I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error;
ERROR 1 : mris_calc compute sym. pct. change (spc) problem?
It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh
The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard?
Thanks, Kevin Department of Neurology University of Wisconsin-Madison
The problem was a bug related to a buffer overflow on the string lengths of command line arguments. Basically, filename/directory names that were too long triggered it.
Nick might know if a newer Mac build is available. In the meantime, you can try re-running the command with shorter file/dir names:
1. Copy your inputs, beta1.mgh and beta2.mgh to some dir, say ~/tmp 2. Run something "shorter" like:
cd ~/tmp mris_calc -o beta_out.mgh beta1.mgh div beta0.mgh mv beta_out.mgh /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh
On 9/19/11 15:47 , Dabbs (Kevin) wrote:
I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error;
ERROR 1 : mris_calc compute sym. pct. change (spc) problem?
It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh
The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard?
Thanks, Kevin Department of Neurology University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
i've put the updated mris_calc for macos leopard here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-in...
On Mon, 2011-09-19 at 14:47 -0500, Dabbs (Kevin) wrote:
I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error;
ERROR 1 : mris_calc compute sym. pct. change (spc) problem?
It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh
The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard?
Thanks, Kevin Department of Neurology University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Freesurfer's
If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice!
Regards, Manish Dalwani
Hello Freesurfer's
If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice!
Regards, Manish Dalwani
P.s. I sent this email out earlier with the wrong subject name...
There is no "convention" for the surfaces. If it is labeled lh, then it is left hemi, etc. doug
Dalwani, Manish wrote:
Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani P.s. I sent this email out earlier with the wrong subject name...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Dabbs (Kevin) -
Dalwani, Manish -
Douglas N Greve -
Nick Schmansky -
Rudolph Pienaar