From huanxiang.lu at philips.com Thu Apr 10 21:29:13 2014 From: huanxiang.lu at philips.com (LU, Huan Xiang HX) Date: Fri, 11 Apr 2014 01:29:13 +0000 Subject: [MINC-users] Lobe atlas of ICBM 2009 brain atlas Message-ID: <8837CB3C4BCB794F86B5B7E812C81A400C7C48FD@DB3PRD9003MB057.MGDPHG.emi.philips.com> Hello, I was trying to use the lobe atlas that is claimed to be included in the ICBM 2009 atlas. However, I could not find the lobe segmentation atlas from the downloaded zip files (I downloaded all three zip files of ICBM 2009c). Does anyone know how to acquire this lobe atlas? Many thanks! Huanxiang ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From vladimir.fonov at gmail.com Fri Apr 11 09:45:11 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 11 Apr 2014 09:45:11 -0400 Subject: [MINC-users] Lobe atlas of ICBM 2009 brain atlas In-Reply-To: <8837CB3C4BCB794F86B5B7E812C81A400C7C48FD@DB3PRD9003MB057.MGDPHG.emi.philips.com> References: <8837CB3C4BCB794F86B5B7E812C81A400C7C48FD@DB3PRD9003MB057.MGDPHG.emi.philips.com> Message-ID: <77CF21AB-C455-4F8A-AA60-A742E7026200@gmail.com> Hello, the lobe atlas is included in symmetric version of ICBM2009 atlas, only in MINC1 and MINC2 format. It is meant to be used with lobe_segment script from minc-toolkit ( there are separate atlases for grey and white matter structures). On Apr 10, 2014, at 9:29 PM, LU, Huan Xiang HX wrote: > Hello, > > I was trying to use the lobe atlas that is claimed to be included in the ICBM 2009 atlas. However, I could not find the lobe segmentation atlas from the downloaded zip files (I downloaded all three zip files of ICBM 2009c). Does anyone know how to acquire this lobe atlas? --- Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info From huanxiang.lu at philips.com Sun Apr 13 22:07:46 2014 From: huanxiang.lu at philips.com (LU, Huan Xiang HX) Date: Mon, 14 Apr 2014 02:07:46 +0000 Subject: [MINC-users] Lobe atlas of ICBM 2009 brain atlas In-Reply-To: <77CF21AB-C455-4F8A-AA60-A742E7026200@gmail.com> References: <8837CB3C4BCB794F86B5B7E812C81A400C7C48FD@DB3PRD9003MB057.MGDPHG.emi.philips.com> <77CF21AB-C455-4F8A-AA60-A742E7026200@gmail.com> Message-ID: <8837CB3C4BCB794F86B5B7E812C81A400C7C51CC@DB3PRD9003MB057.MGDPHG.emi.philips.com> Hi Vladimir, Thanks for your reply. In fact, I tried to use the lobe_segment script. But it requires two xfm files which I couldn't locate in the MINC files. Usage: lobe_segment.pl [options] to_model_nl.xfm to_tal.xfm class.mnc out_labels.mnc Do you have idea how to use this script? Many thanks and best regards, Huanxiang -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV Sent: 2014?4?11? 21:45 To: MINC list Subject: Re: [MINC-users] Lobe atlas of ICBM 2009 brain atlas Hello, the lobe atlas is included in symmetric version of ICBM2009 atlas, only in MINC1 and MINC2 format. It is meant to be used with lobe_segment script from minc-toolkit ( there are separate atlases for grey and white matter structures). On Apr 10, 2014, at 9:29 PM, LU, Huan Xiang HX wrote: > Hello, > > I was trying to use the lobe atlas that is claimed to be included in the ICBM 2009 atlas. However, I could not find the lobe segmentation atlas from the downloaded zip files (I downloaded all three zip files of ICBM 2009c). Does anyone know how to acquire this lobe atlas? --- Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From vikash.gupta at inria.fr Thu Apr 24 12:37:45 2014 From: vikash.gupta at inria.fr (Vikash Gupta) Date: Thu, 24 Apr 2014 18:37:45 +0200 (CEST) Subject: [MINC-users] Error with nu_correct tool In-Reply-To: <654999877.4265781.1398356979673.JavaMail.zimbra@inria.fr> Message-ID: <709864868.4269594.1398357465122.JavaMail.zimbra@inria.fr> Hi MINC-Users, I am trying to use the nu_correct tool and I get this error, defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1033. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1036. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1433. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1439. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1441. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1465. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1617. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1619. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1621. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1623. