From ed.gronenschild at mi.unimaas.nl Tue Jan 3 07:34:14 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Tue, 3 Jan 2006 13:34:14 +0100 Subject: [MINC-users] Volumetry and Talairach boxes Message-ID: <233302FF-1AAF-4D81-83E2-15EFE298EEA5@mi.unimaas.nl> Hi all, First of all, I wish everyone a happy new year. I was wondering if it is possible with the MNI software to perform volumetric measurements of gray and white matter and liquor for the whole brain and within Talairach boxes. Kind regards, Ed From anil.kuchinad at mcgill.ca Thu Jan 5 10:40:51 2006 From: anil.kuchinad at mcgill.ca (Anil Ashok Kuchinad, Mr) Date: Thu, 5 Jan 2006 10:40:51 -0500 Subject: [MINC-users] significance question Message-ID: Hey all, I was wondering what value people use as a threshold for statistical significance in a VBM analysis without any a priori hypotheses. I have heard a t-value of 4.2 being tossed around, but I was led to believe that is for fMRI. Cheers, Anil ---------------------------------------------------- Anil Kuchinad Centre for Research on Pain McGill University Strathcona Anatomy and Dentistry Building 3640 University St., Room M/19 Montreal, Quebec , Canada H3A 2B2 Tel: (514) 398-1271 Email: anil.kuchinad at mcgill.ca From bouffard at bic.mni.mcgill.ca Thu Jan 5 12:04:30 2006 From: bouffard at bic.mni.mcgill.ca (Marc BOUFFARD) Date: Thu, 5 Jan 2006 12:04:30 -0500 Subject: [MINC-users] creating a simple mask Message-ID: How can I easily create a mask as a minc file given that the mask is a rectangular region contained inside another rectangular region. Marc From louis.collins at mcgill.ca Thu Jan 5 13:53:16 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Thu, 05 Jan 2006 13:53:16 -0500 Subject: [MINC-users] creating a simple mask In-Reply-To: References: Message-ID: <0853fac20dea5a310a052d4d7f56fbe6@mcgill.ca> Marc, In the mni_autoreg package, there is a program called make_phantom (or makephantom). It can create rectangular or ellipsoidal shapes inside 3D minc volumes. -Louis On Jan 5, 2006, at 12:04 PM, Marc BOUFFARD wrote: > How can I easily create a mask as a minc file given that the mask is a > rectangular region contained inside another rectangular region. > > Marc > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From louis.collins at mcgill.ca Wed Jan 4 13:59:39 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Wed, 04 Jan 2006 13:59:39 -0500 Subject: [MINC-users] Volumetry and Talairach boxes In-Reply-To: <233302FF-1AAF-4D81-83E2-15EFE298EEA5@mi.unimaas.nl> References: <233302FF-1AAF-4D81-83E2-15EFE298EEA5@mi.unimaas.nl> Message-ID: <04724778b80201f1f2391e685f98835d@mcgill.ca> Ed, This should not be difficult, although no one-line command exists to do what you need. I suggest the following, starting with a subj,mnc in native (scanner) space. mritotal subj.mnc subj_to_tal.xfm mincresample subj.mnc subj_tal.mnc -transformation subj_to_tal.xfm -like icbm_template_1.00mm.mnc classify_clean subj_tal.mnc subj_classes.mnc you'll need a method to strip the skull to create a brain mask. We use minc_bet, a derivative of BET from FSL. minccalc -expression 'A[0]>0.5? A[1] : 0' subj_brain_mask.mnc subj_classes.mnc subj_brain_classes.mnc now the fun part. You'll need to chop up the brain into the twelve Talairach boxes and then use print_all_labels to get the volume of each tissue in each box. For example, to get the right frontal superior block: mincreshape -dimrange zspace=72,85 -dimrange xspace=90,70 -dimrange yspace=126,80 \ subj_brain_classes.mnc block.mnc you'll need to play with the start and extent voxel indexes to get each of the twelve blocks correctly defined. to get the volume of tissue for each block: print_all_labels block.mnc hope this helps, -Louis On Jan 3, 2006, at 7:34 AM, Ed Gronenschild wrote: > Hi all, > > First of all, I wish everyone a happy new year. > > I was wondering if it is possible with the MNI software to perform > volumetric > measurements of gray and white matter and liquor for the whole brain > and > within Talairach boxes. > > Kind regards, > > Ed > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jason at bic.mni.mcgill.ca Fri Jan 6 06:22:08 