From a.janke at gmail.com Tue Nov 1 08:07:19 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 1 Nov 2005 08:07:19 -0500 Subject: [MINC-users] mincmath and vector field (deformation maps) In-Reply-To: <20051027071720.56673.qmail@web60812.mail.yahoo.com> References: <20051027071720.56673.qmail@web60812.mail.yahoo.com> Message-ID: Hi Jamila, mincmath will treat the vector_dimension like all other dimensions. So add, subtract and scale will work. Divide and multiply (presuming you mean the vector equivalents) will require a little more work. Simply split the file into its components and and then use minccalc. a On 27/10/05, Jamila Ahdidan wrote: > > Dear all, > > I'm currently working on deformation maps, and I would like to know how I can perform some operations on them (like divide, multiply, add, substract). When I use the usual mincmath, then it doesn't see that it's a vector field and it only returns one value per voxel. > > Do you know how I can get around this, I need it in order to normalise the deformation with the time elapsed between 2 scans. > > > > Many regards, > > Jamila > > > > --------------------------------- > Yahoo! FareChase - Search multiple travel sites in one click. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From elo at neurorx.com Tue Nov 1 11:25:42 2005 From: elo at neurorx.com (elo@neurorx.com) Date: Tue, 1 Nov 2005 11:25:42 -0500 (EST) Subject: [MINC-users] N3 In-Reply-To: Message-ID: Hi Joel, I'm not able to address all of your issues, but here are some aspects of using nu_correct that you might find helpful: A low number of iterations means that nu_correct is not applying a very strong correction, and this may result in poor quality images. To rectify this you might want to decrease the stopping condition for your scans. I find that -stop 2.e-5 works well, the default is 1.e-3. When the stopping condition is tightened however, the number of iterations may increase greatly - so there is a tradeoff between correction quality and processing time. We in fact find that running nu_correct several times (with the same parameters) yields the best results in terms of image uniformity. This may be because different gaussian modes are targeted and corrected. For our MRI images, applying repeated nu_corrects (about 6 times), produces the best results. Good luck, Ernest Lo NeuroRX Research Montreal, Canada > Date: Mon, 10 Oct 2005 17:16:00 -0500 > From: joel-bruss at uiowa.edu > Subject: [MINC-users] N3 > To: minc-users at bic.mni.mcgill.ca > Message-ID: <1128982560.434ae820b26f4 at webmail2.its.uiowa.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Currently I have data from a GE 1.5T, and Siemens 1.5 and 3T (Avanto and Trio) > scanners. I am looking for a way to bias-correct these images so that they can > be used with Gray/White segmentation and other volumetrics. My data is in > 16-bit Analyze format and I have a minc converter (ana2mnc). When I run > nu_correct, with default parameters (-V1.0) as well as specifying a mask of the > brain image, I get very awful results. In my 124-slice volume, there are > regions where the image is totally washed out (5-10 slice runs) and others where > the brain looks nice but the bias-correction happened outside of the skull. > When specifying for temp files to be saved as well as a tempdir, after > converting the bias field, it looks like a perfectly uniform smoothing kernel > (ovular/egg shape) which is definitely not what the bias appears as (more polar, > specifically in the frontal lobe). I've tried downloading the test data but am > unsure of how to even work with it. I've read Sled et al's IEEE paper but don't > find it that useful in configuring nu_correct. Also, I set the max iteration > for 150 but it runs through 3 iterations (in about 2 minutes) and says that it > is done. Is this really possible? > > Is there a help file, other than the README, or tutorial out there? Any > suggestions on how to configure nu_correct? Should I use a different Minc > converter? Is it OK to use 16-bit images or do they need to be 8-bit? Any help > would be useful right now. > > Thanks for your time > > -Joel > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 11 Oct 2005 09:20:25 -0400 > From: Jason Lerch > Subject: Re: [MINC-users] N3 > To: MINC users mailing list > Message-ID: <434BBC19.90208 at bic.mni.mcgill.ca> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Make sure that the intensity histogram of your volumes is adequate for > N3 - which means that it should not lie between 0 and 1. If the actual > values don't matter to you, try multiplying the volume with a large > enough constant, then run N3. > > Hope this helps, > > Jason > > joel-bruss at uiowa.edu wrote: > > >Currently I have data from a GE 1.5T, and Siemens 1.5 and 3T (Avanto and Trio) > >scanners. I am looking for a way to bias-correct these images so that they can > >be used with Gray/White segmentation and other volumetrics. My data is in > >16-bit Analyze format and I have a minc converter (ana2mnc). When I run > >nu_correct, with default parameters (-V1.0) as well as specifying a mask of the > >brain image, I get very awful results. In my 124-slice volume, there are > >regions where the image is totally washed out (5-10 slice runs) and others where > >the brain looks nice but the bias-correction happened outside of the skull. > >When specifying for temp files to be saved as well as a tempdir, after > >converting the bias field, it looks like a perfectly uniform smoothing kernel > >(ovular/egg shape) which is definitely not what the bias appears as (more polar, > >specifically in the frontal lobe). I've tried downloading the test data but am > >unsure of how to even work with it. I've read Sled et al's IEEE paper but don't > >find it that useful in configuring nu_correct. Also, I set the max iteration > >for 150 but it runs through 3 iterations (in about 2 minutes) and says that it > >is done. Is this really possible? > > > >Is there a help file, other than the README, or tutorial out there? Any > >suggestions on how to configure nu_correct? Should I use a different Minc > >converter? Is it OK to use 16-bit images or do they need to be 8-bit? Any help > >would be useful right now. > > > >Thanks for your time > > > >-Joel > > > > > > > >_______________________________________________ > >MINC-users at bic.mni.mcgill.ca > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > ------------------------------ > > _______________________________________________ > 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 3, Issue 8 > **************************************** > From alex at bic.mni.mcgill.ca Tue Nov 1 14:40:27 2005 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Tue, 01 Nov 2005 14:40:27 -0500 Subject: [MINC-users] N3 In-Reply-To: References: Message-ID: <20051101194027.GA3776@bic.mni.mcgill.ca> On Tue, Nov 01, 2005 at 11:25:42AM -0500, elo at neurorx.com wrote: > > We in fact find that running nu_correct several times (with the same > parameters) yields the best results in terms of image uniformity. This > may be because different gaussian modes are targeted and corrected. For > our MRI images, applying repeated nu_corrects (about 6 times), produces > the best results. This has been reported by others as well, but I still find this puzzling. Given the iterative nature of N3, why would running it multiple times produce results different results from running it longer (more iterations)? Is there something fundamentally different between nu_correct's internal loop, versus imposing an external loop? John (Sled) - any thoughts? -- A From acaroli at fatebenefratelli.it Fri Nov 11 05:53:29 2005 From: acaroli at fatebenefratelli.it (Anna Caroli) Date: Fri, 11 Nov 2005 11:53:29 +0100 Subject: [MINC-users] From .IMA to .mnc Message-ID: <200511111053.jABArXo71990794@shadow.bic.mni.mcgill.ca> Dear MINC user, Does anybody know if there is any possibility to create a .mnc file from .IMA images? I usually create .mnc files starting from DICOM files using dicom_to_minc, is there any analogous command for IMA images? Thanks for your help! Anna Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni di Dio FBF The National Center for Research and Care of Alzheimer's Disease via Pilastroni 4, 25125 - Brescia, Italy Tel: +39 030 3501 361, Fax: +39 02 700 435 727 www.centroAlzheimer.it From jammam2 at yahoo.com Fri Nov 11 07:05:18 2005 From: jammam2 at yahoo.com (Jamila Ahdidan) Date: Fri, 11 Nov 2005 04:05:18 -0800 (PST) Subject: [MINC-users] how to apply an .xfm transformation on a vector field? Message-ID: <20051111120518.38063.qmail@web60823.mail.yahoo.com> Hi all, I have a grid describing a deformation field resulted from the coregistration of an image to an other. Does anyone have an idea about how to apply the transformation of an .xfm file on the grid. I thouht about using minc reshape to separate the components of the vetor at each voxel into 3 different files, and apply the transformation on them using mincresample -transform, and ofcourse rebuilding the vector field again (just don't know how to do that last step!). Can anyone tell me whether this will do it or if it's completely wrong. I really need to find out how to apply an .xfm transformation on a vector field. Looking forward to reading your smart ideas!!! Jamila --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. From marc.schoenwiesner at mcgill.ca Fri Nov 11 07:22:06 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Fri, 11 Nov 2005 07:22:06 -0500 Subject: [MINC-users] emma for matlab 6.5/7? In-Reply-To: <20051111120518.38063.qmail@web60823.mail.yahoo.com> References: <20051111120518.38063.qmail@web60823.mail.yahoo.com> Message-ID: <1131711726.43748cee0ebaa@webmail.mcgill.ca> Hi, is there any chance to get mireadimages to work with matlab 6.5? Most of the programs seem to work fine (miinquire for instance gives the correct image size). It's getting hard to find a matlab 6.1 or older installation. Cheers, Marc From jharlap at bic.mni.mcgill.ca Fri Nov 11 07:46:58 2005 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Fri, 11 Nov 2005 07:46:58 -0500 Subject: [MINC-users] From .IMA to .mnc In-Reply-To: <200511111053.jABArXo71990794@shadow.bic.mni.mcgill.ca> References: <200511111053.jABArXo71990794@shadow.bic.mni.mcgill.ca> Message-ID: <20051111124658.GA1768591@bic.mni.mcgill.ca> I've often seen DICOM files named *.IMA - so you might try dicom_to_minc. If they aren't DICOM, you'll have to figure out what format they're in in order to determine which converter to use. Cheers, Jon On Fri, Nov 11, 2005 at 11:53:29AM +0100, Anna Caroli wrote: > Dear MINC user, > Does anybody know if there is any possibility to create a .mnc file from > .IMA images? > I usually create .mnc files starting from DICOM files using dicom_to_minc, > is there any analogous command for IMA images? > Thanks for your help! > > Anna > > Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni > di Dio FBF > The National Center for Research and Care of Alzheimer's Disease > via Pilastroni 4, 25125 - Brescia, Italy > Tel: +39 030 3501 361, Fax: +39 02 700 435 727 www.centroAlzheimer.it > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From bert at bic.mni.mcgill.ca Fri Nov 11 08:44:25 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 11 Nov 2005 08:44:25 -0500 Subject: [MINC-users] emma for matlab 6.5/7? In-Reply-To: <1131711726.43748cee0ebaa@webmail.mcgill.ca> Message-ID: Hi Marc, EMMA 0.9.7 (and later) should work fine with Matlab 6.5. There are some issues on systems with spaces in filenames, and there are some installation and configuration problems that I have seen on Windows, but otherwise it should work. -bert On Fri, 11 Nov 2005, Marc Schoenwiesner wrote: > Hi, > > is there any