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line 1625. (Maybe you should just omit the defined()?) /usr/local/bin/volume_stats: error while loading shared libraries: libvolume_io2.so.3: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) I tried to look for the files libvolume_io2.so.3 This is not present in the /usr/local/bin/volume_stats I have pre installed minc-2.2.00 and the N3 library from the git repository. ANy help would be really good Thanks Vikash From vladimir.fonov at gmail.com Thu Apr 24 13:00:30 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 24 Apr 2014 13:00:30 -0400 Subject: [MINC-users] Error with nu_correct tool In-Reply-To: <709864868.4269594.1398357465122.JavaMail.zimbra@inria.fr> References: <654999877.4265781.1398356979673.JavaMail.zimbra@inria.fr> <709864868.4269594.1398357465122.JavaMail.zimbra@inria.fr> Message-ID: Hello, I suggest using minc-toolkit : http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit Or https://github.com/BIC-MNI/minc-toolkit if you want to complete from source Best regards, Vladimir S. Fonov ~ sent from my smartphone On Apr 24, 2014 12:38 PM, "Vikash Gupta" wrote: > > > Hi MINC-Users, > > I am trying to use the nu_correct tool and I get this error, > > > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 165. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 170. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 211. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1033. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1036. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1433. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1439. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1441. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1465. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1617. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1619. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1621. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1623. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em line > 1625. > (Maybe you should just omit the defined()?) > /usr/local/bin/volume_stats: error while loading shared libraries: > libvolume_io2.so.3: cannot open shared object file: No such file or > directory > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=32512) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=32512) > > > I tried to look for the files libvolume_io2.so.3 This is not present in > the /usr/local/bin/volume_stats > I have pre installed minc-2.2.00 and the N3 library from the git > repository. > > ANy help would be really good > > Thanks > Vikash > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vikash.gupta at inria.fr Thu Apr 24 13:20:11 2014 From: vikash.gupta at inria.fr (Vikash Gupta) Date: Thu, 24 Apr 2014 19:20:11 +0200 (CEST) Subject: [MINC-users] Error with nu_correct tool In-Reply-To: <787851463.4286380.1398359729169.JavaMail.zimbra@inria.fr> References: <654999877.4265781.1398356979673.JavaMail.zimbra@inria.fr> <709864868.4269594.1398357465122.JavaMail.zimbra@inria.fr> <787851463.4286380.1398359729169.JavaMail.zimbra@inria.fr> Message-ID: <336972210.4289002.1398360011341.JavaMail.zimbra@inria.fr> Hi, Yes I just did that and I get exactly the same error. I am attaching the CMakeCache.txt with the email, in case you want to have a look at certain flags.. Thanks a lot Vikash ----- Original Message ----- > From: "Vikash Gupta" > To: "MINC users mailing list" > Sent: Thursday, April 24, 2014 7:15:29 PM > Subject: Re: [MINC-users] Error with nu_correct tool > > Hi, > Yes I just did that and I get exactly the same error. > > > I am attaching the CMakeCache.txt with the email, in case you want to have a > look at certain flags.. > > > Thanks a lot > Vikash > > ----- Original Message ----- > > From: "Vladimir S. FONOV" > > To: "MINC list" > > Sent: Thursday, April 24, 2014 7:00:30 PM > > Subject: Re: [MINC-users] Error with nu_correct tool > > > > Hello, > > > > I suggest using minc-toolkit : > > http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit > > > > Or https://github.com/BIC-MNI/minc-toolkit if you want to complete from > > source > > > > Best regards, > > Vladimir S. Fonov ~ sent from my smartphone > > On Apr 24, 2014 12:38 PM, "Vikash Gupta" wrote: > > > > > > > > > > > Hi MINC-Users, > > > > > > I am trying to use the nu_correct tool and I get this error, > > > > > > > > > > > > > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 165. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 170. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 211. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1033. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1036. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1433. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1439. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1441. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1465. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1617. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1619. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1621. