From pgravel at bic.mni.mcgill.ca Wed May 13 12:13:20 2015 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Wed, 13 May 2015 12:13:20 -0400 (EDT) Subject: [MINC-users] Segmentation on cygwin In-Reply-To: References: <5542AA46.70405@gmail.com> Message-ID: Dear all, I am trying to run the old segmentation pipeline, i.e. using: 1) mritotal (linear) 2) nu_estimate, nu_evaluate (or nu_correct) 3) mritotal (non_lin) 4) mincresample to STX 5) classify_clean 6) stx_segment on my machine using cygwin (I know CIVET does great things, but I would like to be able to run a few segmentations locally). However, I don't have the nu_estimate, nu_evaluate and/or nu_correct binaries, nor the one for classify_clean. So I was wondering if I could get them from somewhere, or at least the source (I checked on GitHub, but couldn't find anything). Any ideas? Many thanks! Paul From vladimir.fonov at gmail.com Wed May 13 12:40:26 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 13 May 2015 12:40:26 -0400 Subject: [MINC-users] Segmentation on cygwin In-Reply-To: References: <5542AA46.70405@gmail.com> Message-ID: nu_estimate, nu_correct, nu_evaluate is part of N3 https://github.com/BIC-MNI/classify classify_clean is in classify https://github.com/BIC-MNI/classify On Wed, May 13, 2015 at 12:13 PM, Paul GRAVEL wrote: > Dear all, > > I am trying to run the old segmentation pipeline, i.e. using: > 1) mritotal (linear) > 2) nu_estimate, nu_evaluate (or nu_correct) > 3) mritotal (non_lin) > 4) mincresample to STX > 5) classify_clean > 6) stx_segment > > on my machine using cygwin (I know CIVET does great things, but I would > like to be able to run a few segmentations locally). > > However, I don't have the nu_estimate, nu_evaluate and/or nu_correct > binaries, nor the one for classify_clean. So I was wondering if I could get > them from somewhere, or at least the source (I checked on GitHub, but > couldn't find anything). > Any ideas? > > Many thanks! > > Paul > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From pgravel at bic.mni.mcgill.ca Wed May 13 13:23:38 2015 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Wed, 13 May 2015 13:23:38 -0400 (EDT) Subject: [MINC-users] Segmentation on cygwin In-Reply-To: References: <5542AA46.70405@gmail.com> Message-ID: Once again you saved the day, many thanks Vlad! Best, Paul ps. I think for N# you meant: https://github.com/BIC-MNI/N3 ;-)! On Wed, 13 May 2015, Vladimir S. FONOV wrote: > nu_estimate, nu_correct, nu_evaluate is part of N3 > https://github.com/BIC-MNI/classify > classify_clean is in classify https://github.com/BIC-MNI/classify > > On Wed, May 13, 2015 at 12:13 PM, Paul GRAVEL > wrote: > >> Dear all, >> >> I am trying to run the old segmentation pipeline, i.e. using: >> 1) mritotal (linear) >> 2) nu_estimate, nu_evaluate (or nu_correct) >> 3) mritotal (non_lin) >> 4) mincresample to STX >> 5) classify_clean >> 6) stx_segment >> >> on my machine using cygwin (I know CIVET does great things, but I would >> like to be able to run a few segmentations locally). >> >> However, I don't have the nu_estimate, nu_evaluate and/or nu_correct >> binaries, nor the one for classify_clean. So I was wondering if I could get >> them from somewhere, or at least the source (I checked on GitHub, but >> couldn't find anything). >> Any ideas? >> >> Many thanks! >> >> Paul >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Thu May 14 13:25:06 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 14 May 2015 13:25:06 -0400 Subject: [MINC-users] mincreshape with fillvalue outside image range Message-ID: Hi all, As you probably know, mincreshape will fill points outside of the input volume using the argument to -fillvalue (default 0). However, I noticed that if that fillvalue is outside the range of the input volume, it will show some seemingly erratic (and arguably wrong) behaviour. For example, generating a volume with only '1' values: $ minccalc -expression 1 /usr/local/bic/share/mni-models/icbm_avg_152_t1_tal_lin.mnc ones.mnc $ mincstats -min -max ones.mnc Min: 1 Max: 1 Now, let's pad that on one side and check the range of the output: $ mincreshape -start -10,-10,-10 ones.mnc ones_pad.mnc $ mincstats -min -max ones_pad.mnc *** mincstats - reported max (0) doesn't equal header (1) Min: 0 Max: 0 So that is unexpected. Repeating the mincreshape call, this time with -normalize: $ mincreshape -normalize -start -10,-10,-10 ones.mnc ones_pad_norm.mnc $ mincstats -min -max ones_pad_norm.mnc Min: 1 Max: 1 Still wrong. When you modify the image range in either one of these mincreshape calls, you get the expected result: $ mincreshape -start -10,-10,-10 -image_range 0 1 ones.mnc ones_pad_range01.mnc $ mincstats -min -max ones_pad_range01.mnc Min: 0 Max: 1 So, the problem appears