chance to get mireadimages to work with matlab 6.5? Most of the > programs seem to work fine (miinquire for instance gives the correct image > size). It's getting hard to find a matlab 6.1 or older installation. > > Cheers, > Marc > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From bert at bic.mni.mcgill.ca Fri Nov 11 08:47:27 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 11 Nov 2005 08:47:27 -0500 Subject: [MINC-users] From .IMA to .mnc In-Reply-To: <200511111053.jABArXo71990794@shadow.bic.mni.mcgill.ca> Message-ID: Hi Anna, Some .IMA files are in a Siemens proprietary format, others are actually DICOM. This seems to depend upon the version of the software running on the scanner. Our dcm2mnc tool (part of MINC 1.4 and later) should be able to handle either one - it has some code to deal with the Siemens internal format. As Jonathan said, dicom_to_minc will also work with them if they are DICOM files. -bert On Fri, 11 Nov 2005, Anna Caroli wrote: > Dear MINC user, > Does anybody know if there is any possibility to create a .mnc file from > .IMA images? > I usually create .mnc files starting from DICOM files using dicom_to_minc, > is there any analogous command for IMA images? > Thanks for your help! > > Anna > > Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni > di Dio FBF > The National Center for Research and Care of Alzheimer's Disease > via Pilastroni 4, 25125 - Brescia, Italy > Tel: +39 030 3501 361, Fax: +39 02 700 435 727 www.centroAlzheimer.it > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From marc.schoenwiesner at mcgill.ca Sat Nov 12 16:53:53 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Sat, 12 Nov 2005 16:53:53 -0500 Subject: [MINC-users] emma for matlab 6.5/7? Message-ID: <1131832433.43766471bf44f@webmail.mcgill.ca> Hi, I installed emma 0.9.7 on several winXP systems under matlab 6.5 and I always get the following error message: > ??? Error using ==> mireadimages > Unable to read images from file e:\ave3Dtal.mnc Under matlab 6.1 on the same computer this works without problem. Has anyone had similar problems and an idea how to solve this? Cheers, Marc Quoting Robert VINCENT : > Hi Marc, > > EMMA 0.9.7 (and later) should work fine with Matlab 6.5. There are some > issues on systems with spaces in filenames, and there are some > installation and configuration problems that I have seen on Windows, but > otherwise it should work. > > -bert > > On Fri, 11 Nov 2005, Marc Schoenwiesner wrote: > > > Hi, > > > > is there any chance to get mireadimages to work with matlab 6.5? Most of > the > > programs seem to work fine (miinquire for instance gives the correct image > > size). It's getting hard to find a matlab 6.1 or older installation. > > > > Cheers, > > Marc > > _______________________________________________ > > 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 bert at bic.mni.mcgill.ca Sat Nov 12 18:47:29 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Sat, 12 Nov 2005 18:47:29 -0500 Subject: [MINC-users] emma for matlab 6.5/7? In-Reply-To: <1131832433.43766471bf44f@webmail.mcgill.ca> Message-ID: Hi Marc, I'm not sure if this will help, but please take a look at emma 0.9.8, which attempts to correct some possible issues with earlier versions of emma on Windows. You can download it here: http://www.bic.mni.mcgill.ca/~bert/emma-0.9.8-win32.zip Copy all of the DLL and EXE files into a directory on your path, and copy all of the .m files into the normal location you use for emma toolbox files. If you add the emma toolbox to the Matlab path you should be all set. I am able to use mireadimages() with this version of emma and Matlab7. -bert On Sat, 12 Nov 2005, Marc Schoenwiesner wrote: > Hi, > > I installed emma 0.9.7 on several winXP systems under matlab 6.5 and I always > get the following error message: > > ??? Error using ==> mireadimages > > Unable to read images from file e:\ave3Dtal.mnc > Under matlab 6.1 on the same computer this works without problem. Has anyone had > similar problems and an idea how to solve this? > > Cheers, > Marc > > > Quoting Robert VINCENT : > > > Hi Marc, > > > > EMMA 0.9.7 (and later) should work fine with Matlab 6.5. There are some > > issues on systems with spaces in filenames, and there are some > > installation and configuration problems that I have seen on Windows, but > > otherwise it should work. > > > > -bert > > > > On Fri, 11 Nov 2005, Marc Schoenwiesner wrote: > > > > > Hi, > > > > > > is there any chance to get mireadimages to work with matlab 6.5? Most of > > the > > > programs seem to work fine (miinquire for instance gives the correct image > > > size). It's getting hard to find a matlab 6.1 or older installation. > > > > > > Cheers, > > > Marc > > > _______________________________________________ > > > 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 jammam2 at yahoo.com Sun Nov 13 07:08:41 2005 From: jammam2 at yahoo.com (Jamila Ahdidan) Date: Sun, 13 Nov 2005 04:08:41 -0800 (PST) Subject: [MINC-users] Help on how to transform a displacement field!!! Message-ID: <20051113120841.51917.qmail@web60820.mail.yahoo.com> Hi all, I have an urgent question. I need to know if it's ok to mincresample -transform a displacement field? Or is it better to decompose the displacement field using mincreshape and mincresample -transform the 3 different volumes? This question is really important, and I don't really know who to ask, or where to find the answer. Thank you very much for your help! Jamila --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. From marc.schoenwiesner at mcgill.ca Sun Nov 13 15:52:07 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Sun, 13 Nov 2005 15:52:07 -0500 Subject: [MINC-users] emma for matlab 6.5/7? In-Reply-To: References: Message-ID: <1131915127.4377a777a23c8@webmail.mcgill.ca> Hi, thanks, I have gotten a bit closer. mireadimages() does a good job, but the real trouble seems to come from mincextract. If I run mincextract on a slice of any of my volumes or icbm_avg_152_t1_tal_lin.mnc I get an almost random array in return with most of the voxel values at something like -8.5960e+247... If I clamp the output at the correct range I can see a distorted outline of the brain. Any idea what could be causing this? Cheers, Marc Quoting Robert VINCENT : > Hi Marc, > > I'm not sure if this will help, but please take a look at emma 0.9.8, > which attempts to correct some possible issues with earlier versions of > emma on Windows. > > You can download it here: > > http://www.bic.mni.mcgill.ca/~bert/emma-0.9.8-win32.zip > > Copy all of the DLL and EXE files into a directory on your path, and copy > all of the .m files into the normal location you use for emma toolbox > files. If you add the emma toolbox to the Matlab path you should be all > set. I am able to use mireadimages() with this version of emma and > Matlab7. > > -bert > > On Sat, 12 Nov 2005, Marc Schoenwiesner wrote: > > > Hi, > > > > I installed emma 0.9.7 on several winXP systems under matlab 6.5 and I > always > > get the following error message: > > > ??? Error using ==> mireadimages > > > Unable to read images from file e:\ave3Dtal.mnc > > Under matlab 6.1 on the same computer this works without problem. Has > anyone had > > similar problems and an idea how to solve this? > > > > Cheers, > > Marc > > > > > > Quoting Robert VINCENT : > > > > > Hi Marc, > > > > > > EMMA 0.9.7 (and later) should work fine with Matlab 6.5. There are some > > > issues on systems with spaces in filenames, and there are some > > > installation and configuration problems that I have seen on Windows, but > > > otherwise it should work. > > > > > > -bert > > > > > > On Fri, 11 Nov 2005, Marc Schoenwiesner wrote: > > > > > > > Hi, > > > > > > > > is there any chance to get mireadimages to work with matlab 6.5? Most > of > > > the > > > > programs seem to work fine (miinquire for instance gives the correct > image > > > > size). It's getting hard to find a matlab 6.1 or older installation. > > > > > > > > Cheers, > > > > Marc > > > > _______________________________________________ > > > > 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 > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Nov 17 01:46:39 2005 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 17 Nov 2005 07:46:39 +0100 Subject: [MINC-users] Help on how to transform a displacement field!!! In-Reply-To: <20051113120841.51917.qmail@web60820.mail.yahoo.com> References: <20051113120841.51917.qmail@web60820.mail.yahoo.com> Message-ID: Yes. mincresample will "do the right thing" with minc files that contain a vector dimension. Just be aware that what you get will be a non-mass preserving resampling of your deformation field. a On 13/11/05, Jamila Ahdidan wrote: > Hi all, > I have an urgent question. I need to know if it's ok to mincresample -transform a displacement field? Or is it better to decompose the displacement field using mincreshape and mincresample -transform the 3 different volumes? > This question is really important, and I don't really know who to ask, or where to find the answer. > > Thank you very much for your help! > > Jamila > > > --------------------------------- > Yahoo! FareChase - Search multiple travel sites in one click. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From jammam2 at yahoo.com Thu Nov 17 04:19:49 2005 From: jammam2 at yahoo.com (Jamila Ahdidan) Date: Thu, 17 Nov 2005 01:19:49 -0800 (PST) Subject: [MINC-users] Help on how to transform a displacement field!!! In-Reply-To: Message-ID: <20051117091949.56131.qmail@web60815.mail.yahoo.com> Thanks for the answer first. I would like to understand what "a non-mass preserving resampling" means. Does this mean that I won't be able to apply mincblob on the results? Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field. I hope you understand what I mean. Jamila Andrew Janke wrote: Yes. mincresample will "do the right thing" with minc files that contain a vector dimension. Just be aware that what you get will be a non-mass preserving resampling of your deformation field. a On 13/11/05, Jamila Ahdidan wrote: > Hi all, > I have an urgent question. I need to know if it's ok to mincresample -transform a displacement field? Or is it better to decompose the displacement field using mincreshape and mincresample -transform the 3 different volumes? > This question is really important, and I don't really know who to ask, or where to find the answer. > > Thank you very much for your help! > > Jamila > > > --------------------------------- > Yahoo! FareChase - Search multiple travel sites in one click. