Hi Joseph, In freeview you can use "Tools"->"Transform Volume" to reorient volumes.
Best, Ruopeng On 08/11/2015 02:59 PM, Bruce Fischl wrote: > Ruopeng should be able to help you out > > cheers > Bruce > On Tue, 11 Aug 2015, fmri wrote: > >> Is there a wiki instruction block on how to reorient all volumes? >> >> Thanks >> >> On Aug 11, 2015, at 6:13 AM, Bruce Fischl wrote: >> >>> Hi Joseph, >>> >>> no it shouldn't matter to us what the angle is as long as it's in >>> approximately the right orientation. You could reorient the volumes in >>> freeview if you wanted, but I don't think it's necessary >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 10 Aug 2015, fmri wrote: >>> >>>> Hello FreeSurfer experts, >>>> >>>> When MRI slices are not aligned to a more perfect plane of axis as shown >>>> in the 3D render attached. The sagittal slice is Not in-line with the >>>> midsagittal plane of the cerebral cortex. >>>> >>>> All orthogonal slices are viewed in some Uneven angle, this is >>>> demonstrated in the Coronal image attached. >>>> >>>> The coronal slice demonstrates the left hemisphere of the brain in view >>>> Before the right hemisphere. >>>> >>>> This has become trouble some for editing and review purposes. >>>> >>>> The greater concern is that we believe this could be affecting >>>> FreeSurfers' ability to distinguish critical areas in the temporal lobes. >>>> >>>> Does the incorrect alignment of slices -to- brain anatomy matter when >>>> generating segmentations and parcellations? >>>> >>>> If so is there a way to correct these angels before the recons begins to >>>> get better results in labeling segmentations and parcellations? >>>> >>>> Or is there a way to correct these angles for viewing and editing purposes? >>>> >>>> Any thoughts on the matter are appreciated, >>>> >>>> Thanks so much, >>>> >>>> Joseph >>>> >>> _______________________________________________ >>> 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. >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
