Thanks. Does freeview use same approach as what Koen described? Look like both ways need upsampling nu to 0.5x0.5x0.5.
Wayne On 12/07/11 10:29 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > 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" <fis...@nmr.mgh.harvard.edu> 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 <k...@nmr.mgh.harvard.edu> >>> 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 <w...@interchange.ubc.ca> 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" <k...@nmr.mgh.harvard.edu> wrote: >>>>> >>>>> Hi Tricia, >>>>> >>>>> Yes, that summarizes it neatly. :-) >>>>> >>>>> Koen >>>>> >>>>> >>>>> On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley <tmerkl...@yahoo.com> >>>>> 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 >>>>> 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 . 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