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. From o.winz at fz-juelich.de Mon Nov 21 08:30:45 2005 From: o.winz at fz-juelich.de (Oliver Winz) Date: Mon, 21 Nov 2005 14:30:45 +0100 Subject: [MINC-users] nonlinear transformation Message-ID: <4381CC05.9070905@fz-juelich.de> Hello everybody, i have a problem concering nonlinear transformation to stereotaxic space. The final MRI after transformation is very suspect. Maybe i forgot a very important part in the processing steps and someone can give a hint. Here is my complete procedure: > dcm2mnc input*.IMA destdir/ > mritotal inputMRI.mnc outputTrans-Lin.xfm > mritotal -nonlinear -transformation outputTrans-Lin.xfm inputMRI.mnc outputTrans-NonLin.xfm > mincresample -transformation outputTrans-NonLin.xfm -like average305.mnc inputMRI.mnc outputMRI-toTAL.mnc > mritotal -version Program mritotal, built from: Package MNI AutoReg, version 0.98r, compiled by owinz at medpc66 (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14 I'm working on Pentium V 3.0 GHz, running SuSE Linux 9.2 with kernel 2.6.8-24.18-smp I get the DICOM MRI's from a Magneton VISION 1.5 T, Siemens, Erlangen, Germany) using a 3D T1-weighted MPRAGE sequenze (voxel size = 1 x 1 x 1 mm?) Everyone who's interested in a screenshot, please let me know, i will send to you. Thanks in advance!! Greetings, Oliver -- Oliver Winz, M.Sc. Molecular Neuroimaging Group Institute of Medicine (IME) Research Centre Juelich D-52425 Juelich Germany Phone: +49 2461 61-6493 Web: http://www.fz-juelich.de/ime/mni Location: Building 15.9, Room 3010 From U951678 at STUDMED.AU.DK Tue Nov 22 04:17:58 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Tue, 22 Nov 2005 10:17:58 +0100 Subject: [MINC-users] subsampling Message-ID: Hi, What is the fastest way to extract for instance every 2nd slice from a volume? I guess mincresample can be used, but it becomes a little tedious as step sizes and start points have to be given in voxel coordinates. Is there a better way? Best regards Soren From cjb at pet.auh.dk Tue Nov 22 05:42:54 2005 From: cjb at pet.auh.dk (Christopher Bailey) Date: Tue, 22 Nov 2005 11:42:54 +0100 Subject: [MINC-users] subsampling In-Reply-To: References: Message-ID: <1132656174.15524.61.camel@kafka.pet.auh.dk> Would this work? foreach $i (every second slice index) { `mincreshape -dimrange zspace=$i,1 input.mnc /tmp/slice$i.mnc`; push(@slices, "/tmp/slice$i.mnc"); } `mincconcat -concat_dimension zspace @slices output.mnc`; unlink @slices; -Chris On Tue, 2005-11-22 at 10:17 +0100, S?ren Christensen wrote: > Hi, > What is the fastest way to extract for instance every 2nd slice from a volume? > I guess mincresample can be used, but it becomes a little tedious as step sizes and start points have to be given in voxel coordinates. > Is there a better way? > > Best regards > Soren > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Tue Nov 22 08:08:57 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 22 Nov 2005 08:08:57 -0500 Subject: [MINC-users] nonlinear transformation In-Reply-To: <4381CC05.9070905@fz-juelich.de> References: <4381CC05.9070905@fz-juelich.de> Message-ID: Hi Oliver, The approach you are using looks fine to me. Does the registration go "bad" at the linear or nonlinear step? ie: have you checked what the image looks like if you resample with the linear transformation only. a On 21/11/05, Oliver Winz wrote: > Hello everybody, > > i have a problem concering nonlinear transformation to stereotaxic > space. The final MRI after transformation is very suspect. Maybe i > forgot a very important part in the processing steps and someone can > give a hint. > Here is my complete procedure: > > > > dcm2mnc input*.IMA destdir/ > > mritotal inputMRI.mnc outputTrans-Lin.xfm > > mritotal -nonlinear -transformation outputTrans-Lin.xfm inputMRI.mnc > outputTrans-NonLin.xfm > > mincresample -transformation outputTrans-NonLin.xfm -like > average305.mnc inputMRI.mnc outputMRI-toTAL.mnc > > > mritotal -version > Program mritotal, built from: > Package MNI AutoReg, version 0.98r, compiled by owinz at medpc66 > (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14 > > I'm working on Pentium V 3.0 GHz, running SuSE Linux 9.2 with kernel > 2.6.8-24.18-smp > I get the DICOM MRI's from a Magneton VISION 1.5 T, Siemens, Erlangen, > Germany) using a 3D T1-weighted MPRAGE sequenze (voxel size = 1 x 1 x 1 mm?) > > Everyone who's interested in a screenshot, please let me know, i will > send to you. > Thanks in advance!! > Greetings, > Oliver > > > > -- > Oliver Winz, M.Sc. > Molecular Neuroimaging Group > Institute of Medicine (IME) > Research Centre Juelich > D-52425 Juelich > Germany > > Phone: +49 2461 61-6493 > Web: http://www.fz-juelich.de/ime/mni > Location: Building 15.9, Room 3010 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From louis.collins at mcgill.ca Mon Nov 21 10:35:29 2005 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Mon, 21 Nov 2005 10:35:29 -0500 Subject: [MINC-users] nonlinear transformation In-Reply-To: <4381CC05.9070905@fz-juelich.de> References: <4381CC05.9070905@fz-juelich.de> Message-ID: <986c5f681d0280632f9627941d72f533@mcgill.ca> Oliver, Please post a few screen shots of the problem and I should be able to give you some pointers. -Louis On Nov 21, 2005, at 8:30 AM, Oliver Winz wrote: > Hello everybody, > > i have a problem concering nonlinear transformation to stereotaxic > space. The final MRI after transformation is very suspect. Maybe i > forgot a very important part in the processing steps and someone can > give a hint. > Here is my complete procedure: > > >> dcm2mnc input*.IMA destdir/ >> mritotal inputMRI.mnc outputTrans-Lin.xfm >> mritotal -nonlinear -transformation outputTrans-Lin.xfm inputMRI.mnc > outputTrans-NonLin.xfm >> mincresample -transformation outputTrans-NonLin.xfm -like > average305.mnc inputMRI.mnc outputMRI-toTAL.mnc > >> mritotal -version > Program mritotal, built from: > Package MNI AutoReg, version 0.98r, compiled by owinz at medpc66 > (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14 > > I'm working on Pentium V 3.0 GHz, running SuSE Linux 9.2 with kernel > 2.6.8-24.18-smp > I get the DICOM MRI's from a Magneton VISION 1.5 T, Siemens, Erlangen, > Germany) using a 3D T1-weighted MPRAGE sequenze (voxel size = 1 x 1 x > 1 mm?) > > Everyone who's interested in a screenshot, please let me know, i will > send to you. > Thanks in advance!! > Greetings, > Oliver > > > > -- > Oliver Winz, M.Sc. > Molecular Neuroimaging Group > Institute of Medicine (IME) > Research Centre Juelich > D-52425 Juelich > Germany > > Phone: +49 2461 61-6493 > Web: http://www.fz-juelich.de/ime/mni > Location: Building 15.9, Room 3010 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From U951678 at STUDMED.AU.DK Tue Nov 22 18:46:05 2005 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Wed, 23 Nov 2005 00:46:05 +0100 Subject: [MINC-users] subsampling In-Reply-To: <1132656174.15524.61.camel@kafka.pet.auh.dk> References: , <1132656174.15524.61.camel@kafka.pet.auh.dk> Message-ID: That will probably work; i was just thinking if mincreshape alone could have done it, but it probably can't skip slices. Thanks Soren Fra: Christopher Bailey Sendt: ti 22-11-2005 21:42 Til: MINC users mailing list Emne: Re: [MINC-users] subsampling Would this work? foreach $i (every second slice index) { `mincreshape -dimrange zspace=$i,1 input.mnc /tmp/slice$i.mnc`; push(@slices, "/tmp/slice$i.mnc"); } `mincconcat -concat_dimension zspace @slices output.mnc`; unlink @slices; -Chris On Tue, 2005-11-22 at 10:17 +0100, S?ren Christensen wrote: > Hi, > What is the fastest way to extract for instance every 2nd slice from a volume? > I guess mincresample can be used, but it becomes a little tedious as step sizes and start points have to be given in voxel coordinates. > Is there a better way? > > Best regards > Soren > > _______________________________________________ > 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 a.janke at gmail.com Tue Nov 22 08:47:56 2005 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 22 Nov 2005 08:47:56 -0500 Subject: [MINC-users] subsampling In-Reply-To: References: <1132656174.15524.61.camel@kafka.pet.auh.dk> Message-ID: No skipping of slices that I know of. a On 22/11/05, S?ren Christensen wrote: > That will probably work; i was just thinking if mincreshape alone could have done it, but it probably can't skip slices. > > Thanks > Soren > > > > > Fra: Christopher Bailey > Sendt: ti 22-11-2005 21:42 > Til: MINC users mailing list > Emne: Re: [MINC-users] subsampling > > > Would this work? > > foreach $i (every second slice index) { > `mincreshape -dimrange zspace=$i,1 input.mnc /tmp/slice$i.mnc`; > push(@slices, "/tmp/slice$i.mnc"); > } > `mincconcat -concat_dimension zspace @slices output.mnc`; > unlink @slices; > > -Chris > > On Tue, 2005-11-22 at 10:17 +0100, S?ren Christensen wrote: > > Hi, > > What is the fastest way to extract for instance every 2nd slice from a volume? > > I guess mincresample can be used, but it becomes a little tedious as step sizes and start points have to be given in voxel coordinates. > > Is there a better way? > > > > Best regards > > Soren > > > > _______________________________________________ > > 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 > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From louis.collins at mcgill.ca Tue Nov 22 10:13:20 2005 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 22 Nov 2005 10:13:20 -0500 Subject: [MINC-users] nonlinear transformation In-Reply-To: <200511220934.10324.rghassemi@talos.bic.mni.mcgill.ca> References: <200511220934.10324.rghassemi@talos.bic.mni.mcgill.ca> Message-ID: <3eec8541b89ec70da76bc566dc61b346@mcgill.ca> Rezwan, that is pretty funny - the result looks very square. Can you show a result of the linear registration? I'd like to see the same slices if possible. -L On Nov 22, 2005, at 9:34 AM, Rezwan Ghassemi wrote: > Hi, > > I have also tried it. the attached file is output of non-linear > transformation > to stx 305 model. > > Would you please let me know what is wrong with it? > > thanks > Rezwan > --- "D. Louis Collins" wrote: > >> Oliver, >> >> Please post a few screen shots of the problem and I >> should be able to >> give you some pointers. >> >> -Louis >> >> >> On Nov 21, 2005, at 8:30 AM, Oliver Winz wrote: >> >>> Hello everybody, >>> >>> i have a problem concering nonlinear >> transformation to stereotaxic >>> space. The final MRI after transformation is very >> suspect. Maybe i >>> forgot a very important part in the processing >> steps and someone can >>> give a hint. >>> Here is my complete procedure: >>> >>> >>>> dcm2mnc input*.IMA destdir/ >>>> mritotal inputMRI.mnc outputTrans-Lin.xfm >>>> mritotal -nonlinear -transformation >> outputTrans-Lin.xfm inputMRI.mnc >>> outputTrans-NonLin.xfm >>>> mincresample -transformation >> outputTrans-NonLin.xfm -like > >>> average305.mnc inputMRI.mnc outputMRI-toTAL.mnc >>> >>>> mritotal -version >>> Program mritotal, built from: >>> Package MNI AutoReg, version 0.98r, compiled by >> owinz at medpc66 >>> (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14 >>> >>> I'm working on Pentium V 3.0 GHz, running SuSE >> Linux 9.2 with kernel >>> 2.6.8-24.18-smp >>> I get the DICOM MRI's from a Magneton VISION 1.5 >> T, Siemens, Erlangen, >>> Germany) using a 3D T1-weighted MPRAGE sequenze >> (voxel size = 1 x 1 x >>> 1 mm?) >>> >>> Everyone who's interested in a screenshot, please >> let me know, i will >>> send to you. >>> Thanks in advance!! >>> Greetings, >>> Oliver >>> >>> >>> >>> -- >>> Oliver Winz, M.Sc. >>> Molecular Neuroimaging Group >>> Institute of Medicine (IME) >>> Research Centre Juelich >>> D-52425 Juelich >>> Germany >>> >>> Phone: +49 2461 61-6493 >>> Web: http://www.fz-juelich.de/ime/mni >>> Location: Building 15.9, Room 3010 >>> >>> _______________________________________________ >>> 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 louis.collins at mcgill.ca Tue Nov 22 11:57:20 2005 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 22 Nov 2005 11:57:20 -0500 Subject: [MINC-users] nonlinear transformation In-Reply-To: <200511221024.42092.rghassemi@talos.bic.mni.mcgill.ca> References: <200511221024.42092.rghassemi@talos.bic.mni.mcgill.ca> Message-ID: Rezwan, I just realized that you are using the average305 target for non-linear registration. We have stopped using it because of problems similar to those you've shown (but ours have not been as big). Please use one of the newer icbm targets available from packages.bic.mni.mcgill.ca. mni-models-icbm152-lin is better, but you still might have some errors. the best is a new symmetric non-linear average of the 152 icbm subjects. We are working to get it placed on the web. should be soon. -Louis On Nov 22, 2005, at 10:24 AM, Rezwan Ghassemi wrote: > here is the linear registration. > > > --- "D. Louis Collins" wrote: > >> Rezwan, >> >> that is pretty funny - the