to be that mincreshape's fill value (0) falls outside the input range of the volume, causing some fairly unexpected behaviour. It seems to me that in this case, mincreshape should either throw an error (fillvalue outside image range); or perhaps extend the image range to make sure it _can_ represent the fill value? -- A From robert.d.vincent at mcgill.ca Thu May 14 13:31:47 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Thu, 14 May 2015 13:31:47 -0400 Subject: [MINC-users] mincreshape with fillvalue outside image range In-Reply-To: References: Message-ID: I agree that the existing behavior is incorrect. I think extending the range to include the fill value would be reasonable here. On Thu, May 14, 2015 at 1:25 PM, Alex Zijdenbos wrote: > Hi all, > > As you probably know, mincreshape will fill points outside of the input > volume using the argument to -fillvalue (default 0). However, I noticed > that if that fillvalue is outside the range of the input volume, it will > show some seemingly erratic (and arguably wrong) behaviour. For example, > generating a volume with only '1' values: > > $ minccalc -expression 1 > /usr/local/bic/share/mni-models/icbm_avg_152_t1_tal_lin.mnc ones.mnc > $ mincstats -min -max ones.mnc > Min: 1 > Max: 1 > > Now, let's pad that on one side and check the range of the output: > > $ mincreshape -start -10,-10,-10 ones.mnc ones_pad.mnc > $ mincstats -min -max ones_pad.mnc > *** mincstats - reported max (0) doesn't equal header (1) > Min: 0 > Max: 0 > > So that is unexpected. Repeating the mincreshape call, this time with > -normalize: > > $ mincreshape -normalize -start -10,-10,-10 ones.mnc ones_pad_norm.mnc > $ mincstats -min -max ones_pad_norm.mnc > Min: 1 > Max: 1 > > Still wrong. When you modify the image range in either one of these > mincreshape calls, you get the expected result: > > $ mincreshape -start -10,-10,-10 -image_range 0 1 ones.mnc > ones_pad_range01.mnc > $ mincstats -min -max ones_pad_range01.mnc > Min: 0 > Max: 1 > > So, the problem appears to be that mincreshape's fill value (0) falls > outside the input range of the volume, causing some fairly unexpected > behaviour. > > It seems to me that in this case, mincreshape should either throw an error > (fillvalue outside image range); or perhaps extend the image range to make > sure it _can_ represent the fill value? > > -- A > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From redoute at cermep.fr Wed May 20 11:13:02 2015 From: redoute at cermep.fr (=?windows-1252?Q?J=E9r=F4me_Redout=E9?=) Date: Wed, 20 May 2015 17:13:02 +0200 Subject: [MINC-users] using register remotely Message-ID: <555CA47E.60003@cermep.fr> Hi, Minc tools are available on a remote server. I can't run register through ssh -X connection How should I do? Thanks Jerome -- ================================================================== J?r?me Redout? Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 CERMEP - Imagerie du vivant 59 Bd Pinel. 69677 Bron - FRANCE tel : 33 (0)4 72 68 86 18 (bureau) tel : 33 (0)4 72 68 86 00 (standard) fax : 33 (0)4 72 68 86 10 ================================================================== From robert.d.vincent at mcgill.ca Wed May 20 11:20:07 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Wed, 20 May 2015 11:20:07 -0400 Subject: [MINC-users] using register remotely In-Reply-To: <555CA47E.60003@cermep.fr> References: <555CA47E.60003@cermep.fr> Message-ID: Hi Jerome, Can you be more specific about what happens? Normally register should work over an X connection, although it may run quite slowly. -bert On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? wrote: > Hi, > Minc tools are available on a remote server. > I can't run register through ssh -X connection > How should I do? > Thanks > Jerome > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From redoute at cermep.fr Wed May 20 11:34:24 2015 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Wed, 20 May 2015 17:34:24 +0200 Subject: [MINC-users] using register remotely In-Reply-To: References: <555CA47E.60003@cermep.fr> Message-ID: <555CA980.7070204@cermep.fr> here is what I get: > register > X Error of failed request: BadValue (integer parameter out of range > for operation) > Major opcode of failed request: 154 (GLX) > Minor opcode of failed request: 3 (X_GLXCreateContext) > Value in failed request: 0x0 > Serial number of failed request: 17 > Current serial number in output stream: 18 Le 20/05/2015 17:20, Robert D. Vincent a ?crit : > Hi Jerome, > > Can you be more specific about what happens? Normally register should work > over an X connection, although it may run quite slowly. > > -bert > > > On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? wrote: > >> Hi, >> Minc tools are available on a remote server. >> I can't run register through ssh -X connection >> How should I do? >> Thanks >> Jerome >> >> -- >> ================================================================== >> J?r?me Redout? >> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >> CERMEP - Imagerie du vivant >> 59 Bd Pinel. 