I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm?
Josh
Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio
On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:
I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm?
Josh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think the resolution is important. The CA1 subfield is only about 2-2.5 mm thick after all.
If this is a feature request thread now, let me add that it would be nice if the actual training algorithm was integrated into Freesurfer. There is a lot of disagreement about the most appropriate subfield boundaries, and the ability to make custom training sets would be helpful.
Right now there is little guidance on what kind of data-sets are appropriate to use with this algorithm. I am concerned that users are trying to segment subfields with older data-sets that probably aren't appropriate (e.g. 1.5 Tesla or 1.5 mm isotropic data).
Josh
On Tue, May 28, 2013 at 1:44 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio
On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:
I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm?
Josh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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