result looks very square. >> >> Can you show a result of the linear registration? >> I'd like to see the >> same slices if possible. >> >> -L >> >> On Nov 22, 2005, at 9:34 AM, Rezwan Ghassemi wrote: >> >>> Hi, >>> >>> I have also tried it. the attached file is output >> of non-linear >>> transformation >>> to stx 305 model. >>> >>> Would you please let me know what is wrong with >> it? >>> >>> thanks >>> Rezwan >>> --- "D. Louis Collins" >> wrote: >>> >>>> Oliver, >>>> >>>> Please post a few screen shots of the problem and >> I >>>> should be able to >>>> give you some pointers. >>>> >>>> -Louis >>>> >>>> >>>> On Nov 21, 2005, at 8:30 AM, Oliver Winz wrote: >>>> >>>>> Hello everybody, >>>>> >>>>> i have a problem concering nonlinear >>>> transformation to stereotaxic >>>>> space. The final MRI after transformation is >> very >>>> suspect. Maybe i >>>>> forgot a very important part in the processing >>>> steps and someone can >>>>> give a hint. >>>>> Here is my complete procedure: >>>>> >>>>> >>>>>> dcm2mnc input*.IMA destdir/ >>>>>> mritotal inputMRI.mnc outputTrans-Lin.xfm >>>>>> mritotal -nonlinear -transformation >>>> outputTrans-Lin.xfm inputMRI.mnc >>>>> outputTrans-NonLin.xfm >>>>>> mincresample -transformation >>>> outputTrans-NonLin.xfm -like >>> >>>>> average305.mnc inputMRI.mnc outputMRI-toTAL.mnc >>>>> >>>>>> mritotal -version >>>>> Program mritotal, built from: >>>>> Package MNI AutoReg, version 0.98r, compiled by >>>> owinz at medpc66 >>>>> (i686-pc-linux-gnu) on 2005-02-24 at 17:58:14 >>>>> >>>>> I'm working on Pentium V 3.0 GHz, running SuSE >>>> Linux 9.2 with kernel >>>>> 2.6.8-24.18-smp >>>>> I get the DICOM MRI's from a Magneton VISION 1.5 >>>> T, Siemens, Erlangen, >>>>> Germany) using a 3D T1-weighted MPRAGE sequenze >>>> (voxel size = 1 x 1 x >>>>> 1 mm?) >>>>> >>>>> Everyone who's interested in a screenshot, >> please >>>> let me know, i will >>>>> send to you. >>>>> Thanks in advance!! >>>>> Greetings, >>>>> Oliver >>>>> >>>>> >>>>> >>>>> -- >>>>> Oliver Winz, M.Sc. >>>>> Molecular Neuroimaging Group >>>>> Institute of Medicine (IME) >>>>> Research Centre Juelich >>>>> D-52425 Juelich >>>>> Germany >>>>> >>>>> Phone: +49 2461 61-6493 >>>>> Web: http://www.fz-juelich.de/ime/mni >>>>> Location: Building 15.9, Room 3010 >>>>> >>>>> _______________________________________________ >>>>> 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 teodorst at cancerboard.ab.ca Wed Nov 23 14:44:33 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Wed, 23 Nov 2005 12:44:33 -0700 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 9 References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CDE@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, Please, could you help me with the following installation-related problem? I was not able to make mritotal to run properly. I installed (or I tried to install) on my system (Mandriva LE 2005, Intel Xeon) the following packages: netcdf-3.5.0 minc-1.4 Getopt-Tabular-0.3 mni_perllib-0.07 mni_autoreg-0.98r mni_autoreg_model-1.03 with path /mni/local/mni. When I run ./mritotal input.mnc output.xfm I get the following error: Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) Couldn't find program "mincresample" Couldn't find program "mincblur" Couldn't find program "volume_cog" Couldn't find program "minctracc" Couldn't find program "check_scale" Couldn't find program "autocrop" However, I can access their individual man page, e.g. ./mritotal -help. If I run in mni_autoreg-0.98r directory make check I get the following (it couldn't find mincresample): Making check in Proglib make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/Proglib' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/Proglib' Making check in make_phantom make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/make_phantom' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/make_phantom' Making check in mincbbox make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/mincbbox' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/mincbbox' Making check in mincblur make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/mincblur' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/mincblur' Making check in mincchamfer make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/mincchamfer' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/mincchamfer' Making check in minctracc make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc' Making check in Files make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Files' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Files' Making check in Numerical make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Numerical' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Numerical' Making check in Optimize make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Optimize' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Optimize' Making check in Volume make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Volume' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Volume' Making check in Main make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Main' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Main' Making check in Extra_progs make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' make cmpxfm make[3]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' make[3]: `cmpxfm' is up to date. make[3]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' make check-TESTS make[3]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' PASS: param2xfm.tests ================== All 1 tests passed ================== make[3]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc/Extra_progs' make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/minctracc' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc' make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/minctracc' Making check in perl make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/perl' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/perl' Making check in Testing make[1]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/Testing' make ellipse0.mnc ellipse1.mnc ellipse2.mnc ellipse3.mnc ellipse4.mnc warped_ellipse4.mnc ellipse0_dxyz.mnc ellipse1_dxyz.mnc ellipse2_dxyz.mnc ellipse3_dxyz.mnc ellipse4_dxyz.mnc warped_ellipse4_dxyz.mnc ellipse0_slice_x.mnc ellipse0_slice_y.mnc ellipse0_slice_z.mnc test1.xfm test2.xfm test3.xfm make[2]: Entering directory `/home/teo/t5/mni_autoreg-0.98r/Testing' make[2]: `ellipse0.mnc' is up to date. make[2]: `ellipse1.mnc' is up to date. mincresample -clobber -transformation test2.xfm \ -like ellipse0.mnc ellipse0.mnc ellipse2.mnc make[2]: mincresample: Command not found make[2]: *** [ellipse2.mnc] Error 127 make[2]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/Testing' make[1]: *** [check-am] Error 2 make[1]: Leaving directory `/home/teo/t5/mni_autoreg-0.98r/Testing' make: *** [check-recursive] Error 1 Also, in mni_autoreg_model-1.03 the make install step failed with the following message: gunzip: average_305_headmask.mnc already exists; do you wish to overwrite (y or n)? y gunzip: average_305_mask.mnc already exists; do you wish to overwrite (y or n)? y gunzip: average_305.mnc already exists; do you wish to overwrite (y or n)? y /bin/sh: make_model: command not found make: *** [install] Error 127 Thank you for your help in advance. Best regards, Teo This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Wed Nov 23 15:25:40 2005 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 23 Nov 2005 15:25:40 -0500 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 9 In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265CDE@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265CDE@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: Hi Teo, > Please, could you help me with the following installation-related problem? > > I installed (or I tried to install) on my system (Mandriva LE 2005, Intel Xeon) the following packages: > netcdf-3.5.0 > minc-1.4 > Getopt-Tabular-0.3 > mni_perllib-0.07 > mni_autoreg-0.98r > mni_autoreg_model-1.03 > with path /mni/local/mni. > > When I run ./mritotal input.mnc output.xfm I get the following error: > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > Couldn't find program "mincresample" > Couldn't find program "mincblur" > Couldn't find program "volume_cog" > Couldn't find program "minctracc" > Couldn't find program "check_scale" > Couldn't find program "autocrop" > > However, I can access their individual man page, e.g. ./mritotal -help. The ./mritotal would make me think that in order to run mritotal you do this: cd /usr/local/mni/bin ./mritotal -help ? In this case I think the solution is simply that you need to add /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or ~/.cshrc). If you cd to your home directory and type this what happens? cd ~/ which mritotal which mincresample -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From teodorst at cancerboard.ab.ca Thu Nov 24 14:56:43 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Thu, 24 Nov 2005 12:56:43 -0700 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 10 Message-ID: <86A652071AFE5548AA1C648AD489A15E012005C4@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi Andrew, > The ./mritotal would make me think that in order to run mritotal you do this: > > cd /usr/local/mni/bin > ./mritotal -help > > ? Yes, that is correct. > In this case I think the solution is simply that you need to add > /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or > ~/.cshrc). > > If you cd to your home directory and type this what happens? > > cd ~/ > which mritotal > which mincresample Yes, by setting PATH=/usr/local/mni/bin:$PATH the initial problem with mritotal was fixed. Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. If I run ./mritotal in.mnc out.xfm I would get the following error: Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist In /usr/local/mni/share/mni_autoreg there are only 3 files: average_305_headmask.mnc average_305_mask.mnc average_305.mnc. Thank you for your help. Teo This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From tguo at imaging.robarts.ca Thu Nov 24 15:15:13 2005 From: tguo at imaging.robarts.ca ((Jessie) Ting Guo) Date: Thu, 24 Nov 2005 15:15:13 -0500 Subject: [MINC-users] Questions about MNI-Autoreg Message-ID: <006701c5f133$d34d93f0$c32914c6@irus.robarts.ca> Hello everyone, I have a few questions regarding the MNI Autoreg. 