Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this. Thanks! a.y On Tue, 9 Jul 2013, Gundran, Andrew wrote: > Helo all, > > I was finally able to figure out my configuration file problem. But when I > run the first step of pre-processing I receive an error about freesurfer > being unable to read a certain dwi_frame file. > > ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz > /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz > awk: can't open file 1000 > source line number 1 > mri_concat --i > /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz > --mean --o > /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz > niiRead(): error opening file > /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz > ninputs = 1 > Checking inputs > ERROR: reading > /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz > Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: > Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > > > I have also attached the trac-all log. _______________________________________________ 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.
