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: ladofred@gmail.com
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 ladofred@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: ladofred@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 ladofred@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: ladofred@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
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: ladofred@gmail.com
On Jan 2, 2013, at 4:04 PM, Nick Schmansky nicks@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 ladofred@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: ladofred@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
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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
freesurfer@nmr.mgh.harvard.edu
-
Fred Lado -
Nick Schmansky -
Rudolph Pienaar