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 >>>>>> >>>>> >>>> >>>> >>> >> >> > -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick _______________________________________________ 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.
