From maxime.descoteaux at gmail.com Sat Mar 7 14:09:57 2015 From: maxime.descoteaux at gmail.com (Maxime Descoteaux) Date: Sat, 7 Mar 2015 14:09:57 -0500 Subject: [MINC-users] Call for participation: Fiber Tractography Challenge at ISMRM 2015 Message-ID: [SORRY IF THIS IS A DUPLICATE] Dear Colleagues: The Diffusion Study Group is sponsoring a novel Fiber Tractography Challenge to stimulate an interactive discussion on diffusion reconstruction and tractography methods at this year?s study group meeting at ISMRM 2015 in Toronto. The Challenge will use a simulated but highly realistic diffusion-weighted dataset in which 26 specific white matter bundles have been used to generate synthetic data that awaits your processing and analysis. The Challenge, developed by diffusion experts Peter Neher, Jean-Christophe Houde, Emmanuel Caruyer, Alessandro Daducci, Tim Dyrby, Klaus Maier-Hein, Bram Stieltjes, and Maxime Descoteaux has been designed to emulate clinically-realistic acquisition. Several common artifacts have been introduced in the data to probe the strengths and limitations of your processing pipelines. All entries will receive individualized feedback and statistics comparing their results to the ground truth white matter bundles. A discussion of the methods and results will be held at the DSG meeting at ISMRM 2015, scheduled for Monday June 1 from 4:30-6:30pm in Reception Hall 105. For additional details, including information about the data, evaluation methods, and submission procedures, and to download the data, please visit the challenge website at http://www.tractometer.org/ismrm_2015_challenge/ An ISMRM virtual conference (date soon to be announced) will be held to present the Challenge, and one full hour of the study group meeting in Toronto will be dedicated to discussion and result presentations. Further questions regarding the challenge should be directed to tractometer at gmail.com. We look forward to seeing you in Toronto. Ready, track, go! ISMRM Diffusion Study Group From evl2001 at med.cornell.edu Mon Mar 16 13:47:06 2015 From: evl2001 at med.cornell.edu (Eve M LoCastro) Date: Mon, 16 Mar 2015 17:47:06 +0000 Subject: [MINC-users] BEaST - spatial, intensity normalizations Message-ID: <1426528030425.80938@med.cornell.edu> Dear BEaST-masters, I am a newcomer to the MINC toolkit, but I have recently begun testing BEaST for skull-stripping in our pipeline and thoroughly enjoying the results. Thank you for this great tool. I have two questions regarding tweaking and modifying the normalization to MNI space, and the intensity normalization that is applied to the image. 1. With some aged and atrophic brains, sometimes the transformation to MNI is a little bit off when using beast_normalize. Are there any tweaks-to-parameters that I could employ in these subjects to improve the matching to the template. (current command usage: beast_normalize head.mnc head_mni.mnc anat2mni.xfm -modeldir $MincLibPATH) 2. If I am still unsatisfied with the spatial normalization results from the MINC toolkit, can I use a transformed MNI image from an alternate program (ie FSL, SPM)? If so, what kind of intensity normalization do you suggest I apply to best match the smoothed intensity of images in the included libraries? Much thanks, Eve Eve M. LoCastro Staff Associate in Radiology Imaging Data Evaluation and Analytics Lab (IDEAL) Weill Cornell Medical College 515 E. 71st St S118 Tel: 212-746-1289 Fax: 212-746-4189 http://ideal-cornell.com/ From gdevenyi at gmail.com Mon Mar 16 19:48:23 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Mon, 16 Mar 2015 19:48:23 -0400 Subject: [MINC-users] BEaST - spatial, intensity normalizations In-Reply-To: <1426528030425.80938@med.cornell.edu> References: <1426528030425.80938@med.cornell.edu> Message-ID: Hi Eve, I suggest you look into using an alternative method to transform your brain to MNI space, such as mincANTS I wrote a fully automated pipeline that does BeAST with some of the stages improved, see https://github.com/CobraLab/minc-bpipe-library If you take a look at beast_normalize, its a script that consists of an N3 correction, an affine registration and a intensity normalization, all as separate