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 6 Jan 2006 06:22:08 -0500 Subject: [MINC-users] significance question In-Reply-To: References: Message-ID: <7BD1BE8D-6D18-4F93-82F4-DD5873F46D5F@bic.mni.mcgill.ca> Greetings, there is no one threshold to use - and this applies to fMRI as well. You first have to chose the thresholding strategy that you would like to use, then compute the appropriate threshold for the degrees of freedom and number of voxels in your study. The most commonly used method is Keith's random field theory - you can find more information about it by starting matlab on one of the SGIs and typing 'help stat_threshold' Cheers, Jason On 5-Jan-06, at 10:40 AM, Anil Ashok Kuchinad, Mr wrote: > Hey all, > > > > I was wondering what value people use as a threshold for statistical > significance in a VBM analysis without any a priori hypotheses. I have > heard a t-value of 4.2 being tossed around, but I was led to believe > that is for fMRI. > > > > Cheers, > > Anil > > > > ---------------------------------------------------- > > Anil Kuchinad > > Centre for Research on Pain > > McGill University > > Strathcona Anatomy and Dentistry Building > > 3640 University St., Room M/19 > > Montreal, Quebec , Canada > > H3A 2B2 > > Tel: (514) 398-1271 > > Email: anil.kuchinad at mcgill.ca > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From tguo at imaging.robarts.ca Mon Jan 16 12:51:52 2006 From: tguo at imaging.robarts.ca ((Jessie) Ting Guo) Date: Mon, 16 Jan 2006 12:51:52 -0500 Subject: [MINC-users] How to check imaging parameters of a minc image Message-ID: <015a01c61ac5$88382c20$c32914c6@irus.robarts.ca> Hello everyone, Is there a program available to check the imaging parameters (TR, TE, flip angle) of a minc image? Thanks, Jessie From sylvain at bic.mni.mcgill.ca Mon Jan 16 13:03:38 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon, 16 Jan 2006 13:03:38 -0500 Subject: [MINC-users] How to check imaging parameters of a minc image In-Reply-To: <015a01c61ac5$88382c20$c32914c6@irus.robarts.ca> Message-ID: Hi, You could try the following: mincheader MyMri.mnc | grep acqui On Mon, 16 Jan 2006, (Jessie) Ting Guo wrote: > Hello everyone, > > Is there a program available to check the imaging parameters (TR, TE, flip angle) of a minc image? > > Thanks, > > Jessie > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From rghassemi at mrs.mni.mcgill.ca Mon Jan 16 13:25:00 2006 From: rghassemi at mrs.mni.mcgill.ca (Rezwan Ghassemi) Date: Mon, 16 Jan 2006 13:25:00 -0500 Subject: [MINC-users] Quantitative T2 Map Message-ID: <200601161325.00413.rghassemi@talos.bic.mni.mcgill.ca> Hello everyone, Is there any script available to calculate the quantitative T2 map in ROI? thanks Rezwan From rghassemi at mrs.mni.mcgill.ca Mon Jan 16 14:40:55 2006 From: rghassemi at mrs.mni.mcgill.ca (Rezwan Ghassemi) Date: Mon, 16 Jan 2006 14:40:55 -0500 Subject: [MINC-users] Quantitative T2 Map Message-ID: <200601161440.55553.rghassemi@talos.bic.mni.mcgill.ca> Hi, I am using the dual-echo data sets (one set from the early echo [TE1] and one from the late echo [TE2]) and use the following equation to get the t2 signal intensity: (TE2 - TE1)/ln (S1/S2), where S1 and S2 represent the signal intensities for the early and late echoes (PDW and T2W) But output is odd! would you please let me know where is the problem. thanks Rezwan From sean at rogue-research.com Mon Jan 16 17:43:56 2006 From: sean at rogue-research.com (Sean McBride) Date: Mon, 16 Jan 2006 17:43:56 -0500 Subject: [MINC-users] MINE type for MINC? Message-ID: <20060116224356.13612@smtp1.sympatico.ca> Hi all, Is there a MIME type defined for the MINC file format? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From bert at bic.mni.mcgill.ca Mon Jan 16 19:42:46 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Mon, 16 Jan 2006 19:42:46 -0500 Subject: [MINC-users] MINE type for MINC? In-Reply-To: <20060116224356.13612@smtp1.sympatico.ca> Message-ID: Not that I'm aware of. -bert On Mon, 16 Jan 2006, Sean McBride wrote: > Hi all, > > Is there a MIME type defined for the MINC file format? > > Thanks, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From acveilleux at mrs.mni.mcgill.ca Tue Jan 17 12:02:35 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Tue, 17 Jan 2006 12:02:35 -0500 Subject: [MINC-users] MINE type for MINC? In-Reply-To: <20060116224356.13612@smtp1.sympatico.ca>; from sean@rogue-research.com on Mon, Jan 16, 2006 at 05:43:56PM -0500 References: <20060116224356.13612@smtp1.sympatico.ca> Message-ID: <20060117120235.C8899@mrs.mni.mcgill.ca> application/octet-stream would be safe. Netcdf which minc1 is based on has mime type image/x-netcdf Alex On Mon, Jan 16, 2006 at 05:43:56PM -0500, Sean McBride wrote: > From: "Sean McBride" > To: > Date: Mon, 16 Jan 2006 17:43:56 -0500 > X-Mailer: CTM PowerMail version 5.2.1 build 4397 English > > Subject: [MINC-users] MINE type for MINC? > > Hi all, > > Is there a MIME type defined for the MINC file format? > > Thanks, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From tguo at imaging.robarts.ca Wed Jan 18 14:16:23 2006 From: tguo at imaging.robarts.ca ((Jessie) Ting Guo) Date: Wed, 18 Jan 2006 14:16:23 -0500 Subject: [MINC-users] AC-PC based Talairach alignment Message-ID: <002701c61c6f$c0db4160$c32914c6@irus.robarts.ca> Hello everyone, Is there any program available to do the AC-PC based Talairach linear alignment? Many Thanks, Jessie From tguo at imaging.robarts.ca Wed Jan 18 14:53:17 2006 From: tguo at imaging.robarts.ca ((Jessie) Ting Guo) Date: Wed, 18 Jan 2006 14:53:17 -0500 Subject: [MINC-users] AC-PC based Talairach alignment Message-ID: <002801c61c6f$c0e8fd00$c32914c6@irus.robarts.ca> Hello everyone, Is there any program available to do the AC-PC based Talairach linear alignment? Many Thanks, Jessie From sylvain at bic.mni.mcgill.ca Wed Jan 18 16:12:21 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed, 18 Jan 2006 16:12:21 -0500 Subject: [MINC-users] AC-PC based Talairach alignment In-Reply-To: <002801c61c6f$c0e8fd00$c32914c6@irus.robarts.ca> Message-ID: Depending on whether you want to do this manually (Register package) or automatically (mni_autoreg package) Go to http://wiki.bic.mni.mcgill.ca/ and use search keywords like: register, registration, talairach - doing a full-text-search is also useful. Sylvain On Wed, 18 Jan 2006, (Jessie) Ting Guo wrote: > Hello everyone, > > Is there any program available to do the AC-PC based Talairach linear alignment? > > Many Thanks, > Jessie > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From a.janke at gmail.com Wed Jan 18 23:36:29 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 18 Jan 2006 23:36:29 -0500 Subject: [MINC-users] AC-PC based Talairach alignment In-Reply-To: <002801c61c6f$c0e8fd00$c32914c6@irus.robarts.ca> References: <002801c61c6f$c0e8fd00$c32914c6@irus.robarts.ca> Message-ID: Hi Jessie, The only automatic procedure that I know of that does the full "talairach" registration process is the registration tool that is part of AFNI (written by Bob Cox). I think it might even support MINC. a On 18/01/06, (Jessie) Ting Guo wrote: > Hello everyone, > > Is there any program available to do the AC-PC based Talairach linear alignment? > > Many Thanks, > Jessie > _______________________________________________ > 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 jualulno at upvnet.upv.es Tue Jan 24 08:48:18 2006 From: jualulno at upvnet.upv.es (Juanjo Lull (UPV)) Date: Tue, 24 Jan 2006 14:48:18 +0100 Subject: [MINC-users] problems installing mni - N3 Message-ID: <43D63022.6060804@upvnet.upv.es> Hi Jason (or whoever is in charge of N3 by now...), I have been trying to install N3, and after many hours of hard trying I feel desperate because I always get the same error: No EBTKS libraries found. I have those libraries installed, but no way. ./configure says it can't find them and there is no possibility to compile the code. I attach the log file that I got while trying to compile the code. Thanks in advance, Juan -- ________________________________________________________ Juan J. Lull Noguera - jualulno_at_upvnet.upv.es [MI - Medical Imaging Area] BET - Bioengineering, Electronics and Telemedicine Group UPV - Politechnical University of Valencia - Spain ________________________________________________________ [IM - ?rea de Imagen] BET - Grupo de Bioingenier?a, Electr?nica y Telemedicina UPV - Universidad Polit?cnica de Valencia ________________________________________________________ -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: config.log Url: http://www.