69677 Bron - FRANCE >> tel : 33 (0)4 72 68 86 18 (bureau) >> tel : 33 (0)4 72 68 86 00 (standard) >> fax : 33 (0)4 72 68 86 10 >> ================================================================== >> >> >> _______________________________________________ >> 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 > -- ================================================================== J?r?me Redout? Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 CERMEP - Imagerie du vivant 59 Bd Pinel. 69677 Bron - FRANCE tel : 33 (0)4 72 68 86 18 (bureau) tel : 33 (0)4 72 68 86 00 (standard) fax : 33 (0)4 72 68 86 10 ================================================================== From robert.d.vincent at mcgill.ca Wed May 20 11:38:29 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Wed, 20 May 2015 11:38:29 -0400 Subject: [MINC-users] using register remotely In-Reply-To: <555CA980.7070204@cermep.fr> References: <555CA47E.60003@cermep.fr> <555CA980.7070204@cermep.fr> Message-ID: Hi, What operating system is on the remote computer are you using? -bert On Wed, May 20, 2015 at 11:34 AM, J?r?me Redout? wrote: > here is what I get: > > register >> X Error of failed request: BadValue (integer parameter out of range for >> operation) >> Major opcode of failed request: 154 (GLX) >> Minor opcode of failed request: 3 (X_GLXCreateContext) >> Value in failed request: 0x0 >> Serial number of failed request: 17 >> Current serial number in output stream: 18 >> > > > Le 20/05/2015 17:20, Robert D. Vincent a ?crit : > >> Hi Jerome, >> >> Can you be more specific about what happens? Normally register should work >> over an X connection, although it may run quite slowly. >> >> -bert >> >> >> On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? >> wrote: >> >> Hi, >>> Minc tools are available on a remote server. >>> I can't run register through ssh -X connection >>> How should I do? >>> Thanks >>> Jerome >>> >>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> 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 >> >> > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Wed May 20 12:04:55 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 20 May 2015 12:04:55 -0400 Subject: [MINC-users] using register remotely In-Reply-To: <555CA47E.60003@cermep.fr> References: <555CA47E.60003@cermep.fr> Message-ID: <555CB0A7.7000800@gmail.com> Hello, try running with ssh -X -Y On 15-05-20 11:13 AM, J?r?me Redout? wrote: > Hi, > Minc tools are available on a remote server. > I can't run register through ssh -X connection > How should I do? > Thanks > Jerome > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From ayobimpe2004 at gmail.com Wed May 20 13:37:29 2015 From: ayobimpe2004 at gmail.com (Azeez Adebimpe) Date: Wed, 20 May 2015 19:37:29 +0200 Subject: [MINC-users] mesh.nv Message-ID: hello group, please i want to create mesh.nv from my own mri. please help me with link to the tutorial. thanks azeez From redoute at cermep.fr Thu May 21 03:35:31 2015 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Thu, 21 May 2015 09:35:31 +0200 Subject: [MINC-users] using register remotely In-Reply-To: References: <555CA47E.60003@cermep.fr> <555CA980.7070204@cermep.fr> Message-ID: <555D8AC3.4020107@cermep.fr> Le 20/05/2015 17:38, Robert D. Vincent a ?crit : > Hi, > > What operating system is on the remote computer are you using? > > -bert The remote server runs RedHat 5 ssh -X -Y fails too > > > On Wed, May 20, 2015 at 11:34 AM, J?r?me Redout? wrote: > >> here is what I get: >> >> register >>> X Error of failed request: BadValue (integer parameter out of range for >>> operation) >>> Major opcode of failed request: 154 (GLX) >>> Minor opcode of failed request: 3 (X_GLXCreateContext) >>> Value in failed request: 0x0 >>> Serial number of failed request: 17 >>> Current serial number in output stream: 18 >>> >> >> Le 20/05/2015 17:20, Robert D. Vincent a ?crit : >> >>> Hi Jerome, >>> >>> Can you be more specific about what happens? Normally register should work >>> over an X connection, although it may run quite slowly. >>> >>> -bert >>> >>> >>> On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? >>> wrote: >>> >>> Hi, >>>> Minc tools are available on a remote server. >>>> I can't run register through ssh -X connection >>>> How should I do? >>>> Thanks >>>> Jerome >>>> >>>> -- >>>> ================================================================== >>>> J?r?me Redout? >>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>> CERMEP - Imagerie du vivant >>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>> tel : 33 (0)4 72 68 86 00 (standard) >>>> fax : 33 (0)4 72 68 86 10 >>>> ================================================================== >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> -- >> ================================================================== >> J?r?me Redout? >> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >> CERMEP - Imagerie du vivant >> 59 Bd Pinel. 