commands. If you choose to do one of those steps by yourself, you can still use the other stages, while skipping some of the stages (see -help for the "no" options). -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Mon, Mar 16, 2015 at 1:47 PM, Eve M LoCastro wrote: > Dear BEaST-masters, > > I am a newcomer to the MINC toolkit, but I have recently begun testing > BEaST for skull-stripping in our pipeline and thoroughly enjoying the > results. Thank you for this great tool. > > I have two questions regarding tweaking and modifying the normalization to > MNI space, and the intensity normalization that is applied to the image. > > 1. With some aged and atrophic brains, sometimes the transformation to MNI > is a little bit off when using beast_normalize. Are there any > tweaks-to-parameters that I could employ in these subjects to improve the > matching to the template. (current command usage: beast_normalize head.mnc > head_mni.mnc anat2mni.xfm -modeldir $MincLibPATH) > > 2. If I am still unsatisfied with the spatial normalization results from > the MINC toolkit, can I use a transformed MNI image from an alternate > program (ie FSL, SPM)? If so, what kind of intensity normalization do you > suggest I apply to best match the smoothed intensity of images in the > included libraries? > > > Much thanks, > > Eve > > > Eve M. LoCastro > Staff Associate in Radiology > Imaging Data Evaluation and Analytics Lab (IDEAL) > Weill Cornell Medical College > 515 E. 71st St S118 > Tel: 212-746-1289 > Fax: 212-746-4189 > http://ideal-cornell.com/ > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Mon Mar 16 21:24:32 2015 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Mon, 16 Mar 2015 21:24:32 -0400 Subject: [MINC-users] BEaST - spatial, intensity normalizations In-Reply-To: <1426528030425.80938@med.cornell.edu> References: <1426528030425.80938@med.cornell.edu> Message-ID: <55078250.40309@gmail.com> Hello, 1. in our experiments we found that it's more reliable to use a template based on aged population instead of MNI ICBM 2009c, for example we have got ADNI average template. In case of beast_normalize , you can specify -modeldir -modelname model_t1w.mnc 2. you can run beast_normalize with -noreg and use file that was already registered in stereotaxic space. On 15-03-16 01:47 PM, Eve M LoCastro wrote: > Dear BEaST-masters, > > I am a newcomer to the MINC toolkit, but I have recently begun testing BEaST for skull-stripping in our pipeline and thoroughly enjoying the results. Thank you for this great tool. > > I have two questions regarding tweaking and modifying the normalization to MNI space, and the intensity normalization that is applied to the image. > > 1. With some aged and atrophic brains, sometimes the transformation to MNI is a little bit off when using beast_normalize. Are there any tweaks-to-parameters that I could employ in these subjects to improve the matching to the template. (current command usage: beast_normalize head.mnc head_mni.mnc anat2mni.xfm -modeldir $MincLibPATH) > > 2. If I am still unsatisfied with the spatial normalization results from the MINC toolkit, can I use a transformed MNI image from an alternate program (ie FSL, SPM)? If so, what kind of intensity normalization do you suggest I apply to best match the smoothed intensity of images in the included libraries? -- Best regards, Vladimir S. Fonov From gdevenyi at gmail.com Mon Mar 16 22:02:01 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Mon, 16 Mar 2015 22:02:01 -0400 Subject: [MINC-users] BEaST - spatial, intensity normalizations In-Reply-To: <55078250.40309@gmail.com> References: <1426528030425.80938@med.cornell.edu> <55078250.40309@gmail.com> Message-ID: Follow-up, I agree with Vlad that if your subjects are significantly different than the MNI template brain, you will get a far better registration if you use an appropriate target registration template. Sidenote: bpipe-library can easily be adapted to target any MINC file as a target for registration, it works best if head/brainmasks are also available like MNI atlases. -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Mon, Mar 16, 2015 at 9:24 PM, Vladimir S. Fonov wrote: > Hello, > > > 1. in