it of course resamples for overlay, but it doesn't downsample - just uses the vox2ras matrices from the two volumes to compute a common space
On Tue, 12 Jul 2011, Wayne Su wrote: > Thank you Koen. We're investigating the VR Space volume in each hippocampal > subfield. Your suggestion is just what I'm looking for, very helpful. > > Yes, I can use freeview to display them as an overlay. don't how freeview > achieves that. Are you sure no resampling there for the command: > freeview nu.mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt > > > Wayne > > > On 12/07/11 5:33 AM, "Bruce Fischl" <[email protected]> wrote: > >> Or you could use freeview to display them as an overlay without any >> resampling. What is it you are trying to do? >> >> On Jul 12, 2011, at 5:56 AM, Koen Van Leemput <[email protected]> >> wrote: >> >>> Hi Wayne, >>> >>> You're right: It will be difficult to somehow shoehorn the probability >>> images with voxel size 0.5mm isotropic into the orginal 1mm isotropic >>> FreeSurfer volumes. The other way around, by resampling the 1mm input >>> image onto the correct 0.5mm grid is easy, though: >>> >>> >>> kvlUpsample nu.mgz 2 >>> kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0 >>> >>> will result in the files nu_upsampled_2_2_2.mgz and >>> posterior_left_presubiculum_resampled.mgz that are both in the same >>> space and contain 2^3 = 8 times more voxels than the original 1mm >>> voxels. >>> >>> Hope this helps - please let me know if you need more information. >>> >>> Koen >>> >>> >>> >>> On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su <[email protected]> wrote: >>>> Hi Koen, >>>> Look like the outputs (posterior_*.mgz) are probability kind of images. How >>>> can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into >>>> one >>>> image without overlapping? >>>> Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I >>>> achieve this? >>>> Thanks, >>>> Wayne >>>> >>>> >>>> On 06/07/11 5:59 AM, "Koen Van Leemput" <[email protected]> wrote: >>>> >>>> Hi Tricia, >>>> >>>> Yes, that summarizes it neatly. :-) >>>> >>>> Koen >>>> >>>> >>>> On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley <[email protected]> >>>> wrote: >>>> >>>> Hi, >>>> >>>> I understand that the models for the hippocampal subfield segmentation were >>>> created using high resolution MRI scans. But it sounds like this procedure >>>> can be used for scans with 1mm ^3 resolution, right? The resulting values >>>> would just need to be divided by 8 in order to get the subfield volumes in >>>> 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. >>>> Is that correct? >>>> >>>> Thanks, >>>> Tricia Merkley >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> 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 . 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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 >>>> [email protected] >>>> 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 . 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