69677 Bron - FRANCE >> tel : 33 (0)4 72 68 86 18 (bureau) >> tel : 33 (0)4 72 68 86 00 (standard) >> fax : 33 (0)4 72 68 86 10 >> ================================================================== >> >> >> _______________________________________________ >> 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 > -- ================================================================== J?r?me Redout? Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 CERMEP - Imagerie du vivant 59 Bd Pinel. 69677 Bron - FRANCE tel : 33 (0)4 72 68 86 18 (bureau) tel : 33 (0)4 72 68 86 00 (standard) fax : 33 (0)4 72 68 86 10 ================================================================== From mishkind at gmail.com Thu May 21 05:01:07 2015 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Wed, 20 May 2015 23:01:07 -1000 Subject: [MINC-users] using register remotely In-Reply-To: <555D8AC3.4020107@cermep.fr> References: <555CA47E.60003@cermep.fr> <555CA980.7070204@cermep.fr> <555D8AC3.4020107@cermep.fr> Message-ID: here are a few things I've tried in the past when my ssh doesn't work as I'd like: 1. add -rgb to the register command, i.e., ssh -X register -rgb 2. Not sure if this is mac specific, but edit /etc/sshd_config on your host machine. Uncomment the line that says X11Forwarding no and change it so it says X11Forwarding yes 3. edit /etc/ssh_config on your host machine. Uncomment the line that says ForwardX11 no and change it to ForwardX11 yes 4. use ssh -Y as vlad suggested On Wed, May 20, 2015 at 9:35 PM, J?r?me Redout? wrote: > Le 20/05/2015 17:38, Robert D. Vincent a ?crit : >> >> Hi, >> >> What operating system is on the remote computer are you using? >> >> -bert > > > The remote server runs RedHat 5 > > ssh -X -Y fails too > > > >> >> >> On Wed, May 20, 2015 at 11:34 AM, J?r?me Redout? >> wrote: >> >>> here is what I get: >>> >>> register >>>> >>>> X Error of failed request: BadValue (integer parameter out of range for >>>> operation) >>>> Major opcode of failed request: 154 (GLX) >>>> Minor opcode of failed request: 3 (X_GLXCreateContext) >>>> Value in failed request: 0x0 >>>> Serial number of failed request: 17 >>>> Current serial number in output stream: 18 >>>> >>> >>> Le 20/05/2015 17:20, Robert D. Vincent a ?crit : >>> >>>> Hi Jerome, >>>> >>>> Can you be more specific about what happens? Normally register should >>>> work >>>> over an X connection, although it may run quite slowly. >>>> >>>> -bert >>>> >>>> >>>> On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? >>>> wrote: >>>> >>>> Hi, >>>>> >>>>> Minc tools are available on a remote server. >>>>> I can't run register through ssh -X connection >>>>> How should I do? >>>>> Thanks >>>>> Jerome >>>>> >>>>> -- >>>>> ================================================================== >>>>> J?r?me Redout? >>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>> CERMEP - Imagerie du vivant >>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>> fax : 33 (0)4 72 68 86 10 >>>>> ================================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> 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 >> > > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From robert.d.vincent at mcgill.ca Thu May 21 05:34:03 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Thu, 21 May 2015 05:34:03 -0400 Subject: [MINC-users] using register remotely In-Reply-To: <555D8AC3.4020107@cermep.fr> References: <555CA47E.60003@cermep.fr> <555CA980.7070204@cermep.fr> <555D8AC3.4020107@cermep.fr> Message-ID: What is the OS on your local machine? The -rgb flag might help, depending on the version of register. On May 21, 2015 3:36 AM, "J?r?me Redout?" wrote: > Le 20/05/2015 17:38, Robert D. Vincent a ?crit : > >> Hi, >> >> What operating system is on the remote computer are you using? >> >> -bert >> > > The remote server runs RedHat 5 > > ssh -X -Y fails too > > > >> >> On Wed, May 20, 2015 at 11:34 AM, J?r?me Redout? >> wrote: >> >> here is what I get: >>> >>> register >>> >>>> X Error of failed request: BadValue (integer parameter out of range for >>>> operation) >>>> Major opcode of failed request: 154 (GLX) >>>> Minor opcode of failed request: 3 (X_GLXCreateContext) >>>> Value in failed request: 0x0 >>>> Serial number of failed request: 17 >>>> Current serial number in output stream: 