Re: [Freesurfer] fscalc / mris_calc problem
Thank Nick, when I try mris_calc, I get the following error: /Users/Lado 1 mris_calc /usr/local/freesurfer/bin/mris_calc: Exec format error. Binary file not executable. I applied chmod/chown/chgrp to the executable files to resemble the other freesurfer executables, the prior mris_calc file was renamed to mris_calc.old, shown below for comparison: /Users/Lado 10 ls -l /usr/local/freesurfer/bin/mris_calc* -rwxr-xr-x 1 root wheel 5936512 Aug 13 19:53 /usr/local/freesurfer/bin/mris_calc -rwxr-xr-x 1 root wheel 5903448 May 26 2011 /usr/local/freesurfer/bin/mris_calc.old Not sure what I'm missing, any suggestions? -Fred Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladof...@gmail.com On Jan 2, 2013, at 4:04 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fred, You can try an updated mris_calc for the mac found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ Nick On Mon, 2012-12-31 at 13:21 +0200, Rudolph Pienaar wrote: Hi Fred -- I'm currently traveling and have limited internet connectivity. I'll be back at the office later in the week and will take a look then. In the meantime, has this ever worked for you previously? I know that older versions of 'mris_calc' were somewhat particular about filename lengths and filename conventions, and you might be seeing the same bug here... Best -=R Sent from my iPad On Dec 28, 2012, at 7:50, Fred Lado ladof...@gmail.com wrote: Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... -- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladof...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fscalc / mris_calc problem
That error typically means you're trying to run a binary file compiled for a different architecture (i.e. running a Linux binary on a Mac or vice versa). You can easily check what 'mris_calc' is compiled for. # On a Mac: $cd $FREESURFER_HOME/bin $file mris_calc mris_calc: Mach-O 64-bit executable x86_64 # On Linux: $cd $FREESURFER_HOME/bin $file mris_calc mris_calc: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.24, BuildID[sha1]=0x9323298c405a28417aa0700d979713651437a416, not stripped Can you confirm what architecture your 'mris_calc' is compiled for? Best -=R On 1/3/13 13:38 , Fred Lado wrote: Thank Nick, when I try mris_calc, I get the following error: /Users/Lado 1 mris_calc /usr/local/freesurfer/bin/mris_calc: Exec format error. Binary file not executable. I applied chmod/chown/chgrp to the executable files to resemble the other freesurfer executables, the prior mris_calc file was renamed to mris_calc.old, shown below for comparison: /Users/Lado 10 ls -l /usr/local/freesurfer/bin/mris_calc* -rwxr-xr-x 1 root wheel 5936512 Aug 13 19:53 /usr/local/freesurfer/bin/mris_calc -rwxr-xr-x 1 root wheel 5903448 May 26 2011 /usr/local/freesurfer/bin/mris_calc.old Not sure what I'm missing, any suggestions? -Fred -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] fscalc / mris_calc problem
Fred, You can try an updated mris_calc for the mac found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ Nick On Mon, 2012-12-31 at 13:21 +0200, Rudolph Pienaar wrote: Hi Fred -- I'm currently traveling and have limited internet connectivity. I'll be back at the office later in the week and will take a look then. In the meantime, has this ever worked for you previously? I know that older versions of 'mris_calc' were somewhat particular about filename lengths and filename conventions, and you might be seeing the same bug here... Best -=R Sent from my iPad On Dec 28, 2012, at 7:50, Fred Lado ladof...@gmail.com wrote: Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... -- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladof...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] fscalc / mris_calc problem
Hi Fred -- I'm currently traveling and have limited internet connectivity. I'll be back at the office later in the week and will take a look then. In the meantime, has this ever worked for you previously? I know that older versions of 'mris_calc' were somewhat particular about filename lengths and filename conventions, and you might be seeing the same bug here... Best -=R Sent from my iPad On Dec 28, 2012, at 7:50, Fred Lado ladof...@gmail.com wrote: Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... -- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladof...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] fscalc / mris_calc problem
Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... -- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladof...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
