Hi Anastasia,
Thanks so much for your help. I was able to correct this problem in my configuration file. I have now run into another error- "bvecs and bvals don't have the same number of entries." I have read other postings about this error and can see that my bvec file is not formatted correctly when I import into Excel. However, I am not sure how to correctly fix this formatting. I know that I have 28 bval entries and 84 bvec entries, so the overall number is correct. I am just unclear on how to fix the formatting of the bvec file so that it corresponds correctly to the ordering in the bval file (which order the bvec entries should appear in within the three columns). Do you have any resources on this?
Thank you again for your help, Allison
Quoting Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:
Hi Allison - The mri_convert command at the top of your log file is trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to a nifti file. From the name of that nifti file, it looks like it's expecting to find a field map and not finding it.
Hope this helps, a.y
On Tue, 8 Jan 2013, Allison Gruber wrote:
Dear Freesurfer experts,
I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this.
Selection from log:
mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013
Please let me know if this is not enough information. Thank you for your help.
Allison _______________________________________________ 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.
Hi Allison - Instead of using excel, I would use a unix-based text editor, whichever is available on the system where you are running the analyses. This way you can ensure that unix commands read your text files properly.
The 3 values for each diffusion gradient vector are its x, y, z components, so I wouldn't change their order, unless you have reason to believe that the order is not correct the way it was given to you.
Hope this helps, a.y
On Wed, 9 Jan 2013, Allison Gruber wrote:
Hi Anastasia,
Thanks so much for your help. I was able to correct this problem in my configuration file. I have now run into another error- "bvecs and bvals don't have the same number of entries." I have read other postings about this error and can see that my bvec file is not formatted correctly when I import into Excel. However, I am not sure how to correctly fix this formatting. I know that I have 28 bval entries and 84 bvec entries, so the overall number is correct. I am just unclear on how to fix the formatting of the bvec file so that it corresponds correctly to the ordering in the bval file (which order the bvec entries should appear in within the three columns). Do you have any resources on this?
Thank you again for your help, Allison
Quoting Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:
Hi Allison - The mri_convert command at the top of your log file is trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to a nifti file. From the name of that nifti file, it looks like it's expecting to find a field map and not finding it.
Hope this helps, a.y
On Tue, 8 Jan 2013, Allison Gruber wrote:
Dear Freesurfer experts,
I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this.
Selection from log:
mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013
Please let me know if this is not enough information. Thank you for your help.
Allison _______________________________________________ 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.
Hi I add the same problem; It finally worked :
- using libreoffice instead of excel to transpose the bvec/bval files ; - with english as linguisitic parameter, - save the file as cvs document, with the filter parameters box checked - in the filer option choose "space" as field separator; " as text separator, "unicode UTF-8" as encoding
cheers
freesurfer@nmr.mgh.harvard.edu
-
Allison Gruber -
Anastasia Yendiki -
Christophe Destrieux