18 >>>> >>>> >>> Le 20/05/2015 17:20, Robert D. Vincent a ?crit : >>> >>> Hi Jerome, >>>> >>>> Can you be more specific about what happens? Normally register should >>>> work >>>> over an X connection, although it may run quite slowly. >>>> >>>> -bert >>>> >>>> >>>> On Wed, May 20, 2015 at 11:13 AM, J?r?me Redout? >>>> wrote: >>>> >>>> Hi, >>>> >>>>> Minc tools are available on a remote server. >>>>> I can't run register through ssh -X connection >>>>> How should I do? >>>>> Thanks >>>>> Jerome >>>>> >>>>> -- >>>>> ================================================================== >>>>> J?r?me Redout? >>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>> CERMEP - Imagerie du vivant >>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>> fax : 33 (0)4 72 68 86 10 >>>>> ================================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> 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 >> >> > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu May 21 08:03:27 2015 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 21 May 2015 22:03:27 +1000 Subject: [MINC-users] using register remotely In-Reply-To: <555CA47E.60003@cermep.fr> References: <555CA47E.60003@cermep.fr> Message-ID: Hi Jerome, Changes in the underlying GLUT libraries mean that this at times can be painful, is there an option to use VNC or something of the ilk instead? a On 21 May 2015 at 01:13, J?r?me Redout? wrote: > Hi, > Minc tools are available on a remote server. > I can't run register through ssh -X connection > How should I do? > Thanks > Jerome > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From redoute at cermep.fr Thu May 21 11:05:26 2015 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Thu, 21 May 2015 17:05:26 +0200 Subject: [MINC-users] using register remotely In-Reply-To: References: <555CA47E.60003@cermep.fr> Message-ID: <555DF436.8020104@cermep.fr> Thanks for your responses... the local machine runs Ubuntu x64 15.04 the -rgb option fails too I switched my local machine from windows to ubuntu to escape from VNC sessions.... but I'm afraid I ll have to get them back if I want to use register :( Le 21/05/2015 14:03, Andrew Janke a ?crit : > Hi Jerome, > > Changes in the underlying GLUT libraries mean that this at times can > be painful, is there an option to use VNC or something of the ilk > instead? > > a > > > > On 21 May 2015 at 01:13, J?r?me Redout? wrote: >> Hi, >> Minc tools are available on a remote server. >> I can't run register through ssh -X connection >> How should I do? >> Thanks >> Jerome >> >> -- >> ================================================================== >> J?r?me Redout? >> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >> CERMEP - Imagerie du vivant >> 59 Bd Pinel. 69677 Bron - FRANCE >> tel : 33 (0)4 72 68 86 18 (bureau) >> tel : 33 (0)4 72 68 86 00 (standard) >> fax : 33 (0)4 72 68 86 10 >> ================================================================== >> >> >> _______________________________________________ >> 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 > -- ================================================================== J?r?me Redout? Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 CERMEP - Imagerie du vivant 59 Bd Pinel. 69677 Bron - FRANCE tel : 33 (0)4 72 68 86 18 (bureau) tel : 33 (0)4 72 68 86 00 (standard) fax : 33 (0)4 72 68 86 10 ================================================================== From sorench at gmail.com Thu May 21 11:17:33 2015 From: sorench at gmail.com (Soren Christensen) Date: Thu, 21 May 2015 08:17:33 -0700 Subject: [MINC-users] using register remotely In-Reply-To: <555DF436.8020104@cermep.fr> References: <555CA47E.60003@cermep.fr> <555DF436.8020104@cermep.fr> Message-ID: Why not install locally? Running locally generally involves less lag in my experience. Soren On Thu, May 21, 2015 at 8:05 AM, J?r?me Redout? wrote: > Thanks for your responses... > the local machine runs Ubuntu x64 15.04 > > the -rgb option fails too > > > I switched my local machine from windows to ubuntu to escape from VNC > sessions.... but I'm afraid I ll have to get them back if I want to use > register :( > > > Le 21/05/2015 14:03, Andrew Janke a ?crit : > >> Hi Jerome, >> >> Changes in the underlying GLUT libraries mean that this at times can >> be painful, is there an option to use VNC or something of the ilk >> instead? >> >> a >> >> >> >> On 21 May 2015 at 01:13, J?r?me Redout? wrote: >> >>> Hi, >>> Minc tools are available on a remote server. >>> I can't run register through ssh -X connection >>> How should I do? >>> Thanks >>> Jerome >>> >>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> 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 >> >> > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From