From davids at bic.mni.mcgill.ca Fri Dec 4 11:33:25 2009 From: davids at bic.mni.mcgill.ca (David SEMINOWICZ) Date: Fri, 4 Dec 2009 11:33:25 -0500 (EST) Subject: [MINC-users] 64-bit mincbet Message-ID: Hello, does anyone know if there is a 64-bit version of mincbet? Thanks, Dave From dale at bic.mni.mcgill.ca Fri Dec 4 13:01:21 2009 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Fri, 4 Dec 2009 13:01:21 -0500 Subject: [MINC-users] 64-bit mincbet In-Reply-To: References: Message-ID: Hello, I dont have any experience with it, but I just downloaded the source and built it :} What OS/Arch are you working on? The source can be found here. http://www.bic.mni.mcgill.ca/software/pipeline_extras/ Cheers! dale On 4-Dec-09, at 11:33 AM, David SEMINOWICZ wrote: > Hello, does anyone know if there is a 64-bit version of mincbet? > Thanks, > Dave > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From shahin at bic.mni.mcgill.ca Tue Dec 8 13:15:16 2009 From: shahin at bic.mni.mcgill.ca (Shahin Zangenehpour) Date: Tue, 8 Dec 2009 13:15:16 -0500 Subject: [MINC-users] Question regarding get_meansd_voi Message-ID: <41340E1B-A3DA-47C4-98FC-1D5B35A1138F@bic.mni.mcgill.ca> Hi all, I remember being able to use get_meansd_voi command to extract raw values from minc files when I logged into yorick a few years back. Not only can I not log into yorick anymore (here is the response from the server: ssh_exchange_identification: Connection closed by remote host), the command is not apparently available on the general BIC server (login.bic.mni.mcgill.ca) as I get the following msg: grumio 201% get_meansd_voi get_meansd_voi: Command not found. Can anyone please help? Thanks Shahin From shahin at bic.mni.mcgill.ca Tue Dec 8 13:12:08 2009 From: shahin at bic.mni.mcgill.ca (Shahin Zangenehpour) Date: Tue, 8 Dec 2009 13:12:08 -0500 Subject: [MINC-users] Question regarding get_meansd_voi Message-ID: <4B70B4B7-42DC-4EA7-98D7-502381D83D84@bic.mni.mcgill.ca> Hi all, I remember being able to use get_meansd_voi command to extract raw values from minc files when I logged into yorick a few years back. Not only can I not log into yorick anymore (here is the response from the server: ssh_exchange_identification: Connection closed by remote host), the command is not apparently available on the general BIC server (login.bic.mni.mcgill.ca) as I get the following msg: grumio 201% get_meansd_voi get_meansd_voi: Command not found. Can anyone please help? Thanks Shahin From sylvain at bic.mni.mcgill.ca Tue Dec 8 13:37:13 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 8 Dec 2009 13:37:13 -0500 (EST) Subject: [MINC-users] Question regarding get_meansd_voi In-Reply-To: <4B70B4B7-42DC-4EA7-98D7-502381D83D84@bic.mni.mcgill.ca> References: <4B70B4B7-42DC-4EA7-98D7-502381D83D84@bic.mni.mcgill.ca> Message-ID: that product is not yet available for linux - no ETA but you can hope for early 2010. In the meantime, login to yorick - you should be able to login now, but only within the BIC subnet. S On Tue, 8 Dec 2009, Shahin Zangenehpour wrote: > Hi all, > > I remember being able to use get_meansd_voi command to extract raw values from minc files when I logged into yorick a few years back. Not only can I not log into yorick anymore (here is the response from the server: ssh_exchange_identification: Connection closed by remote host), the command is not apparently available on the general BIC server (login.bic.mni.mcgill.ca) as I get the following msg: > > grumio 201% get_meansd_voi > get_meansd_voi: Command not found. > > Can anyone please help? > Thanks > Shahin > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From nikelski at bic.mni.mcgill.ca Tue Dec 8 20:26:21 2009 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Tue, 8 Dec 2009 20:26:21 -0500 Subject: [MINC-users] Unusually colorful Register display Message-ID: Hi all, I'm currently rebuilding my minc tools under OS X (10.5.8) in preparation for a cold and windy winter. All of the bits and pieces build without much complaint, but whenever I launch Register or Display, all of the windows have a distinct pink-ish, purple-ish hue. Festive yes! ... but not what I really need right now. Any ideas? I thought that it might be due to recent changes in the bicpl, however rebuilding with older bicpl versions makes no difference. Has anyone seen this