Hi Doug, All other things being equal, if you switch from AP to RL phase encoding in an axial acquisition, then the PE direction will switch from the y-axis to the x-axis in the images. It doesn't really have anything to do with Siemens, since the images are written out in a standard anatomical orientation, not according to which axis was readout and which was phase encode.
Hope that helps, -MH Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 11/13/12 3:46 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >I guess it is possible that Siemens is doing something funny with the >images. I've never used sagittal before. > >On 11/13/2012 12:51 PM, Clark Fisher wrote: >> I'm using a script that calls unpacksdcmdir. Maybe there is some >>setting in our config file that forces the orientation? Nothing obvious >>though. >> >> >> On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: >> >>> I'm a little confused as to why the rows are not the phase encode >>>direction to begin with. What did you use to convert the dicoms to >>>nifti? >>> doug >>> >>> On 11/13/2012 11:59 AM, Clark Fisher wrote: >>>> Thanks Doug, >>>> >>>> Would the proper way to handle this then be to switch the rows and >>>>columns before unwarping, then switch them back before the further >>>>processing steps? >>>> >>>> -Clark >>>> >>>> >>> -- >>> 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 >>> Outgoing: >>>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> >>> >>> 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. >>> >> >> > >-- >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 >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
