is nearly complete other than one outstanding > problem that I have. > > The PET images that I am using are converted from MINC and have a 4th > (time) dimension and are converted from ECAT using ecattominc. If you want a simple way to read things all in and then out and not worry about the voxel data type, then if you are sticking with MINC 1.X I have attached a few files that should give some examples of how to do this with volume_io. The first gives a quick howto with volume_io, the second is a makefile to suit and the third is not as well commented but shows what to do to extend the first example to 4D. the volume_io manuals and the likes are here: http://en.wikibooks.org/wiki/MINC/Reference/MINC1-volumeio-programmers-reference However I would recommend that you use MINC 2.0 instead but it is probably a little late for that now! There are some examples for that here: http://en.wikibooks.org/wiki/MINC/Tutorials#Programming_with_the_MINC_toolkit Good luck! -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883