Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you. Please see attached.
-S
On Wed, Mar 6, 2013 at 12:40 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - Can you send your trac-all.log and dmrirc files? Thanks! a.y On Wed, 6 Mar 2013, Salil Soman wrote: Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil SomanThe 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%C2%A0. 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.