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1623. > > > (Maybe you should just omit the defined()?) > > > defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em > > > line > > > 1625. > > > (Maybe you should just omit the defined()?) > > > /usr/local/bin/volume_stats: error while loading shared libraries: > > > libvolume_io2.so.3: cannot open shared object file: No such file or > > > directory > > > nu_estimate_np_and_em: crashed while running volume_stats (termination > > > status=32512) > > > nu_correct: crashed while running nu_estimate_np_and_em (termination > > > status=32512) > > > > > > > > > I tried to look for the files libvolume_io2.so.3 This is not present in > > > the /usr/local/bin/volume_stats > > > I have pre installed minc-2.2.00 and the N3 library from the git > > > repository. > > > > > > ANy help would be really good > > > > > > Thanks > > > Vikash > > > _______________________________________________ > > > 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 > > > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CMakeCache.txt URL: From vladimir.fonov at gmail.com Fri Apr 25 10:09:02 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 25 Apr 2014 10:09:02 -0400 Subject: [MINC-users] Error with nu_correct tool In-Reply-To: <336972210.4289002.1398360011341.JavaMail.zimbra@inria.fr> References: <654999877.4265781.1398356979673.JavaMail.zimbra@inria.fr> <709864868.4269594.1398357465122.JavaMail.zimbra@inria.fr> <787851463.4286380.1398359729169.JavaMail.zimbra@inria.fr> <336972210.4289002.1398360011341.JavaMail.zimbra@inria.fr> Message-ID: <344783AE-3418-4202-A750-C0EACF8665FB@gmail.com> Hello, so, what happens when you run make test ? On Apr 24, 2014, at 1:20 PM, Vikash Gupta wrote: > Hi, > Yes I just did that and I get exactly the same error. > I am attaching the CMakeCache.txt with the email, in case you want to have a > look at certain flags.. > > Thanks a lot > Vikash > > ----- Original Message ----- >> From: "Vikash Gupta" >> To: "MINC users mailing list" >> Sent: Thursday, April 24, 2014 7:15:29 PM >> Subject: Re: [MINC-users] Error with nu_correct tool >> >> Hi, >> Yes I just did that and I get exactly the same error. >> >> >> I am attaching the CMakeCache.txt with the email, in case you want to have a >> look at certain flags.. >> >> >> Thanks a lot >> Vikash >> >> ----- Original Message ----- >>> From: "Vladimir S. FONOV" >>> To: "MINC list" >>> Sent: Thursday, April 24, 2014 7:00:30 PM >>> Subject: Re: [MINC-users] Error with nu_correct tool >>> >>> Hello, >>> >>> I suggest using minc-toolkit : >>> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit >>> >>> Or https://github.com/BIC-MNI/minc-toolkit if you want to complete from >>> source >>> >>> Best regards, >>> Vladimir S. Fonov ~ sent from my smartphone >>> On Apr 24, 2014 12:38 PM, "Vikash Gupta" wrote: >>> >>>> >>>> >>>> Hi MINC-Users, >>>> >>>> I am trying to use the nu_correct tool and I get this error, >>>> >>>> >>>> >>>> >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 165. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 170. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 211. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1033. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1036. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1433. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1439. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1441. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1465. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1617. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1619. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1621. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1623. >>>> (Maybe you should just omit the defined()?) >>>> defined(@array) is deprecated at /usr/local/bin/nu_estimate_np_and_em >>>> line >>>> 1625. >>>> (Maybe you should just omit the defined()?) >>>> /usr/local/bin/volume_stats: error while loading shared libraries: >>>> libvolume_io2.so.3: cannot open shared object file: No such file or >>>> directory >>>> nu_estimate_np_and_em: crashed while running volume_stats (termination >>>> status=32512) >>>> nu_correct: crashed while running nu_estimate_np_and_em (termination >>>> status=32512) >>>> >>>> >>>> I tried to look for the files libvolume_io2.so.3 This is not present in >>>> the /usr/local/bin/volume_stats >>>> I have pre installed minc-2.2.00 and the N3 library from the git >>>> repository. >>>> >>>> ANy help would be really good >>>> >>>> Thanks >>>> Vikash >>>> _______________________________________________ >>>> 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 --- Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info