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? Thanks a lot! Jessie From a.janke at gmail.com Thu Nov 24 20:40:32 2005 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 24 Nov 2005 20:40:32 -0500 Subject: [MINC-users] Questions about MNI-Autoreg In-Reply-To: <006701c5f133$d34d93f0$c32914c6@irus.robarts.ca> References: <006701c5f133$d34d93f0$c32914c6@irus.robarts.ca> Message-ID: > I have a few questions regarding the MNI Autoreg. > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? packages.bic.mni.mcgill.ca/tgz > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? Intensity cross correlation by default. > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? sbrain? I'm afraid you lost me.. :) -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Thu Nov 24 20:43:23 2005 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 24 Nov 2005 20:43:23 -0500 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 10 In-Reply-To: <86A652071AFE5548AA1C648AD489A15E012005C4@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E012005C4@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. What was the error in the install process? Looks to me (from the below) that the install didn't complete and only files were copied. i suspect again this is because make_model (part of the mni_autoreg install) was not on your path when you installed the model files package. > If I run ./mritotal in.mnc out.xfm I would get the following error: > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > average_305_headmask.mnc > average_305_mask.mnc > average_305.mnc. So, now that you have fixed your path you can either re-install the model files or do this: cd /usr/loca/mni/share/mni_autoreg make_model average_305 -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Thu Nov 24 22:40:25 2005 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 24 Nov 2005 22:40:25 -0500 Subject: [MINC-users] Help on how to transform a displacement field!!! In-Reply-To: <20051117091949.56131.qmail@web60815.mail.yahoo.com> References: <20051117091949.56131.qmail@web60815.mail.yahoo.com> Message-ID: > I would like to understand what "a non-mass > preserving resampling" means. It is the notion of preserving signal as it relates to area in the original image. ie: if you shrink an area by 10% you increase its signal by 10%. Thus if you integrate across an area both before and after resampling you will get the same result. Sometimes you want to do this and sometimes you dont..... > Does this mean that I won't be able to apply mincblob on the results? no > Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field. why? This is in effect what mincresample does. -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From teodorst at cancerboard.ab.ca Fri Nov 25 17:50:37 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Fri, 25 Nov 2005 15:50:37 -0700 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 11 References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CF0@ACBEXCHANGE.ad.cancerboard.ab.ca> > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 > >directory. > What was the error in the install process? Looks to me (from the > below) that the install didn't complete and only files were copied. i > suspect again this is because make_model (part of the mni_autoreg > install) was not on your path when you installed the model files > package. The error I got is: gunzip: average_305_headmask.mnc already exists; do you wish to overwrite (y or n)? y gunzip: average_305_mask.mnc already exists; do you wish to overwrite (y or n)? y gunzip: average_305.mnc already exists; do you wish to overwrite (y or n)? y /bin/sh: /usr/local/mni/bin/make_model: /bin/csh: bad interpreter: No such file or directory make: *** [install] Error 126 > So, now that you have fixed your path you can either re-install the > model files or do this: > > cd /usr/loca/mni/share/mni_autoreg > make_model average_305 I fixed the path, I re-installed the model but I got the same error (please see above). I also tried make_model in /usr/loca/mni/share/mni_autoreg but I got the error: bash: /usr/local/mni/bin/make_model: /bin/csh: bad interpreter: No such file or directory Teo. This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Sat Nov 26 20:27:15 2005 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 26 Nov 2005 20:27:15 -0500 Subject: [MINC-users] MINC-users Digest, Vol 4, Issue 11 In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265CF0@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265CF0@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: Hi, You have two options: 1) install csh or tcsh 2) use a later version of mni_autoreg in which I have converted the make_model script from csh to sh. a On 25/11/05, Teodor Stanescu wrote: > > > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 > > >directory. > > > What was the error in the install process? Looks to me (from the > > below) that the install didn't complete and only files were copied. i > > suspect again this is because make_model (part of the mni_autoreg > > install) was not on your path when you installed the model files > > package. > > The error I got is: > > gunzip: average_305_headmask.mnc already exists; do you wish to overwrite (y or n)? y > gunzip: average_305_mask.mnc already exists; do you wish to overwrite (y or n)? y > gunzip: average_305.mnc already exists; do you wish to overwrite (y or n)? y > /bin/sh: /usr/local/mni/bin/make_model: /bin/csh: bad interpreter: No such file or directory > make: *** [install] Error 126 > > > So, now that you have fixed your path you can either re-install the > > model files or do this: > > > > cd /usr/loca/mni/share/mni_autoreg > > make_model average_305 > > I fixed the path, I re-installed the model but I got the same error (please see above). > I also tried make_model in /usr/loca/mni/share/mni_autoreg but I got the error: > > bash: /usr/local/mni/bin/make_model: /bin/csh: bad interpreter: No such file or directory > > Teo. > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From marc.schoenwiesner at mcgill.ca Sun Nov 27 07:37:05 2005 From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner) Date: Sun, 27 Nov 2005 07:37:05 -0500 Subject: [MINC-users] cortical surface inflation Message-ID: <1133095025.4389a871a6971@webmail.mcgill.ca> Hi, in his BIC seminar talk some weeks ago Alan Evans mentioned the possible advantages of coregistering anatomical volumes on a sphere to decrease intersubject variability for fMRI analysis. Once the cortical surfaces are extracted how would one proceed to do this with the MINC tools? The cortical surfaces need to be inflated into spheres and a transformation to get from the volume- to spherical space and back in needed, I guess. Cheers, Marc =============================== Marc Schoenwiesner, PhD Department of Neuropsychology Montreal Neurological Institute 3801 Rue University Montr?al, Qu?bec __o Canada, H3A 2B4 _`\<,_ tel: 514-398-2579 (+)/ (+) fax: 514-398-1338 www.bic.mni.mcgill.ca/~marcs lab website: www.zlab.mcgill.ca =============================== From jharlap at bic.mni.mcgill.ca Sun Nov 27 11:21:43 2005 From: jharlap at bic.mni.mcgill.ca (Jonathan Harlap) Date: Sun, 27 Nov 2005 11:21:43 -0500 Subject: [MINC-users] cortical surface inflation In-Reply-To: <1133095025.4389a871a6971@webmail.mcgill.ca> References: <1133095025.4389a871a6971@webmail.mcgill.ca> Message-ID: <4389DD17.5020000@bic.mni.mcgill.ca> I believe the idea was more that you can take a signal measured on the surface (or mapped to the surface from the volumetric data) and then perform registration and subsequent analyses with the surface data. i.e., you don't map back from the surface to a volume. Inflating a surface to a sphere is actually pretty trivial due to the way that the cortices are extracted, in that a sphere is shrinkwrapped down onto the cortex. Thus, the function that maps vertices in your cortical surface back to vertices on the inflated sphere is simply the identity. In other words, once you have a signal at each vertex on the cortex you can simply use the same signal on a sphere of identical structure (such as, say, the one used to generate the cortical surface) and you will have mapped the signal onto a sphere. Surface registration is a topic I really can't comment on with any authority. As to signals on the surface, Jason Lerch wrote about cortical thickness analysis on the wiki (http://wiki.bic.mni.mcgill.ca/index.php/CorticalThickness). Noting that cortical thickness is just one example signal you can have on the surface, most of the information there should be easily applicable to other signals. J Marc Schoenwiesner wrote: > Hi, > > in his BIC seminar talk some weeks ago Alan Evans mentioned the possible > advantages of coregistering anatomical volumes on a sphere to decrease > intersubject variability for fMRI analysis. Once the cortical surfaces are > extracted how would one proceed to do this with the MINC tools? The cortical > surfaces need to be inflated into spheres and a transformation to get from the > volume- to spherical space and back in needed, I guess. > > Cheers, > Marc > > =============================== > Marc Schoenwiesner, PhD > Department of Neuropsychology > Montreal Neurological Institute > 3801 Rue University > Montr?al, Qu?bec __o > Canada, H3A 2B4 _`\<,_ > tel: 514-398-2579 (+)/ (+) > fax: 514-398-1338 > www.bic.mni.mcgill.ca/~marcs > lab website: www.zlab.mcgill.ca > =============================== > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From steven.robbins at videotron.ca Mon Nov 28 01:10:20 2005 From: steven.robbins at videotron.ca (Steve M. Robbins) Date: Mon, 28 Nov 2005 01:10:20 -0500 Subject: [MINC-users] cortical surface inflation In-Reply-To: <1133095025.4389a871a6971@webmail.mcgill.ca> References: <1133095025.4389a871a6971@webmail.mcgill.ca> Message-ID: <20051128061016.GP5067@nyongwa.montreal.qc.ca> On Sun, Nov 27, 2005 at 07:37:05AM -0500, Marc Schoenwiesner wrote: > in his BIC seminar talk some weeks ago Alan Evans mentioned the > possible advantages of coregistering anatomical volumes on a sphere > to decrease intersubject variability for fMRI analysis. Once the > cortical surfaces are extracted how would one proceed to do this > with the MINC tools? The cortical surfaces need to be inflated into > spheres As Jonathan Harlap suggested, inflation is the easy part. > and a transformation to get from the volume- to spherical space This is the non-trivial part. The extracted cortical surface is thin so you'll need to do some kind of projection of the volume data onto the surface. I have done this with sulcal label data, but never with anything like fMRI. For labels I used simple heuristics like: label the surface node closest to the voxel. > and back in needed, I guess. Going from the 2D sphere to the 3D volume isn't too hard and is only for visualization, anyway. Once you have each subject's data on the sphere, my "mni_surfreg" code can be used to register them all to a standard space/template. This should reduce the intersubject anatomical variability and improve the analysis. This registration has been used in thickness analyses like those that Jonathan mentioned. -Steve From schwarz at cba.muni.cz Mon Nov 28 11:37:45 2005 From: schwarz at cba.muni.cz (Daniel Schwarz) Date: Mon, 28 Nov 2005 17:37:45 +0100 Subject: [MINC-users] mincmorph problem Message-ID: <200511281637.jASGbnT4026695@tirith.ics.muni.cz> Dear minc-users, I have afollowing problem with running mincmorph. All I would like to do is to prepare mask files for my native MRI data. I would like to use these mask files in nu_correct. After the command: mincmorph -dilation test-segmented.mnc test-dilated.mnc I get the message: Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Copy_volume(): copying cached volumes not implemented. Segmentation fault (core dumped) I tried two ways to construct test-segmented.mnc: mincmath -segment -const2 100 4096 -byte -unsigned -range 0 1 test.mnc test-segmented.mnc mincmorph -binarise -range 100 4096 test.mnc test-segmented.mnc with the same result from dilation. I guess that the problem is is in the messages Copy_volume...., as the messages Not implemented yet in.... are quite frequent. Can anyone give me a suggestion to solve that problem? Is there another way to do the mask files for nu_correct from native MRI? I could do also nu_correct in stx space, where the maskfiles are prepared, but the image intensities are already blurred by interpolation...and phpwiki also suggests to perform nu_correct on native MRI. Thanks for any replay. Regards. Daniel Schwarz From teodorst at cancerboard.ab.ca Mon Nov 28 18:44:38 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Mon, 28 Nov 2005 16:44:38 -0700 Subject: [MINC-users] dicom to minc converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CF4@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, I tried to convert some dicom images (Philips, Intera 3T) into mnc format using dcm2mnc and I got the following error: Checking file types... File /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm appears to be DICOM (CD/Export). Parsing 28 files |<--Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm, which is not in theexpected format. ->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513198175.dcm, which is not in the expected format. -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513204176.dcm, which is not in the expected format. -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513210177.dcm, which is not in the expected format. [...] Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311531998201.dcm, which is not in the expected format. Sorting 0 files... Done sorting files. Processing files, one series at a time... Done processing files. Can anyone help me with some suggestions? Thank you. Teo -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca Sent: Fri 11/25/2005 10:00 AM To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 4, Issue 11 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. Re: MINC-users Digest, Vol 4, Issue 10 (Teodor Stanescu) 2. Questions about MNI-Autoreg ((Jessie) Ting Guo) 3. Re: Questions about MNI-Autoreg (Andrew Janke) 4. Re: MINC-users Digest, Vol 4, Issue 10 (Andrew Janke) 5. Re: Help on how to transform a displacement field!!! (Andrew Janke) ---------------------------------------------------------------------- Message: 1 Date: Thu, 24 Nov 2005 12:56:43 -0700 From: "Teodor Stanescu" Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 To: Message-ID: <86A652071AFE5548AA1C648AD489A15E012005C4 at ACBEXCHANGE.ad.cancerboard.ab.ca> Content-Type: text/plain; charset="iso-8859-1" Hi Andrew, > The ./mritotal would make me think that in order to run mritotal you do this: > > cd /usr/local/mni/bin > ./mritotal -help > > ? Yes, that is correct. > In this case I think the solution is simply that you need to add > /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or > ~/.cshrc). > > If you cd to your home directory and type this what happens? > > cd ~/ > which mritotal > which mincresample Yes, by setting PATH=/usr/local/mni/bin:$PATH the initial problem with mritotal was fixed. Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. If I run ./mritotal in.mnc out.xfm I would get the following error: Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist In /usr/local/mni/share/mni_autoreg there are only 3 files: average_305_headmask.mnc average_305_mask.mnc average_305.mnc. Thank you for your help. Teo This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. ------------------------------ Message: 2 Date: Thu, 24 Nov 2005 15:15:13 -0500 From: "\(Jessie\) Ting Guo" Subject: [MINC-users] Questions about MNI-Autoreg To: Message-ID: <006701c5f133$d34d93f0$c32914c6 at irus.robarts.ca> Content-Type: text/plain; charset="iso-8859-1" Hello everyone, I have a few questions regarding the MNI Autoreg. 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? Thanks a lot! Jessie ------------------------------ Message: 3 Date: Thu, 24 Nov 2005 20:40:32 -0500 From: Andrew Janke Subject: Re: [MINC-users] Questions about MNI-Autoreg To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 > I have a few questions regarding the MNI Autoreg. > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? packages.bic.mni.mcgill.ca/tgz > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? Intensity cross correlation by default. > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? sbrain? I'm afraid you lost me.. :) -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 ------------------------------ Message: 4 Date: Thu, 24 Nov 2005 20:43:23 -0500 From: Andrew Janke Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. What was the error in the install process? Looks to me (from the below) that the install didn't complete and only files were copied. i suspect again this is because make_model (part of the mni_autoreg install) was not on your path when you installed the model files package. > If I run ./mritotal in.mnc out.xfm I would get the following error: > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > average_305_headmask.mnc > average_305_mask.mnc > average_305.mnc. So, now that you have fixed your path you can either re-install the model files or do this: cd /usr/loca/mni/share/mni_autoreg make_model average_305 -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 ------------------------------ Message: 5 Date: Thu, 24 Nov 2005 22:40:25 -0500 From: Andrew Janke Subject: Re: [MINC-users] Help on how to transform a displacement field!!! To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 > I would like to understand what "a non-mass > preserving resampling" means. It is the notion of preserving signal as it relates to area in the original image. ie: if you shrink an area by 10% you increase its signal by 10%. Thus if you integrate across an area both before and after resampling you will get the same result. Sometimes you want to do this and sometimes you dont..... > Does this mean that I won't be able to apply mincblob on the results? no > Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field. why? This is in effect what mincresample does. -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 ------------------------------ _______________________________________________ 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 4, Issue 11 ***************************************** This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Mon Nov 28 20:59:25 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 28 Nov 2005 20:59:25 -0500 Subject: [MINC-users] dicom to minc converter In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265CF4@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265CF4@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: It would appear (from the error) that the files are not even dicom. Can they be opened with anything else? imageJ/Osirix? a On 28/11/05, Teodor Stanescu wrote: > Hi, > > I tried to convert some dicom images (Philips, Intera 3T) into mnc format using dcm2mnc and I got the following error: > > Checking file types... > File /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm appears to be DICOM (CD/Export). > Parsing 28 files |<--Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm, which is not in theexpected format. > ->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513198175.dcm, which is not in the expected format. > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513204176.dcm, which is not in the expected format. > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513210177.dcm, which is not in the expected format. > > [...] > > Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311531998201.dcm, which is not in the expected format. > Sorting 0 files... Done sorting files. > Processing files, one series at a time... > Done processing files. > > Can anyone help me with some suggestions? > Thank you. > > Teo > > > -----Original Message----- > From: minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca > Sent: Fri 11/25/2005 10:00 AM > To: minc-users at bic.mni.mcgill.ca > Subject: MINC-users Digest, Vol 4, Issue 11 > > 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. Re: MINC-users Digest, Vol 4, Issue 10 (Teodor Stanescu) > 2. Questions about MNI-Autoreg ((Jessie) Ting Guo) > 3. Re: Questions about MNI-Autoreg (Andrew Janke) > 4. Re: MINC-users Digest, Vol 4, Issue 10 (Andrew Janke) > 5. Re: Help on how to transform a displacement field!!! > (Andrew Janke) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Nov 2005 12:56:43 -0700 > From: "Teodor Stanescu" > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 > To: > Message-ID: > <86A652071AFE5548AA1C648AD489A15E012005C4 at ACBEXCHANGE.ad.cancerboard.ab.ca> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Andrew, > > > The ./mritotal would make me think that in order to run mritotal you do this: > > > > cd /usr/local/mni/bin > > ./mritotal -help > > > > ? > > Yes, that is correct. > > > In this case I think the solution is simply that you need to add > > /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or > > ~/.cshrc). > > > > If you cd to your home directory and type this what happens? > > > > cd ~/ > > which mritotal > > which mincresample > > Yes, by setting PATH=/usr/local/mni/bin:$PATH the initial problem with mritotal was fixed. > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. > If I run ./mritotal in.mnc out.xfm I would get the following error: > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > average_305_headmask.mnc > average_305_mask.mnc > average_305.mnc. > > Thank you for your help. > > Teo > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > ------------------------------ > > Message: 2 > Date: Thu, 24 Nov 2005 15:15:13 -0500 > From: "\(Jessie\) Ting Guo" > Subject: [MINC-users] Questions about MNI-Autoreg > To: > Message-ID: <006701c5f133$d34d93f0$c32914c6 at irus.robarts.ca> > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone, > > I have a few questions regarding the MNI Autoreg. > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? > > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? > > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? > > Thanks a lot! > > Jessie > > ------------------------------ > > Message: 3 > Date: Thu, 24 Nov 2005 20:40:32 -0500 > From: Andrew Janke > Subject: Re: [MINC-users] Questions about MNI-Autoreg > To: MINC users mailing list > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1 > > > I have a few questions regarding the MNI Autoreg. > > > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? > > packages.bic.mni.mcgill.ca/tgz > > > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? > > Intensity cross correlation by default. > > > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? > > sbrain? I'm afraid you lost me.. :) > > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > > > ------------------------------ > > Message: 4 > Date: Thu, 24 Nov 2005 20:43:23 -0500 > From: Andrew Janke > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 > To: MINC users mailing list > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1 > > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. > > What was the error in the install process? Looks to me (from the > below) that the install didn't complete and only files were copied. i > suspect again this is because make_model (part of the mni_autoreg > install) was not on your path when you installed the model files > package. > > > If I run ./mritotal in.mnc out.xfm I would get the following error: > > > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > > average_305_headmask.mnc > > average_305_mask.mnc > > average_305.mnc. > > So, now that you have fixed your path you can either re-install the > model files or do this: > > cd /usr/loca/mni/share/mni_autoreg > make_model average_305 > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > > > ------------------------------ > > Message: 5 > Date: Thu, 24 Nov 2005 22:40:25 -0500 > From: Andrew Janke > Subject: Re: [MINC-users] Help on how to transform a displacement > field!!! > To: MINC users mailing list > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1 > > > I would like to understand what "a non-mass > > preserving resampling" means. > > It is the notion of preserving signal as it relates to area in the > original image. ie: if you shrink an area by 10% you increase its > signal by 10%. Thus if you integrate across an area both before and > after resampling you will get the same result. Sometimes you want to > do this and sometimes you dont..... > > > Does this mean that I won't be able to apply mincblob on the results? > > no > > > Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field. > > why? This is in effect what