assemlal at cim.mcgill.ca Fri May 22 07:08:32 2015 From: assemlal at cim.mcgill.ca (Haz-Edine) Date: Fri, 22 May 2015 07:08:32 -0400 Subject: [MINC-users] RE : Re: using register remotely Message-ID: <7wqvyh3g50vn0rlx6d7t8dpc.1432292670118@email.android.com> Hi,Remote access to OpenGL applications like register or Display is a bit of hit or miss. It depends on the compatibility between the X server/client video card drivers. In my experience Nvidia drivers works fairly well. You may try compiling register statically to the MESA drivers (software implementation of OpenGL) and use that binary remotely. Thanks,Haz-Edine? -------- Message d'origine -------- De : Soren Christensen Date : 05/21/2015 11:17 AM (GMT-05:00) ? : MINC users mailing list Objet : Re: [MINC-users] using register remotely Why not install locally?? Running locally generally involves less lag in my experience. Soren On Thu, May 21, 2015 at 8:05 AM, J?r?me Redout? wrote: > Thanks for your responses... > the local machine runs Ubuntu x64 15.04 > > the -rgb option fails too > > > I switched my local machine from windows to ubuntu to escape from VNC > sessions.... but I'm afraid I ll have to get them back if I want to use > register :( > > > Le 21/05/2015 14:03, Andrew Janke a ?crit : > >> Hi Jerome, >> >> Changes in the underlying GLUT libraries mean that this at times can >> be painful, is there an option to use VNC or something of the ilk >> instead? >> >> a >> >> >> >> On 21 May 2015 at 01:13, J?r?me Redout? wrote: >> >>> Hi, >>> Minc tools are available on a remote server. >>> I can't run register through ssh -X connection >>> How should I do? >>> Thanks >>> Jerome >>> >>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> 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 >> >> > > -- > ================================================================== > J?r?me Redout? > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > CERMEP - Imagerie du vivant > 59 Bd Pinel. 69677 Bron - FRANCE > tel : 33 (0)4 72 68 86 18 (bureau) > tel : 33 (0)4 72 68 86 00 (standard) > fax : 33 (0)4 72 68 86 10 > ================================================================== > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users, ??? From zijdenbos at gmail.com Fri May 22 07:48:48 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Fri, 22 May 2015 07:48:48 -0400 Subject: [MINC-users] RE : Re: using register remotely In-Reply-To: <7wqvyh3g50vn0rlx6d7t8dpc.1432292670118@email.android.com> References: <7wqvyh3g50vn0rlx6d7t8dpc.1432292670118@email.android.com> Message-ID: By the way, NoMachine/NX is far superior to VNC for remote desktop sessions. Unfortunately ever since they completely rewrote it (and botched it for the longest time), they also started charging for it with version 4. But you can still find/use v3, and there are some alternatives, such as OpenNX. -- A On Fri, May 22, 2015 at 7:08 AM, Haz-Edine wrote: > Hi,Remote access to OpenGL applications like register or Display is a bit > of hit or miss. It depends on the compatibility between the X server/client > video card drivers. In my experience Nvidia drivers works fairly well. > You may try compiling register statically to the MESA drivers (software > implementation of OpenGL) and use that binary remotely. > Thanks,Haz-Edine > > -------- Message d'origine -------- > De : Soren Christensen > Date : 05/21/2015 11:17 AM (GMT-05:00) > ? : MINC users mailing list > Objet : Re: [MINC-users] using register remotely > > Why not install locally? Running locally generally involves less lag in my > experience. > > Soren > > On Thu, May 21, 2015 at 8:05 AM, J?r?me Redout? wrote: > > > Thanks for your responses... > > the local machine runs Ubuntu x64 15.04 > > > > the -rgb option fails too > > > > > > I switched my local machine from windows to ubuntu to escape from VNC > > sessions.... but I'm afraid I ll have to get them back if I want to use > > register :( > > > > > > Le 21/05/2015 14:03, Andrew Janke a ?crit : > > > >> Hi Jerome, > >> > >> Changes in the underlying GLUT libraries mean that this at times can > >> be painful, is there an option to use VNC or something of the ilk > >> instead? > >> > >> a > >> > >> > >> > >> On 21 May 2015 at 01:13, J?r?me Redout? wrote: > >> > >>> Hi, > >>> Minc tools are available on a remote server. > >>> I can't run register through ssh -X connection > >>> How should I do? > >>> Thanks > >>> Jerome > >>> > >>> -- > >>> ================================================================== > >>> J?r?me Redout? > >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > >>> CERMEP - Imagerie du vivant > >>> 59 Bd Pinel. 