how do you get all the image files to align with the one that you realign ?
On Aug 11, 2015, at 12:07 PM, Ruopeng Wang wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
