Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug
On 11/13/2012 07:32 AM, Clark Fisher wrote: > Hi everyone, > > I recently switched the phase encoding direction of the functional sequence > I've been using from F>> H to R>> L and ran into a problem with > epidewarp.fsl (in version 4). The unwarping was still happening along the > F>> H axis in the new images where phase encoding was R>> L. > > (Note: I'm working with NHPs in sphinx position, but I'll describe my problem > in standard coordinates to keep everything somewhat simpler) > > Because thought that epidewarp.fsl might be having a difficult time > determining the phase encoding direction, I swapped the position of the F>> > H and R>> L dimensions in my nifti file (going from LIP to IRP) and the > dewarping now seems to work. > > Is there something going wrong in the unpacking such that the phase encoding > information is lost? Also, is the phase encoding information stored anywhere > in the nifti, so that I can automatically detect and correct cases like this? > > Thanks for the help, > Clark > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
