hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it?
cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > 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. > >
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