what does mri_info say about them (and the rawavg.mgz) On Fri, 13 Jan 2012, Anthony Dick wrote:
> It was created from the ahuman_1_do_shft.nii volume, which was what was > input to recon-all in Freesurfer. And these volumes (the overlay and > underlay) align in other viewers (e.g., AFNI and mricron). > > On 1/13/12 2:40 PM, Douglas N Greve wrote: >> What volume was human_1_do_shft.nii created from? >> >> Anthony Dick wrote: >>> Here is the command, in case I didn't run it right. >>> >>> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>> chuman_1_do_shft_new.nii >>> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>> chuman_1_do_shft_new.nii >>> reading info from orig.mgz... >>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>> reading from chuman_1_do_shft.nii... >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> volume sizes do not match >>> >>> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, >>> 102, 1) >>> >>> orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) >>> adick% >>> >>> >>> An image of the tkmedit output is attached. Thanks for any suggestions. >>> >>> Anthony >>> >>> >>> On 1/13/12 2:15 PM, Douglas N Greve wrote: >>>> Try changing the header information in your parcellation, something >>>> like >>>> mri_convert yourparcellation.mgh --in_like orig.mgz >>>> yourparcellation.new.mgh >>>> doug >>>> >>>> Anthony Dick wrote: >>>>> Good question. The parcellation is created outside of Freesurfer >>>>> (the data were shared from another lab and I don't know which >>>>> program they used to create the parcellation; of course I can find >>>>> out if this would be helpful). At any rate, the anatomy and >>>>> parcellation align when viewed in AFNI. >>>>> >>>>> Anthony >>>>> >>>>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>>>> Hi Anthony, how are you creating the parcellation? Are you >>>>>> generating it off the orig.mgz? >>>>>> doug >>>>>> >>>>>> Anthony Dick wrote: >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to train a cerebellar atlas based on 20 manually >>>>>>> parcellated cerebellums. I have run the anatomical through >>>>>>> freesurfer. When I try to load the overlay (parcellation) in >>>>>>> tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay >>>>>>> (the parcellation) are no longer in alignment. >>>>>>> >>>>>>> However, loaded in AFNI the underlay and overlay of course align. >>>>>>> Is there a quick fix to get them in alignment? >>>>>>> >>>>>>> Anthony >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >> > > > _______________________________________________ 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.