mincresample does. > > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > > > ------------------------------ > > _______________________________________________ > 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 4, Issue 11 > ***************************************** > > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Nov 28 21:35:41 2005 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 28 Nov 2005 21:35:41 -0500 Subject: [MINC-users] mincmorph problem In-Reply-To: <200511281637.jASGbnT4026695@tirith.ics.muni.cz> References: <200511281637.jASGbnT4026695@tirith.ics.muni.cz> Message-ID: Hi daniel, I presume test-segmented.mnc is a somewhat large file? volume_io has provision for on-disk caching when working on large files. unfortunately it was never completely implemented (as you have discovered) this is mainly as memory is now cheap. Which version of minc are you running? later version have this "functionality" essentially disabled by setting the cache threshold rather large. You could test this by doing something like this in your ~/.bashrc export VOLUME_CACHE_THRESHOLD 1000000000 a On 28/11/05, Daniel Schwarz wrote: > Dear minc-users, > > I have afollowing problem with running mincmorph. All I would like to do is > to prepare mask files for my native MRI data. I would like to use these mask > files in nu_correct. > > After the command: > > mincmorph -dilation test-segmented.mnc test-dilated.mnc > > I get the message: > > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Copy_volume(): copying cached volumes not implemented. > Segmentation fault (core dumped) > > I tried two ways to construct test-segmented.mnc: > > mincmath -segment -const2 100 4096 -byte -unsigned -range 0 1 test.mnc > test-segmented.mnc > mincmorph -binarise -range 100 4096 test.mnc test-segmented.mnc > > with the same result from dilation. > I guess that the problem is is in the messages Copy_volume...., as the > messages Not implemented yet in.... are quite frequent. > > > Can anyone give me a suggestion to solve that problem? > Is there another way to do the mask files for nu_correct from native MRI? > I could do also nu_correct in stx space, where the maskfiles are prepared, > but the image intensities are already blurred by interpolation...and phpwiki > also suggests to perform nu_correct on native MRI. > > Thanks for any replay. > > Regards. > > Daniel Schwarz > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From bert at bic.mni.mcgill.ca Mon Nov 28 21:58:18 2005 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Mon, 28 Nov 2005 21:58:18 -0500 Subject: [MINC-users] dicom to minc converter In-Reply-To: Message-ID: Hi Teodor, The code is written to skip over files it doesn't recognize as being consistent with the first DICOM file it finds. This could be misbehaving for some reason with your files. Is there any way you could send me a few examples? -bert On Mon, 28 Nov 2005, Andrew Janke wrote: > It would appear (from the error) that the files are not even dicom. > Can they be opened with anything else? imageJ/Osirix? > > > a > > On 28/11/05, Teodor Stanescu wrote: > > Hi, > > > > I tried to convert some dicom images (Philips, Intera 3T) into mnc format using dcm2mnc and I got the following error: > > > > Checking file types... > > File /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm appears to be DICOM (CD/Export). > > Parsing 28 files |<--Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm, which is not in theexpected format. > > ->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513198175.dcm, which is not in the expected format. > > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513204176.dcm, which is not in the expected format. > > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513210177.dcm, which is not in the expected format. > > > > [...] > > > > Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311531998201.dcm, which is not in the expected format. > > Sorting 0 files... Done sorting files. > > Processing files, one series at a time... > > Done processing files. > > > > Can anyone help me with some suggestions? > > Thank you. > > > > Teo > > > > > > -----Original Message----- > > From: minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca > > Sent: Fri 11/25/2005 10:00 AM > > To: minc-users at bic.mni.mcgill.ca > > Subject: MINC-users Digest, Vol 4, Issue 11 > > > > 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. Re: MINC-users Digest, Vol 4, Issue 10 (Teodor Stanescu) > > 2. Questions about MNI-Autoreg ((Jessie) Ting Guo) > > 3. Re: Questions about MNI-Autoreg (Andrew Janke) > > 4. Re: MINC-users Digest, Vol 4, Issue 10 (Andrew Janke) > > 5. Re: Help on how to transform a displacement field!!! > > (Andrew Janke) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 24 Nov 2005 12:56:43 -0700 > > From: "Teodor Stanescu" > > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 > > To: > > Message-ID: > > <86A652071AFE5548AA1C648AD489A15E012005C4 at ACBEXCHANGE.ad.cancerboard.ab.ca> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Andrew, > > > > > The ./mritotal would make me think that in order to run mritotal you do this: > > > > > > cd /usr/local/mni/bin > > > ./mritotal -help > > > > > > ? > > > > Yes, that is correct. > > > > > In this case I think the solution is simply that you need to add > > > /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or > > > ~/.cshrc). > > > > > > If you cd to your home directory and type this what happens? > > > > > > cd ~/ > > > which mritotal > > > which mincresample > > > > Yes, by setting PATH=/usr/local/mni/bin:$PATH the initial problem with mritotal was fixed. > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. > > If I run ./mritotal in.mnc out.xfm I would get the following error: > > > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > > average_305_headmask.mnc > > average_305_mask.mnc > > average_305.mnc. > > > > Thank you for your help. > > > > Teo > > > > > > This e-mail and any attachments may contain confidential and > > privileged information. If you are not the intended recipient, > > please notify the sender immediately by return e-mail, delete this > > e-mail and destroy any copies. Any dissemination or use of this > > information by a person other than the intended recipient is > > unauthorized and may be illegal. > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 24 Nov 2005 15:15:13 -0500 > > From: "\(Jessie\) Ting Guo" > > Subject: [MINC-users] Questions about MNI-Autoreg > > To: > > Message-ID: <006701c5f133$d34d93f0$c32914c6 at irus.robarts.ca> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello everyone, > > > > I have a few questions regarding the MNI Autoreg. > > > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? > > > > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? > > > > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? > > > > Thanks a lot! > > > > Jessie > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 24 Nov 2005 20:40:32 -0500 > > From: Andrew Janke > > Subject: Re: [MINC-users] Questions about MNI-Autoreg > > To: MINC users mailing list > > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > > > > I have a few questions regarding the MNI Autoreg. > > > > > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version? > > > > packages.bic.mni.mcgill.ca/tgz > > > > > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that? > > > > Intensity cross correlation by default. > > > > > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy? > > > > sbrain? I'm afraid you lost me.. :) > > > > > > -- > > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > > Canada->Montreal Cell: +1 (514) 924 2012 > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 24 Nov 2005 20:43:23 -0500 > > From: Andrew Janke > > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10 > > To: MINC users mailing list > > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > > > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory. > > > > What was the error in the install process? Looks to me (from the > > below) that the install didn't complete and only files were copied. i > > suspect again this is because make_model (part of the mni_autoreg > > install) was not on your path when you installed the model files > > package. > > > > > If I run ./mritotal in.mnc out.xfm I would get the following error: > > > > > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg > > > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) > > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist > > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist > > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist > > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist > > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist > > > > > > In /usr/local/mni/share/mni_autoreg there are only 3 files: > > > average_305_headmask.mnc > > > average_305_mask.mnc > > > average_305.mnc. > > > > So, now that you have fixed your path you can either re-install the > > model files or do this: > > > > cd /usr/loca/mni/share/mni_autoreg > > make_model average_305 > > > > -- > > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > > Canada->Montreal Cell: +1 (514) 924 2012 > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Thu, 24 Nov 2005 22:40:25 -0500 > > From: Andrew Janke > > Subject: Re: [MINC-users] Help on how to transform a displacement > > field!!! > > To: MINC users mailing list > > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > > > > I would like to understand what "a non-mass > > > preserving resampling" means. > > > > It is the notion of preserving signal as it relates to area in the > > original image. ie: if you shrink an area by 10% you increase its > > signal by 10%. Thus if you integrate across an area both before and > > after resampling you will get the same result. Sometimes you want to > > do this and sometimes you dont..... > > > > > Does this mean that I won't be able to apply mincblob on the results? > > > > no > > > > > Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field. > > > > why? This is in effect what mincresample does. > > > > > > -- > > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > > Canada->Montreal Cell: +1 (514) 924 2012 > > > > > > > > ------------------------------ > > > > _______________________________________________ > > 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 4, Issue 11 > > ***************************************** > > > > > > > > This e-mail and any attachments may contain confidential and > > privileged information. If you are not the intended recipient, > > please notify the sender immediately by return e-mail, delete this > > e-mail and destroy any copies. Any dissemination or use of this > > information by a person other than the intended recipient is > > unauthorized and may be illegal. > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 2012 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From schwarz at cba.muni.cz Tue Nov 29 02:56:48 2005 From: schwarz at cba.muni.cz (Daniel Schwarz) Date: Tue, 29 Nov 2005 08:56:48 +0100 Subject: [MINC-users] mincmorph problem In-Reply-To: Message-ID: <200511290756.jAT7us4X032226@tirith.ics.muni.cz> Hi Andrew, Thanks for your advice. It fixed the problem. I use the package made for Cygwin by Dylan D. Wagner (I am not sure which version of minc tools is there). Daniel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke Sent: Tuesday, November 29, 2005 3:36 AM To: MINC users mailing list Subject: Re: [MINC-users] mincmorph problem Hi daniel, I presume test-segmented.mnc is a somewhat large file? volume_io has provision for on-disk caching when working on large files. unfortunately it was never completely implemented (as you