our experiments we found that it's more reliable to use a template > based on aged population instead of MNI ICBM 2009c, for example we have got > ADNI average template. In case of beast_normalize , you can specify > -modeldir -modelname model_t1w.mnc > > 2. you can run beast_normalize with -noreg and use file that was already > registered in stereotaxic space. > > > On 15-03-16 01:47 PM, Eve M LoCastro wrote: > >> Dear BEaST-masters, >> >> I am a newcomer to the MINC toolkit, but I have recently begun testing >> BEaST for skull-stripping in our pipeline and thoroughly enjoying the >> results. Thank you for this great tool. >> >> I have two questions regarding tweaking and modifying the normalization >> to MNI space, and the intensity normalization that is applied to the image. >> >> 1. With some aged and atrophic brains, sometimes the transformation to >> MNI is a little bit off when using beast_normalize. Are there any >> tweaks-to-parameters that I could employ in these subjects to improve the >> matching to the template. (current command usage: beast_normalize head.mnc >> head_mni.mnc anat2mni.xfm -modeldir $MincLibPATH) >> >> 2. If I am still unsatisfied with the spatial normalization results from >> the MINC toolkit, can I use a transformed MNI image from an alternate >> program (ie FSL, SPM)? If so, what kind of intensity normalization do you >> suggest I apply to best match the smoothed intensity of images in the >> included libraries? >> > > > -- > > Best regards, > > Vladimir S. Fonov > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jessieguo80 at hotmail.com Tue Mar 17 17:22:10 2015 From: jessieguo80 at hotmail.com (ting guo) Date: Wed, 18 Mar 2015 05:22:10 +0800 Subject: [MINC-users] mincreshape +direction Message-ID: Dear Minc Users, I was trying to use mincreshape to flip a image to give positive yspace, but it didn't work. The following are what I did and what I got as results. As you can see, the image remains unchanged. Am I missing certain important options? How can I flip the image and have positive yspace? I would really appreciate your suggestions. Thank you very much! Jessie $ mincinfo ImageA.mnc file: ImageA.mnc image: unsigned short 0 to 4095 image dimensions: yspace zspace xspace dimension name length step start -------------- ------ ---- ----- yspace 128 -1 13.7688 zspace 192 -1.04167 115.005 xspace 88 -1.04167 38.0225 $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc Copying chunks:................................................................................................................................Done. $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image dimensions: yspace zspace xspace dimension name length step start -------------- ------ ---- ----- yspace 128 -1 13.7688 zspace 192 -1.04167 115.005 xspace 88 -1.04167 38.0225 From zijdenbos at gmail.com Tue Mar 17 18:10:12 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Tue, 17 Mar 2015 23:10:12 +0100 Subject: [MINC-users] mincreshape +direction In-Reply-To: References: Message-ID: Hi Jessie, Having bitten by this (rather counter-intuitive I'll admit) behaviour more than once mysefl, I can answer your question: mincreshape's +/-direction options only work on image dimensions, which are the two fastest-varying dimensions. In your case, yspace is not an "image dimension" as it is the slowest-varyinhg dimension. You'll need to convert yspace to be an image dimension first - check the mincreshape man page and examples for how exactly to do that. -- Alex On Tue, Mar 17, 2015 at 10:22 PM, ting guo wrote: > Dear Minc Users, > I was trying to use mincreshape to flip a image to give positive yspace, > but it didn't work. The following are what I did and what I got as results. > As you can see, the image remains unchanged. Am I missing certain important > options? How can I flip the image and have positive yspace? I would really > appreciate your suggestions. > Thank you very much! > Jessie > $ mincinfo ImageA.mnc > > > > > > > > file: ImageA.mnc > image: unsigned short 0 to 4095 > image dimensions: yspace zspace xspace > dimension name length step start > -------------- ------ ---- ----- > yspace 128 -1 13.7688 > zspace 192 -1.04167 115.005 > xspace 88 -1.04167 38.0225 > > > > > > > > > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc > > > > > > > > > > > > > > > > Copying > chunks:................................................................................................................................Done. > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image > dimensions: yspace zspace xspace dimension name length > step start -------------- ------ ---- > ----- yspace 128 -1 13.7688 zspace > 192 -1.04167 115.005 > > > > > > > > > > > > > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From Oury.Monchi at ucalgary.ca Tue Mar 17 18:35:44 2015 From: Oury.Monchi at ucalgary.ca (Oury Monchi) Date: Tue, 17 Mar 2015 22:35:44 +0000 Subject: [MINC-users] IT position in neuroimaging at University of Calgary Message-ID: Dear all, I would like to bring to your attention to the following Neuroimaging IT support position to work with Dr. Bruce Pike and myself at the University of Calgary: http://careers.ucalgary.ca/jobs/3484069-neuroimaging-it-system-support-radiology-cumming-school-of-medicine Best, Oury. Oury Monchi, PhD Professor and Tourmaline Chair in Parkinson?s Disease, Research Director of the Movement Disorders Program, Director of Clinical Research, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary. Tel: 403-2208048 http://pcanlab.ca/ From vladimir.fonov at gmail.com Wed Mar 18 00:04:41 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 18 Mar 2015 00:04:41 -0400 Subject: [MINC-users] mincreshape +direction In-Reply-To: References: Message-ID: to convert to the "image dimension" use -dimsize yspace=-1 On Tue, Mar 17, 2015 at 6:10 PM, Alex Zijdenbos wrote: > Hi Jessie, > > Having bitten by this (rather counter-intuitive I'll admit) behaviour more > than once mysefl, I can answer your question: mincreshape's +/-direction > options only work on image dimensions, which are the two fastest-varying > dimensions. In your case, yspace is not an "image dimension" as it is the > slowest-varyinhg dimension. > > You'll need to convert yspace to be an image dimension first - check the > mincreshape man page and examples for how exactly to do that. > > -- Alex > > On Tue, Mar 17, 2015 at 10:22 PM, ting guo > wrote: > > > Dear Minc Users, > > I was trying to use mincreshape to flip a image to give positive yspace, > > but it didn't work. The following are what I did and what I got as > results. > > As you can see, the image remains unchanged. Am I missing certain > important > > options? How can I flip the image and have positive yspace? I would > really > > appreciate your suggestions. > > Thank you very much! > > Jessie > > $ mincinfo ImageA.mnc > > > > > > > > > > > > > > > > file: ImageA.mnc > > image: unsigned short 0 to 4095 > > image dimensions: yspace zspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > yspace 128 -1 13.7688 > > zspace 192 -1.04167 115.005 > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Copying > > > chunks:................................................................................................................................Done. > > > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to > 65535image > > dimensions: yspace zspace xspace dimension name length > > step start -------------- ------ ---- > > ----- yspace 128 -1 13.7688 > zspace > > 192 -1.04167 115.005 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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 > -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From jessieguo80 at hotmail.com Thu Mar 19 12:18:07 2015 From: jessieguo80 at hotmail.com (ting guo) Date: Fri, 20 Mar 2015 00:18:07 +0800 Subject: [MINC-users] mincreshape +direction (Alex & Vladimir) In-Reply-To: References: Message-ID: Hi Alex and Vladimir, Thank you guys for your prompt reply. That helped me solve the problem. Many thanks, Jessie > From: minc-users-request at bic.mni.mcgill.ca > Subject: MINC-users Digest, Vol 115, Issue 3 > To: minc-users at bic.mni.mcgill.ca > Date: Wed, 18 Mar 2015 12:00:01 -0400 > > Send MINC-users mailing list submissions to > minc-users at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 1. mincreshape +direction (ting