Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar
are you sure they are using the same binary? The bash shell probably pushes a new shell, which sources your dot files, etc...
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, thanks for the hint. If I force version 5.1 by specifying the full path to mri_convert, it works. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are you sure they are using the same binary? The bash shell probably pushes a new shell, which sources your dot files, etc...
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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what version failed? On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce, thanks for the hint. If I force version 5.1 by specifying the full path to mri_convert, it works. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are you sure they are using the same binary? The bash shell probably pushes a new shell, which sources your dot files, etc...
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar _______________________________________________ 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.
version 4.5 gives me the segmentation fault, even when I specify the complete path. version 5.1 works if I specify the full path. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
what version failed?
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce, thanks for the hint. If I force version 5.1 by specifying the full path to mri_convert, it works. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are you sure they are using the same binary? The bash shell probably pushes a new shell, which sources your dot files, etc...
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar _______________________________________________ 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.
phew. I thought it was a 5.3 bug. Glad to declare it fixed post-hoc! On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
version 4.5 gives me the segmentation fault, even when I specify the complete path. version 5.1 works if I specify the full path. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
what version failed?
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce, thanks for the hint. If I force version 5.1 by specifying the full path to mri_convert, it works. Caspar
2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are you sure they are using the same binary? The bash shell probably pushes a new shell, which sources your dot files, etc...
On Wed, 19 Jun 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar _______________________________________________ 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Caspar M. Schwiedrzik