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20060124/d17b2e5b/config.ksh From bert at bic.mni.mcgill.ca Wed Jan 25 08:01:22 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Wed, 25 Jan 2006 08:01:22 -0500 Subject: [MINC-users] problems installing mni - N3 In-Reply-To: <43D63022.6060804@upvnet.upv.es> Message-ID: Hi, How did you install EBTKS? Was it from a binary, or from source? -bert On Tue, 24 Jan 2006, Juanjo Lull (UPV) wrote: > Hi Jason (or whoever is in charge of N3 by now...), > I have been trying to install N3, and after many hours of hard trying I > feel desperate because I always get the same error: No EBTKS libraries > found. I have those libraries installed, but no way. ./configure says it > can't find them and there is no possibility to compile the code. > I attach the log file that I got while trying to compile the code. > Thanks in advance, > Juan > > -- > ________________________________________________________ > Juan J. Lull Noguera - jualulno_at_upvnet.upv.es > [MI - Medical Imaging Area] > BET - Bioengineering, Electronics and Telemedicine Group > UPV - Politechnical University of Valencia - Spain > ________________________________________________________ > [IM - ?rea de Imagen] > BET - Grupo de Bioingenier?a, Electr?nica y Telemedicina > UPV - Universidad Polit?cnica de Valencia > ________________________________________________________ > > From spmlxf at yahoo.com Wed Jan 25 14:07:34 2006 From: spmlxf at yahoo.com (xingfeng lee) Date: Wed, 25 Jan 2006 11:07:34 -0800 (PST) Subject: [MINC-users] fmr_preprocess for motion correction Message-ID: <20060125190734.1323.qmail@web50111.mail.yahoo.com> Dear list, Does anyone know which algorithm is using in fmr_preprocess for fMRI time series motion correction? Are there reference papers for the algorithm? Thank you very much. All the best, Li --------------------------------- Do you Yahoo!? With a free 1 GB, there's more in store with Yahoo! Mail. From jarv0075 at umn.edu Thu Jan 26 12:51:06 2006 From: jarv0075 at umn.edu (Tim Jarvis) Date: Thu, 26 Jan 2006 11:51:06 CST Subject: [MINC-users] Removing per-slice scaling from a MNC volume Message-ID: <200601261751.k0QHp69L020381@sarge.software.umn.edu> What is the most efficient way to remove this from a MNC volume? --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu --------------------------------------- From sylvain at bic.mni.mcgill.ca Thu Jan 26 12:58:33 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Thu, 26 Jan 2006 12:58:33 -0500 Subject: [MINC-users] Removing per-slice scaling from a MNC volume In-Reply-To: <200601261751.k0QHp69L020381@sarge.software.umn.edu> Message-ID: I believe the following should do the trick: mincresample -keep_real_range in.mnc out.mnc On Thu, 26 Jan 2006, Tim Jarvis wrote: > > What is the most efficient way to remove this from a MNC volume? > > --------------------------------------- > Timothy R. Jarvis > --------------------------------------- > Graduate Research Assistant > International Neuroimaging Consortium > VA Medical Center > 612-467-2619 > http://www.neurovia.umn.edu > --------------------------------------- > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From louis.collins at mcgill.ca Thu Jan 26 13:14:56 2006 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Thu, 26 Jan 2006 13:14:56 -0500 Subject: [MINC-users] Removing per-slice scaling from a MNC volume In-Reply-To: References: Message-ID: also mincreshape -normalize in.mnc out.mnc -L On Jan 26, 2006, at 12:58 PM, Sylvain MILOT wrote: > > I believe the following should do the trick: > > mincresample -keep_real_range in.mnc out.mnc > > > On Thu, 26 Jan 2006, Tim Jarvis wrote: > >> >> What is the most efficient way to remove this from a MNC volume? >> >> --------------------------------------- >> Timothy R. Jarvis >> --------------------------------------- >> Graduate Research