guo) > 2. Re: mincreshape +direction (Alex Zijdenbos) > 3. IT position in neuroimaging at University of Calgary (Oury Monchi) > 4. Re: mincreshape +direction (Vladimir S. FONOV) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Mar 2015 05:22:10 +0800 > From: ting guo > To: "minc-users at bic.mni.mcgill.ca" > Subject: [MINC-users] mincreshape +direction > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Minc Users, > I was trying to use mincreshape to flip a image to give positive yspace, but it didn't work. The following are what I did and what I got as results. As you can see, the image remains unchanged. Am I missing certain important options? How can I flip the image and have positive yspace? I would really appreciate your suggestions. > Thank you very much! > Jessie > $ mincinfo ImageA.mnc > > > > > > > > file: ImageA.mnc > image: unsigned short 0 to 4095 > image dimensions: yspace zspace xspace > dimension name length step start > -------------- ------ ---- ----- > yspace 128 -1 13.7688 > zspace 192 -1.04167 115.005 > xspace 88 -1.04167 38.0225 > > > > > > > > > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc > > > > > > > > > > > > > > > > Copying chunks:................................................................................................................................Done. > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image dimensions: yspace zspace xspace dimension name length step start -------------- ------ ---- ----- yspace 128 -1 13.7688 zspace 192 -1.04167 115.005 > > > > > > > > > > > > > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 17 Mar 2015 23:10:12 +0100 > From: Alex Zijdenbos > To: MINC users mailing list > Subject: Re: [MINC-users] mincreshape +direction > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Jessie, > > Having bitten by this (rather counter-intuitive I'll admit) behaviour more > than once mysefl, I can answer your question: mincreshape's +/-direction > options only work on image dimensions, which are the two fastest-varying > dimensions. In your case, yspace is not an "image dimension" as it is the > slowest-varyinhg dimension. > > You'll need to convert yspace to be an image dimension first - check the > mincreshape man page and examples for how exactly to do that. > > -- Alex > > On Tue, Mar 17, 2015 at 10:22 PM, ting guo wrote: > > > Dear Minc Users, > > I was trying to use mincreshape to flip a image to give positive yspace, > > but it didn't work. The following are what I did and what I got as results. > > As you can see, the image remains unchanged. Am I missing certain important > > options? How can I flip the image and have positive yspace? I would really > > appreciate your suggestions. > > Thank you very much! > > Jessie > > $ mincinfo ImageA.mnc > > > > > > > > > > > > > > > > file: ImageA.mnc > > image: unsigned short 0 to 4095 > > image dimensions: yspace zspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > yspace 128 -1 13.7688 > > zspace 192 -1.04167 115.005 > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Copying > > chunks:................................................................................................................................Done. > > > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image > > dimensions: yspace zspace xspace dimension name length > > step start -------------- ------ ---- > > ----- yspace 128 -1 13.7688 zspace > > 192 -1.04167 115.005 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 17 Mar 2015 22:35:44 +0000 > From: Oury Monchi > To: MINC users mailing list > Cc: "G. Bruce Pike" > Subject: [MINC-users] IT position in neuroimaging at University of > Calgary > Message-ID: > Content-Type: text/plain; charset="Windows-1252" > > Dear all, > > I would like to bring to your attention to the following Neuroimaging IT support position to work with Dr. Bruce Pike and myself at the University of Calgary: > > http://careers.ucalgary.ca/jobs/3484069-neuroimaging-it-system-support-radiology-cumming-school-of-medicine > > Best, > Oury. > > Oury Monchi, PhD > > Professor and Tourmaline Chair in Parkinson?s Disease, > > Research Director of the Movement Disorders Program, > > Director of Clinical