69677 Bron - FRANCE > >>> tel : 33 (0)4 72 68 86 18 (bureau) > >>> tel : 33 (0)4 72 68 86 00 (standard) > >>> fax : 33 (0)4 72 68 86 10 > >>> ================================================================== > >>> > >>> > >>> _______________________________________________ > >>> 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 > >> > >> > > > > -- > > ================================================================== > > J?r?me Redout? > > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > > CERMEP - Imagerie du vivant > > 59 Bd Pinel. 69677 Bron - FRANCE > > tel : 33 (0)4 72 68 86 18 (bureau) > > tel : 33 (0)4 72 68 86 00 (standard) > > fax : 33 (0)4 72 68 86 10 > > ================================================================== > > > > > > _______________________________________________ > > 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 gdevenyi at gmail.com Fri May 22 08:03:56 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Fri, 22 May 2015 08:03:56 -0400 Subject: [MINC-users] RE : Re: using register remotely In-Reply-To: References: <7wqvyh3g50vn0rlx6d7t8dpc.1432292670118@email.android.com> Message-ID: X2go is an alternative implementation which is free and works well On May 22, 2015 7:49 AM, "Alex Zijdenbos" wrote: > By the way, NoMachine/NX is far superior to VNC for remote desktop > sessions. Unfortunately ever since they completely rewrote it (and botched > it for the longest time), they also started charging for it with version 4. > But you can still find/use v3, and there are some alternatives, such as > OpenNX. > > -- A > > On Fri, May 22, 2015 at 7:08 AM, Haz-Edine wrote: > > > Hi,Remote access to OpenGL applications like register or Display is a bit > > of hit or miss. It depends on the compatibility between the X > server/client > > video card drivers. In my experience Nvidia drivers works fairly well. > > You may try compiling register statically to the MESA drivers (software > > implementation of OpenGL) and use that binary remotely. > > Thanks,Haz-Edine > > > > -------- Message d'origine -------- > > De : Soren Christensen > > Date : 05/21/2015 11:17 AM (GMT-05:00) > > ? : MINC users mailing list > > Objet : Re: [MINC-users] using register remotely > > > > Why not install locally? Running locally generally involves less lag in > my > > experience. > > > > Soren > > > > On Thu, May 21, 2015 at 8:05 AM, J?r?me Redout? > wrote: > > > > > Thanks for your responses... > > > the local machine runs Ubuntu x64 15.04 > > > > > > the -rgb option fails too > > > > > > > > > I switched my local machine from windows to ubuntu to escape from VNC > > > sessions.... but I'm afraid I ll have to get them back if I want to use > > > register :( > > > > > > > > > Le 21/05/2015 14:03, Andrew Janke a ?crit : > > > > > >> Hi Jerome, > > >> > > >> Changes in the underlying GLUT libraries mean that this at times can > > >> be painful, is there an option to use VNC or something of the ilk > > >> instead? > > >> > > >> a > > >> > > >> > > >> > > >> On 21 May 2015 at 01:13, J?r?me Redout? wrote: > > >> > > >>> Hi, > > >>> Minc tools are available on a remote server. > > >>> I can't run register through ssh -X connection > > >>> How should I do? > > >>> Thanks > > >>> Jerome > > >>> > > >>> -- > > >>> ================================================================== > > >>> J?r?me Redout? > > >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > > >>> CERMEP - Imagerie du vivant > > >>> 59 Bd Pinel. 69677 Bron - FRANCE > > >>> tel : 33 (0)4 72 68 86 18 (bureau) > > >>> tel : 33 (0)4 72 68 86 00 (standard) > > >>> fax : 33 (0)4 72 68 86 10 > > >>> ================================================================== > > >>> > > >>> > > >>> _______________________________________________ > > >>> 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 > > >> > > >> > > > > > > -- > > > ================================================================== > > > J?r?me Redout? > > > Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 > > > CERMEP - Imagerie du vivant > > > 59 Bd Pinel. 69677 Bron - FRANCE > > > tel : 33 (0)4 72 68 86 18 (bureau) > > > tel : 33 (0)4 72 68 86 00 (standard) > > > fax : 33 (0)4 72 68 86 10 > > > ================================================================== > > > > > > > > > _______________________________________________ > > > 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 gdevenyi at gmail.com Fri May 22 13:26:43 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Fri, 22 May 2015 13:26:43 -0400 Subject: [MINC-users] Fixing wrapped-around MINC files Message-ID: Hi all, I have a collection of minc files which for some reason have their data wrapped around one of the dimensions (i.e the brain is on the edge of the volume and the other half is on the opposite side) Is there a way I can edit the minc properties to fix this? Thanks! -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com