before? -Jim -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University From nikelski at bic.mni.mcgill.ca Wed Dec 9 22:50:09 2009 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Wed, 9 Dec 2009 22:50:09 -0500 Subject: [MINC-users] Unusually colorful Register display In-Reply-To: References: Message-ID: Hi all, OK, I've narrowed it down. Building ... hdf5-1.6.5 netcdf-3.6.2 minc-2.0.14 / minc-2.0.15 / minc-2.0.16 / minc-2.0.17 / minc-2.0.18 bicpl-1.4.6 Register-1.3.6 The problem shows up with minc-2.0.17 and minc-2.0.18, *not* with minc-2.0.16 or earlier. Thus, something happened in minc-2.0.17 that's effecting my Register (and Display) display. Can anyone take a peak into the minc-2.0.17 changes and see what might have contributed to this? I stand ready to do a test build ... In case it helps, my particulars are: Model Name: MacBook Pro Model Identifier: MacBookPro3,1 Processor Name: Intel Core 2 Duo Processor Speed: 2.2 GHz Number Of Processors: 1 Total Number Of Cores: 2 L2 Cache: 4 MB Memory: 4 GB Bus Speed: 800 MHz System Version: Mac OS X 10.5.8 (9L31a) Kernel Version: Darwin 9.8.0 -Jim On Tue, Dec 8, 2009 at 8:26 PM, EJ Nikelski wrote: > Hi all, > > ? I'm currently rebuilding my minc tools under OS X (10.5.8) in > preparation for a cold and windy winter. ?All of the bits and pieces > build without much complaint, but whenever I launch Register or > Display, all of the windows have a distinct pink-ish, purple-ish hue. > Festive yes! ... but not what I really need right now. > > ?Any ideas? ?I thought that it might be due to recent changes in the > bicpl, however rebuilding with older bicpl versions makes no > difference. ?Has anyone seen this before? > > -Jim > > -- > ================================= > Jim Nikelski, Ph.D. > Postdoctoral Research Fellow > Bloomfield Centre for Research in Aging > Lady Davis Institute for Medical Research > Sir Mortimer B. Davis - Jewish General Hospital > McGill University > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University From nikelski at bic.mni.mcgill.ca Thu Dec 10 13:03:32 2009 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Thu, 10 Dec 2009 13:03:32 -0500 Subject: [MINC-users] Unusually colorful Register display In-Reply-To: References: Message-ID: Hi mincy list, OK, we have a solution. Claude provided me with a version of minc-2.0.19 from cvs head, which fixes my problem. So, for any of you Mac users who are *not* experiencing this problem because your tools were built on top of minc-2.0.16 (or less), hold off rebuilding until minc-2.0.19 gets released. Perhaps we can hope for a Christmas release of minc? -Jim On Tue, Dec 8, 2009 at 8:26 PM, EJ Nikelski wrote: > Hi all, > > ? I'm currently rebuilding my minc tools under OS X (10.5.8) in > preparation for a cold and windy winter. ?All of the bits and pieces > build without much complaint, but whenever I launch Register or > Display, all of the windows have a distinct pink-ish, purple-ish hue. > Festive yes! ... but not what I really need right now. > > ?Any ideas? ?I thought that it might be due to recent changes in the > bicpl, however rebuilding with older bicpl versions makes no > difference. ?Has anyone seen this before? > > -Jim > > -- > ================================= > Jim Nikelski, Ph.D. > Postdoctoral Research Fellow > Bloomfield Centre for Research in Aging > Lady Davis Institute for Medical Research > Sir Mortimer B. Davis - Jewish General Hospital > McGill University > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University From jchen at bic.mni.mcgill.ca Thu Dec 10 18:19:37 2009 From: jchen at bic.mni.mcgill.ca (Jeni Chen) Date: Thu, 10 Dec 2009 18:19:37 -0500 (EST) Subject: [MINC-users] CIVET classification problem Message-ID: Hi all, Upon checking the results of the classified images after running CIVET, I notice that quite often, small portions of the grey matter in the frontal pole or the orbitofrontal area gets cut off. I tried playing with the N3 parameters and re-ran CIVET but it didn't help. I was also told that the problem might reside in the algorithm used to extract the brain to make the mask (mincbet, I presume?). Are there options/parameters that we can specify to improve the result of classification? Also when looking at the verify.png file- is there a reference value to the ones that are indicated. In