Research, > > Department of Clinical Neurosciences, > > Hotchkiss Brain Institute, > > Cumming School of Medicine, University of Calgary. > Tel: 403-2208048 > http://pcanlab.ca/ > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 18 Mar 2015 00:04:41 -0400 > From: "Vladimir S. FONOV" > To: MINC users mailing list > Subject: Re: [MINC-users] mincreshape +direction > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > to convert to the "image dimension" use -dimsize yspace=-1 > > > On Tue, Mar 17, 2015 at 6:10 PM, Alex Zijdenbos wrote: > > > Hi Jessie, > > > > Having bitten by this (rather counter-intuitive I'll admit) behaviour more > > than once mysefl, I can answer your question: mincreshape's +/-direction > > options only work on image dimensions, which are the two fastest-varying > > dimensions. In your case, yspace is not an "image dimension" as it is the > > slowest-varyinhg dimension. > > > > You'll need to convert yspace to be an image dimension first - check the > > mincreshape man page and examples for how exactly to do that. > > > > -- Alex > > > > On Tue, Mar 17, 2015 at 10:22 PM, ting guo > > wrote: > > > > > Dear Minc Users, > > > I was trying to use mincreshape to flip a image to give positive yspace, > > > but it didn't work. The following are what I did and what I got as > > results. > > > As you can see, the image remains unchanged. Am I missing certain > > important > > > options? How can I flip the image and have positive yspace? I would > > really > > > appreciate your suggestions. > > > Thank you very much! > > > Jessie > > > $ mincinfo ImageA.mnc > > > > > > > > > > > > > > > > > > > > > > > > file: ImageA.mnc > > > image: unsigned short 0 to 4095 > > > image dimensions: yspace zspace xspace > > > dimension name length step start > > > -------------- ------ ---- ----- > > > yspace 128 -1 13.7688 > > > zspace 192 -1.04167 115.005 > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Copying > > > > > chunks:................................................................................................................................Done. > > > > > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to > > 65535image > > > dimensions: yspace zspace xspace dimension name length > > > step start -------------- ------ ---- > > > ----- yspace 128 -1 13.7688 > > zspace > > > 192 -1.04167 115.005 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > xspace 88 -1.04167 38.0225 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > > > ------------------------------ > > _______________________________________________ > MINC-users mailing list > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest, Vol 115, Issue 3 > ****************************************** From patelraihaan at gmail.com Mon Mar 23 10:33:01 2015 From: patelraihaan at gmail.com (Raihaan Patel) Date: Mon, 23 Mar 2015 10:33:01 -0400 Subject: [MINC-users] Surface Object Correction Message-ID: Hi All, I'm looking for any advice/input on correcting a surface object (.obj). Specifically, I am wondering how to: - remove/correct any intersecting faces - remove/correct any faces that have an area of 0 Thanks very much, Raihaan From eskild at gmail.com Wed Mar 25 06:16:05 2015 From: eskild at gmail.com (Simon Eskildsen) Date: Wed, 25 Mar 2015 11:16:05 +0100 Subject: [MINC-users] Surface Object Correction In-Reply-To: References: Message-ID: Hi Raihaan, What you're asking for is far from trivial. Can you provide more details? How did you create the object - how did the intersections happen? Are we talking about a triangular mesh? In general, the best strategy is to prevent these unwanted features to happen in the first place. Simon On Mon, Mar 23, 2015 at 3:33 PM, Raihaan Patel wrote: > Hi All, > > I'm looking for any advice/input on correcting a surface object (.obj). > Specifically, I am wondering how to: > > - remove/correct any intersecting faces > - remove/correct any faces that have an area of 0 > > Thanks very much, > Raihaan > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Wed Mar 25 09:01:44 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Wed, 25 Mar 2015 09:01:44 -0400 Subject: [MINC-users] Surface Object Correction In-Reply-To: References: Message-ID: Hi Raihaan, Agreeing with Simon - probably better to avoid these in the first place; but for editing meshes, you may want to take a look at Meshlab, it has a variety of options for cleaning/remeshing/etc. -- A On Wed, Mar 25, 2015 at 6:16 AM, Simon Eskildsen wrote: > Hi Raihaan, > > What you're asking for is far from trivial. Can you provide more details? > How did you create the object - how did the intersections happen? Are we > talking about a triangular mesh? > In general, the best strategy is to prevent these unwanted features to > happen in the first place. > > Simon > > On Mon, Mar 23, 2015 at 3:33 PM, Raihaan Patel > wrote: > > > Hi All, > > > > I'm looking for any advice/input on correcting a surface object (.obj). > > Specifically, I am wondering how to: > > > > - remove/correct any intersecting faces > > - remove/correct any faces that have an area of 0 > > > > Thanks very much, > > Raihaan > > _______________________________________________ > > 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 patelraihaan at gmail.com Wed Mar 25 12:20:27 2015 From: patelraihaan at gmail.com (Raihaan Patel) Date: Wed, 25 Mar 2015 12:20:27 -0400 Subject: [MINC-users] Surface Object Correction In-Reply-To: References: Message-ID: Hi Alex and Simon, Thank you both for your replies. Alex - a quick look at the Meshlab docs looks promising and I will certainly give it a try. Simon - the object was created using a label.mnc file and Display, then downsampled using Amira. 1. Display label.mnc 2. In Create Surface menu (G), use Volume Bin-Isosurf (S) to isolate ROI and extract surface 3. In Polygons menu (Z), perform one iteration of Smooth Polygon (C) 4. Save as .obj file 5. Downsampled the .obj file using Amira software, reducing the number of faces The downsampled .obj file is a triangular mesh. Raihaan On Wed, Mar 25, 2015 at 9:01 AM, Alex Zijdenbos wrote: > Hi Raihaan, > > Agreeing with Simon - probably better to avoid these in the first place; > but for editing meshes, you may want to take a look at Meshlab, it has a > variety of options for cleaning/remeshing/etc. > > -- A > > On Wed, Mar 25, 2015 at 6:16 AM, Simon Eskildsen wrote: > > > Hi Raihaan, > > > > What you're asking for is far from trivial. Can you provide more details? > > How did you create the object - how did the intersections happen? Are we > > talking about a triangular mesh? > > In general, the best strategy is to prevent these unwanted features to > > happen in the first place. > > > > Simon > > > > On Mon, Mar 23, 2015 at 3:33 PM, Raihaan Patel > > wrote: > > > > > Hi All, > > > > > > I'm looking for any advice/input on correcting a surface object (.obj). > > > Specifically, I am wondering how to: > > > > > > - remove/correct any intersecting faces > > > - remove/correct any faces that have an area of 0 > > > > > > Thanks very much, > > > Raihaan > > > _______________________________________________ > > > 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 > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Mon Mar 30 23:29:33 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Mon, 30 Mar 2015 23:29:33 -0400 Subject: [MINC-users] mincresample -like bug? Message-ID: I seem to have stumbled into something unusual: a failure of mincresample. [by the way, according to the GMail spell checker, the correct spelling of 'mincresample' is 'creaminess'. duh.] Anyways, I have this: $ mincinfo in.mnc model.mnc file: in.mnc image: unsigned short 0 to 65535 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 96 2 -321.707 yspace 134 2 -202.414 xspace 134 2 -132.414 file: model.