From robert.d.vincent at mcgill.ca Fri May 22 13:33:00 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Fri, 22 May 2015 13:33:00 -0400 Subject: [MINC-users] Fixing wrapped-around MINC files In-Reply-To: References: Message-ID: Hi, That sounds like a conversion problem - it's the sort of thing one sees when the data in the image is incorrectly aligned. How were these files created? It probably isn't trivial to fix. It might be possible to script some combination of minctoraw -> rawtominc to fix the misaligned data, if the error is consistent in size and direction. -bert On Fri, May 22, 2015 at 1:26 PM, Gabriel A. Devenyi wrote: > Hi all, > > I have a collection of minc files which for some reason have their data > wrapped around one of the dimensions (i.e the brain is on the edge of the > volume and the other half is on the opposite side) > > Is there a way I can edit the minc properties to fix this? Thanks! > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > McGill University > t: 514.761.6131x4781 > e: gdevenyi at gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Fri May 22 20:19:44 2015 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 23 May 2015 10:19:44 +1000 Subject: [MINC-users] Fixing wrapped-around MINC files In-Reply-To: References: Message-ID: hi Gabriel, I have a Perl script called volunfold that fixes this semi magically. I'll put it up on github when I get home for you. a On 23/05/2015 3:28 AM, "Gabriel A. Devenyi" wrote: > Hi all, > > I have a collection of minc files which for some reason have their data > wrapped around one of the dimensions (i.e the brain is on the edge of the > volume and the other half is on the opposite side) > > Is there a way I can edit the minc properties to fix this? Thanks! > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > McGill University > t: 514.761.6131x4781 > e: gdevenyi at gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Fri May 22 22:33:03 2015 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 23 May 2015 12:33:03 +1000 Subject: [MINC-users] Fixing wrapped-around MINC files In-Reply-To: References: Message-ID: Hi Gabriel, Script is here: https://github.com/BIC-MNI/minc-widgets/blob/master/volunfold/volunfold YMWV but at least you can make use of the mincreshape logic to fix your files up if needs be. a On 23 May 2015 at 10:19, Andrew Janke wrote: > hi Gabriel, > > I have a Perl script called volunfold that fixes this semi magically. I'll > put it up on github when I get home for you. > > a > > On 23/05/2015 3:28 AM, "Gabriel A. Devenyi" wrote: >> >> Hi all, >> >> I have a collection of minc files which for some reason have their data >> wrapped around one of the dimensions (i.e the brain is on the edge of the >> volume and the other half is on the opposite side) >> >> Is there a way I can edit the minc properties to fix this? Thanks! >> >> -- >> Gabriel A. Devenyi B.Eng. Ph.D. >> Research Computing Associate >> Computational Brain Anatomy Laboratory >> Cerebral Imaging Center >> Douglas Mental Health University Institute >> McGill University >> t: 514.761.6131x4781 >> e: gdevenyi at gmail.com >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From gdevenyi at gmail.com Sat May 23 20:36:22 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Sat, 23 May 2015 20:36:22 -0400 Subject: [MINC-users] Fixing wrapped-around MINC files In-Reply-To: References: Message-ID: Cheers, I'll give that a try! -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Fri, May 22, 2015 at 10:33 PM, Andrew Janke wrote: > Hi Gabriel, > > Script is here: > > https://github.com/BIC-MNI/minc-widgets/blob/master/volunfold/volunfold > > YMWV but at least you can make use of the mincreshape logic to fix > your files up if needs be. > > > a > > On 23 May 2015 at 10:19, Andrew Janke wrote: > > hi Gabriel, > > > > I have a Perl script called volunfold that fixes this semi magically. > I'll > > put it up on github when I get home for you. > > > > a > > > > On 23/05/2015 3:28 AM, "Gabriel A. Devenyi" wrote: > >> > >> Hi all, > >> > >> I have a collection of minc files which for some reason have their data > >> wrapped around one of the dimensions (i.e the brain is on the edge of > the > >> volume and the other half is on the opposite side) > >> > >> Is there a way I can edit the minc properties to fix this? Thanks! > >> > >> -- > >> Gabriel A. Devenyi B.Eng. Ph.D. > >> Research Computing Associate > >> Computational Brain Anatomy Laboratory > >> Cerebral Imaging Center > >> Douglas Mental Health University Institute > >> McGill University > >> t: 514.761.6131x4781 > >> e: gdevenyi at gmail.com > >> _______________________________________________ > >> 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 >