other words, when I see for example, classified image CSF 7.24% GM 49.79% WM 42.97% native skull mask in stx space (8.75%) what do I make of these % numbers, does that tell me whether the classified images are within a standard range? Thanks! Jeni *********** Jen-I Chen, MSc. Agente de recherche Universite de Montreal 514.343.6111 x4359 From claude at bic.mni.mcgill.ca Thu Dec 10 20:46:50 2009 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Thu, 10 Dec 2009 20:46:50 -0500 Subject: [MINC-users] CIVET classification problem In-Reply-To: Message-ID: <200912110146.nBB1koST002750@grumio.bic.mni.mcgill.ca> Hi Jeni, Can you repost at civet-users and follow the thread from there? If you are not a member, simply subscribe to the group. This is a CIVET related topic and its answer will interest the CIVET community. Yours, Claude > From minc-users-bounces at bic.mni.mcgill.ca Thu Dec 10 18:21:14 2009 > X-Authentication-Warning: grumio.bic.mni.mcgill.ca: jchen owned process doing > -bs > Date: Thu, 10 Dec 2009 18:19:37 -0500 (EST) > From: Jeni Chen > To: minc-users at bic.mni.mcgill.ca > MIME-Version: 1.0 > X-Spam-Status: No, score=-4.9 required=5.0 tests=ALL_TRUSTED,AWL,BAYES_00 > autolearn=ham version=3.0.3 > X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on > mail.bic.mni.mcgill.ca > X-Virus-Scanned: ClamAV 0.91.2/10149/Thu Dec 10 17:26:20 2009 on > mail.bic.mni.mcgill.ca > X-Virus-Status: Clean > X-Greylist: Message whitelisted by Sendmail access database, not delayed by > milter-greylist-4.0 (mail.bic.mni.mcgill.ca [132.206.178.34]); > Thu, 10 Dec 2009 18:19:49 -0500 (EST) > Subject: [MINC-users] CIVET classification problem > X-BeenThere: minc-users at bic.mni.mcgill.ca > X-Mailman-Version: 2.1.9 > Precedence: list > Reply-To: MINC users mailing list > List-Id: MINC users mailing list > List-Unsubscribe: , > > List-Archive: > List-Post: > List-Help: > List-Subscribe: , > > Content-Type: text/plain; charset="us-ascii" > Content-Transfer-Encoding: 7bit > Sender: minc-users-bounces at bic.mni.mcgill.ca > Errors-To: minc-users-bounces at bic.mni.mcgill.ca > > Hi all, > > Upon checking the results of the classified images after running CIVET, I > notice that quite often, small portions of the grey matter in the frontal > pole or the orbitofrontal area gets cut off. I tried playing with the N3 > parameters and re-ran CIVET but it didn't help. I was also told that the > problem might reside in the algorithm used to extract the brain to make > the mask (mincbet, I presume?). Are there options/parameters that we can > specify to improve the result of classification? > > Also when looking at the verify.png file- is there a reference value to > the ones that are indicated. In other words, when I see for example, > > classified image CSF 7.24% GM 49.79% WM 42.97% > native skull mask in stx space (8.75%) > > what do I make of these % numbers, does that tell me whether the > classified images are within a standard range? > > Thanks! > > Jeni > > *********** > Jen-I Chen, MSc. > Agente de recherche > Universite de Montreal > 514.343.6111 x4359 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From matthijs at phenogenomics.ca Thu Dec 31 15:42:36 2009 From: matthijs at phenogenomics.ca (Matthijs van Eede) Date: Thu, 31 Dec 2009 15:42:36 -0500 Subject: [MINC-users] mincresample - what is the expected behavior Message-ID: <4B3D0CBC.3060503@phenogenomics.ca> Hi All, I have a question about the expected behavior of mincresample when using a transformation file with a combination of rotations and translations. The problem is as follows. There is a source file which has its center of gravity in -510,0,0 and a target file which has its center of gravity in 0,0,0. The source image should be translated to the target image and then rotated by -4,1,-13. If I specify two transformation (xfm) files, one for the translation and one for the rotation and apply these sequentially, the resulting transformation is correct., i.e., it has its center of gravity in the origin and rotated around that. However, if I create one transformation file which contains both transformations, I "loose" my file; its new center of gravity is not in 0,0,0 but in 14,118,2 suggesting that the rotation was applied before the transformation. Is this the expected behavior for mincresample? Thank you, Matthijs