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 94 2 -319.707 yspace 132 2 -200.414 xspace 132 2 -130.414 Now I resample in.mnc like model.mnc: $ mincresample -like model.mnc in.mnc res.mnc Transforming slices:..............................................................................................Done $ mincinfo res.mnc file: res.mnc image: unsigned short 0 to 65535 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 94 1 0 yspace 132 2 -200.414 xspace 132 2 -130.414 Clearly, the zspace step and start of the resampled volume (yellow) don't look at all like those of the -like volume (green). I suspect a numerical precision issue causing the start/step calculation to go wrong, but I'm not sure. In case anybody wants to play, you can get in.mnc and model.mnc from the URLs in the first mincinfo call. -- A From a.janke at gmail.com Mon Mar 30 23:55:35 2015 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 31 Mar 2015 14:55:35 +1100 Subject: [MINC-users] mincresample -like bug? In-Reply-To: References: Message-ID: Do either of the files have irregular slice spacing in z ? a On 31/03/2015 2:30 PM, "Alex Zijdenbos" wrote: > I seem to have stumbled into something unusual: a failure of mincresample. > > [by the way, according to the GMail spell checker, the correct spelling of > 'mincresample' is 'creaminess'. duh.] > > Anyways, I have this: > > $ mincinfo in.mnc > model.mnc > file: in.mnc > image: unsigned short 0 to 65535 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 96 2 -321.707 > yspace 134 2 -202.414 > xspace 134 2 -132.414 > > > file: model.mnc > image: signed__ short -32768 to 32767 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 94 2 -319.707 > yspace 132 2 -200.414 > xspace 132 2 -130.414 > > Now I resample in.mnc like model.mnc: > > $ mincresample -like model.mnc in.mnc res.mnc > Transforming > > slices:..............................................................................................Done > > $ mincinfo res.mnc > file: res.mnc > image: unsigned short 0 to 65535 > image dimensions: zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > zspace 94 1 0 > yspace 132 2 -200.414 > xspace 132 2 -130.414 > > Clearly, the zspace step and start of the resampled volume (yellow) don't > look at all like those of the -like volume (green). I suspect a numerical > precision issue causing the start/step calculation to go wrong, but I'm not > sure. > > In case anybody wants to play, you can get in.mnc and model.mnc from the > URLs in the first mincinfo call. > > -- A > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Tue Mar 31 09:43:48 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Tue, 31 Mar 2015 09:43:48 -0400 Subject: [MINC-users] mincresample -like bug? In-Reply-To: References: Message-ID: ! yes. You win the prize - the model volume indeed has irregular z-spacing (and a bizarre series at that). Should mincresample perhaps warn about this - or rather, what should the correct behaviour be, if it is passed -like ? -- A On Mon, Mar 30, 2015 at 11:55 PM, Andrew Janke wrote: > Do either of the files have irregular slice spacing in z ? > > a > On 31/03/2015 2:30 PM, "Alex Zijdenbos" wrote: > > > I seem to have stumbled into something unusual: a failure of > mincresample. > > > > [by the way, according to the GMail spell checker, the correct spelling > of > > 'mincresample' is 'creaminess'. duh.] > > > > Anyways, I have this: > > > > $ mincinfo in.mnc > > > model.mnc > > file: in.mnc > > image: unsigned short 0 to 65535 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 96 2 -321.707 > > yspace 134 2 -202.414 > > xspace 134 2 -132.414 > > > > > > file: model.mnc > > image: signed__ short -32768 to 32767 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 94 2 -319.707 > > yspace 132 2 -200.414 > > xspace 132 2 -130.414 > > > > Now I resample in.mnc like model.mnc: > > > > $ mincresample -like model.mnc in.mnc res.mnc > > Transforming > > > > > slices:..............................................................................................Done > > > > $ mincinfo res.mnc > > file: res.mnc > > image: unsigned short 0 to 65535 > > image dimensions: zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > zspace 94 1 0 > > yspace 132 2 -200.414 > > xspace 132 2 -130.414 > > > > Clearly, the zspace step and start of the resampled volume (yellow) don't > > look at all like those of the -like volume (green). I suspect a numerical > > precision issue causing the start/step calculation to go wrong, but I'm > not > > sure. > > > > In case anybody wants to play, you can get in.mnc and model.mnc from the > > URLs in the first mincinfo call. > > > > -- A > > _______________________________________________ > > 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 > >