have discovered) this is mainly as memory is now cheap. Which version of minc are you running? later version have this "functionality" essentially disabled by setting the cache threshold rather large. You could test this by doing something like this in your ~/.bashrc export VOLUME_CACHE_THRESHOLD 1000000000 a On 28/11/05, Daniel Schwarz wrote: > Dear minc-users, > > I have afollowing problem with running mincmorph. All I would like to > do is to prepare mask files for my native MRI data. I would like to > use these mask files in nu_correct. > > After the command: > > mincmorph -dilation test-segmented.mnc test-dilated.mnc > > I get the message: > > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Copy_volume(): copying cached volumes not implemented. > Segmentation fault (core dumped) > > I tried two ways to construct test-segmented.mnc: > > mincmath -segment -const2 100 4096 -byte -unsigned -range 0 1 > test.mnc test-segmented.mnc mincmorph -binarise -range 100 4096 > test.mnc test-segmented.mnc > > with the same result from dilation. > I guess that the problem is is in the messages Copy_volume...., as the > messages Not implemented yet in.... are quite frequent. > > > Can anyone give me a suggestion to solve that problem? > Is there another way to do the mask files for nu_correct from native MRI? > I could do also nu_correct in stx space, where the maskfiles are > prepared, but the image intensities are already blurred by > interpolation...and phpwiki also suggests to perform nu_correct on native MRI. > > Thanks for any replay. > > Regards. > > Daniel Schwarz > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From teodorst at cancerboard.ab.ca Tue Nov 29 11:06:52 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Tue, 29 Nov 2005 09:06:52 -0700 Subject: [MINC-users] dicom to minc converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CF6@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi Bert, To open/analyze these images I used: eFilm (Dicom transfer), DicomWorks/dcmtk (alter Dicom tags) and Matlab/Mipav (image processing). I am going to send you few samples on private. Thanks. Teo > Hi Teodor, > > The code is written to skip over files it doesn't recognize as being > consistent with the first DICOM file it finds. This could be misbehaving > for some reason with your files. Is there any way you could send me a few > examples? > > -bert This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From teodorst at cancerboard.ab.ca Tue Nov 29 11:15:01 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Tue, 29 Nov 2005 09:15:01 -0700 Subject: [MINC-users] dicom to minc converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CF8@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi Andrew, Yes, I can open them with no problem in Matlab, Mipav, DicomWorks, eFilm ... I got the same error message with both 1.5T and 3T images (Philips Intera). Teo > It would appear (from the error) that the files are not even dicom. > Can they be opened with anything else? imageJ/Osirix? > > > a This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From acveilleux at mrs.mni.mcgill.ca Tue Nov 29 11:26:22 2005 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Tue, 29 Nov 2005 11:26:22 -0500 Subject: [MINC-users] dicom to minc converter In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265CF8@ACBEXCHANGE.ad.cancerboard.ab.ca>; from teodorst@cancerboard.ab.ca on Tue, Nov 29, 2005 at 09:15:01AM -0700 References: <86A652071AFE5548AA1C648AD489A15E01265CF8@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: <20051129112622.A8782@mrs.mni.mcgill.ca> On Tue, Nov 29, 2005 at 09:15:01AM -0700, Teodor Stanescu wrote: > > Yes, I can open them with no problem in Matlab, Mipav, DicomWorks, eFilm ... I got the same error message with both 1.5T and 3T images (Philips Intera). If I can drop in, there's a few questions I'd have: 1) Did you try dicom_to_minc (Peter neelin's version) ? 2) Did you try dicom_to_minc3.pl (Jonathan Harlap's version using the DICOMperl library) ? 3) What is the encoding used? I assume that it's native little endian. I also have some bits of codes to reorder dicom files to fix a very similar issue with dicom_to_minc. However that code requires a modified DICOMperl lib to run. I have the "chance" of having dealt with tricky conversions from probably every scanner model made in the last 15 yeas ;-). Alex From teodorst at cancerboard.ab.ca Tue Nov 29 12:18:47 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Tue, 29 Nov 2005 10:18:47 -0700 Subject: [MINC-users] dicom to minc converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265CFD@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi Alex, 1) I haven't had the chance to try dicom_to_minc, yet. 2) I ran dicom3_to_minc and I got the following error: Reading headers from file "/home/teo/imags" Wrong number of bits allocated per image () Error reading file "/home/teo/imags". Skipping to next. Cleaning up temporary files. 3) Yes, the encoding is little endian. Thanks. Teo > If I can drop in, there's a few questions I'd have: > > 1) Did you try dicom_to_minc (Peter neelin's version) ? > > 2) Did you try dicom_to_minc3.pl (Jonathan Harlap's version using the > DICOMperl library) ? > > 3) What is the encoding used? I assume that it's native little endian. > > I also have some bits of codes to reorder dicom files to fix > a very similar issue with dicom_to_minc. However that code requires > a modified DICOMperl lib to run. > > I have the "chance" of having dealt with tricky conversions > from probably every scanner model made in the last 15 yeas ;-). > > Alex This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From acveilleux at mrs.mni.mcgill.ca Tue Nov 29 12:59:15 2005 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Tue, 29 Nov 2005 12:59:15 -0500 Subject: [MINC-users] dicom to minc converter In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265CFD@ACBEXCHANGE.ad.cancerboard.ab.ca>; from teodorst@cancerboard.ab.ca on Tue, Nov 29, 2005 at 10:18:47AM -0700 References: <86A652071AFE5548AA1C648AD489A15E01265CFD@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: <20051129125915.A12778@mrs.mni.mcgill.ca> On Tue, Nov 29, 2005 at 10:18:47AM -0700, Teodor Stanescu wrote: > > 3) Yes, the encoding is little endian. You can get the exact encoding by the following method: strings | grep 1.2.840.10008.1. The output will be a UID starting by the numeric string above. It's meaning can be derived from Section 6 of the DICOM standard ( http://medical.nema.org/dicom/2004/04_06PU.PDF Table A-1, Page 83.) 1.2.840.10008.1.2.1 (Little Endian, native encoding) and 1.2.840.10008.1.2.2 (Big Endian, native encoding) are the only ones accepted by the dicom_to_minc tools. Any UID starting with 1.2.840.10008.1.2.4. is for a compressed image and it would need to be processed through a decompresser ( dcmdjpeg for example). Otherwise, a pair of sample slices (contiguous) could be useful. Alex > > Thanks. > > Teo > > > > If I can drop in, there's a few questions I'd have: > > > > 1) Did you try dicom_to_minc (Peter neelin's version) ? > > > > 2) Did you try dicom_to_minc3.pl (Jonathan Harlap's version using the > > DICOMperl library) ? > > > > 3) What is the encoding used? I assume that it's native little endian. > > > > I also have some bits of codes to reorder dicom files to fix > > a very similar issue with dicom_to_minc. However that code requires > > a modified DICOMperl lib to run. > > > > I have the "chance" of having dealt with tricky conversions > > from probably every scanner model made in the last 15 yeas ;-). > > > > Alex > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From teodorst at cancerboard.ab.ca Tue Nov 29 13:21:12 2005 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Tue, 29 Nov 2005 11:21:12 -0700 Subject: [MINC-users] dicom to minc converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265D02@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi Alex, This is what I got: $ strings 1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm | grep 1.2.840.10008.1. 1.2.840.10008.1.2 I guess it is bis endian (and not little endian as I previously mentioned). Teo This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From acveilleux at mrs.mni.mcgill.ca Tue Nov 29 14:58:05 2005 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Tue, 29 Nov 2005 14:58:05 -0500 Subject: [MINC-users] dicom to minc converter In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265D02@ACBEXCHANGE.ad.cancerboard.ab.ca>; from teodorst@cancerboard.ab.ca on Tue, Nov 29, 2005 at 11:21:12AM -0700 References: <86A652071AFE5548AA1C648AD489A15E01265D02@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: <20051129145805.C17489@mrs.mni.mcgill.ca> On Tue, Nov 29, 2005 at 11:21:12AM -0700, Teodor Stanescu wrote: > > This is what I got: > $ strings 1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm | grep 1.2.840.10008.1. > 1.2.840.10008.1.2 > > I guess it is bis endian (and not little endian as I previously mentioned). No, you were correct. This is the plainest encoding available. You image data itself should be the last 131072 bytes of the file (for 256x256 images encoded over 2 bytes per voxel.) A dicom header or two would be useful. If you have dicom3_to_minc.pl, you might also have dicom.pl which can dump the header. From the error message generated from dicom3_to_minc.pl, it seems it can't figure out the bit depeth and bit encoding of the image but it's hard to tell without an header. OsiriX and eFilm both have options to show the dicom header, I think. Alex From runa at medphys.ucl.ac.uk Wed Nov 30 16:59:56 2005 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Wed, 30 Nov 2005 21:59:56 +0000 Subject: [MINC-users] help on using rawtominc and n3 Message-ID: <5.2.0.9.0.20051130211322.00bbf3b8@pop3-server> Hi, I have several question to run this package: 1. I have coronal slices, dimension: 256x256x170, cubic voxel :1mm, T1 weighted. I could not understand how I could give the command when changing from rawtominc? also in world coordinate space? the command line I use: rawtominc -coronal -short -unsigned -origin 0 0 0 -range 0 32767 -real_range 0 32767 -orange 0 32767 -ystep 1 -zstep 1 -xstep 1 -xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1 -mri data_pix_out.mnc 171 256 256 < data_pix_in.img I am worried about the right way of mentioning dimension and also what would be the first voxel of the data in world coordinate. 2. In mincresample, what would be the position of centre of first voxel along each of the world dimensions? the command line I use: mincresample data_pix_out.mnc data_pix_resample.mnc -transform data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range 0 32767 -nearest_neighbour -nelements 171 256 256 The volume of the output in this stage is almost half of the rawtominc output? 3. In display, the image is showed in some tilting position. Also I would like to know when the image_range is used, what would be value of the voxel when viewing the image in Display? 4. Also after applying nu_correct, the program runs only for 2 iteration and given CV: 0.000878881, is it OK? 5. As it is stopped after 2 iterations, I use the command: nu_correct -iterations 100 -stop 2.e-5 data_pix_resample.mnc data_pix_nu.mnc it stopped after 37 iterations and CV of field changes: 1.61641e-05. Also, in Display, the view of the image in tilting position. Also I would like to know how I could understand the non-uniformity has been corrected? I really need your suggestion in these regards, and early reply is sincerely appreciable. Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * e-mail: runa at medphys.ucl.ac.uk ** *********************************************************************