Assistant >> International Neuroimaging Consortium >> VA Medical Center >> 612-467-2619 >> http://www.neurovia.umn.edu >> --------------------------------------- >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > Webster 2B, Room 208 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From alex at bic.mni.mcgill.ca Thu Jan 26 16:53:44 2006 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Thu, 26 Jan 2006 16:53:44 -0500 Subject: [MINC-users] signal normalization Message-ID: <20060126215344.GA4433@bic.mni.mcgill.ca> Hello, I'm looking for ways to perform non-linear (!) signal normalization on MRI data, as in, match signal and contrast between scans which may have (possibly subtle) contrast differences (due to scanner/sequence/ biology/whatever). If you have ideas for or experience with this, please let me know - any pointers are welcome - and useable minc code is even better ;-) Thanks, -- Alex From a.janke at gmail.com Thu Jan 26 17:11:53 2006 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 26 Jan 2006 17:11:53 -0500 Subject: [MINC-users] signal normalization In-Reply-To: <20060126215344.GA4433@bic.mni.mcgill.ca> References: <20060126215344.GA4433@bic.mni.mcgill.ca> Message-ID: Sylvain Prima worked on this whilst he was in Louis Lab. (He originally used it for robust registration). The code goes by the name of Polfit and generates a polynomial fit based upon a joint histogram between the two files. The ouput is an equation that can be fed directly into minccalc. It seemed to work pretty well. Andrew On 26/01/06, Alex ZIJDENBOS wrote: > Hello, > > I'm looking for ways to perform non-linear (!) signal normalization on > MRI data, as in, match signal and contrast between scans which may > have (possibly subtle) contrast differences (due to scanner/sequence/ > biology/whatever). > > If you have ideas for or experience with this, please let me know - > any pointers are welcome - and useable minc code is even better ;-) > > Thanks, > > -- Alex > _______________________________________________ > 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 pellegrinis at ninds.nih.gov Fri Jan 27 10:46:43 2006 From: pellegrinis at ninds.nih.gov (Pellegrini, Stefano (NIH/NINDS) [F]) Date: Fri, 27 Jan 2006 10:46:43 -0500 Subject: [MINC-users] problem with nu_estimate Message-ID: Hi all, I have a problem running (nu_coorect and) nu_estimate. I have converted the dicom images using the dicomTOminc procedure. Trying to run nu_correct ( > nu_correct AXIALVOLUME.mnc uot.mnc ) or nu_estimate on the mnc file I get from the conversion, I have this result micopy_all_var_values: MINC package entry point nu_estimate_np_and_em: crashed while running mincresample (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) Does anybody know what can be the problem? Stefano Pellegrini NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 From a.janke at gmail.com Mon Jan 30 02:07:23 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 30 Jan 2006 02:07:23 -0500 Subject: [MINC-users] fmr_preprocess for motion correction In-Reply-To: <20060125190734.1323.qmail@web50111.mail.yahoo.com> References: <20060125190734.1323.qmail@web50111.mail.yahoo.com> Message-ID: fmr_preprocess is a script that wraps up a number of calls to minctracc that is part of the mni_autoreg package written by louis collins. http://www.bic.mni.mcgill.ca/users/louis/MNI_AUTOREG_home/readme/ The page above lists some references for it. a On 25/01/06, xingfeng lee wrote: > Dear list, > Does anyone know which algorithm is using in fmr_preprocess for fMRI time series motion correction? > Are there reference papers for the algorithm? > Thank you very much. > All the best, > Li > > > > --------------------------------- > Do you Yahoo!? > With a free 1 GB, there's more in store with Yahoo! Mail. > _______________________________________________ > 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 ed.gronenschild at mi.unimaas.nl Mon Jan 30 02:26:37 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Mon, 30 Jan 2006 08:26:37 +0100 Subject: [MINC-users] signal normalization In-Reply-To: References: Message-ID: <256DB872-0ABB-4687-80EA-1AF40C70E436@mi.unimaas.nl> Dear Alex, The group of Jay Udupa (University of Pennsylvania) developed a technique for intensity standardisation. References: L. Ny?l and J. Udupa: Magn Reson. Med vol 42, 1072-1081, 1999 L. Ny?l, J. Udupa and X. Zhang: IEEE Trans. Med. Imag vol 19, 143-150, 2000 A Madabhushi and J. Udupa: IEEE Trans. Med. Imag vol 24, 561-576, 2005 Hope this will help. Kind regards, Ed On 27 Jan 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote: > Message: 4 > Date: Thu, 26 Jan 2006 16:53:44 -0500 > From: Alex ZIJDENBOS > Subject: [MINC-users] signal normalization > To: minc-users at bic.mni.mcgill.ca > Message-ID: <20060126215344.GA4433 at bic.mni.mcgill.ca> > Content-Type: text/plain; charset=us-ascii > > Hello, > > I'm looking for ways to perform non-linear (!) signal normalization on > MRI data, as in, match signal and contrast between scans which may > have (possibly subtle) contrast differences (due to scanner/sequence/ > biology/whatever). > > If you have ideas for or experience with this, please let me know - > any pointers are welcome - and useable minc code is even better ;-) > > Thanks, > > -- Alex > From a.janke at gmail.com Mon Jan 30 22:05:02 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 30 Jan 2006 22:05:02 -0500 Subject: [MINC-users] problem with nu_estimate In-Reply-To: References: Message-ID: Hi Stefano, There is a known problem with older versions of N3 and minc files with large headers (when converted from DICOM for example). Which version of N3 are you using? the current version is 1.10 and can be found here: packages.bic.mni.mcgill.ca/tgz Andrew On 27/01/06, Pellegrini, Stefano (NIH/NINDS) [F] wrote: > Hi all, > > I have a problem running (nu_coorect and) nu_estimate. I have converted the dicom images using the dicomTOminc procedure. Trying to run nu_correct ( > nu_correct AXIALVOLUME.mnc uot.mnc ) or nu_estimate on the mnc file I get from the conversion, I have this result > > micopy_all_var_values: MINC package entry point > nu_estimate_np_and_em: crashed while running mincresample (termination status=768) > nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) > > Does anybody know what can be the problem? > > Stefano Pellegrini > > NINDS-NIH > 10 Center Drive > Building 10, Room 5B16 > Bethesda, MD, 20892 > USA > ph #: 001-301-402.6391 > fax #: 001-301-402.0373 > > > _______________________________________________ > 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 pellegrinis at ninds.nih.gov Tue Jan 31 09:22:53 2006 From: pellegrinis at ninds.nih.gov (Pellegrini, Stefano (NIH/NINDS) [F]) Date: Tue, 31 Jan 2006 09:22:53 -0500 Subject: [MINC-users] problem with nu_estimate References: Message-ID: thanks Andrew, Robert Vincent already helped me and now nu_correct seems to work. In fact the problem was about the header. thanks anyway! Stefano Pellegrini NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Andrew Janke [mailto:a.janke at gmail.com] Sent: Mon 1/30/2006 10:05 PM To: MINC users mailing list Subject: Re: [MINC-users] problem with nu_estimate Hi Stefano, There is a known problem with older versions of N3 and minc files with large headers (when converted from DICOM for example). Which version of N3 are you using? the current version is 1.10 and can be found here: packages.bic.mni.mcgill.ca/tgz Andrew On 27/01/06, Pellegrini, Stefano (NIH/NINDS) [F] wrote: > Hi all, > > I have a problem running (nu_coorect and) nu_estimate. I have converted the dicom images using the dicomTOminc procedure. Trying to run nu_correct ( > nu_correct AXIALVOLUME.mnc uot.mnc ) or nu_estimate on the mnc file I get from the conversion, I have this result > > micopy_all_var_values: MINC package entry point > nu_estimate_np_and_em: crashed while running mincresample (termination status=768) > nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) > > Does anybody know what can be the problem? > > Stefano Pellegrini > > NINDS-NIH > 10 Center Drive > Building 10, Room 5B16 > Bethesda, MD, 20892 > USA > ph #: 001-301-402.6391 > fax #: 001-301-402.0373 > > > _______________________________________________ > 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/m