Dear Mojmir, using ~400 subjects, we found that the subfield module was a bit better than the ASEG volumes at discriminating Alzheimer’s patients from controls (see the Neuorimage paper). But, in any case, the difference is small. Regarding longitudinal segmentation: we just got a paper about this accepted, see http://www.nmr.mgh.harvard.edu/~iglesias/pdf/Neuroimage_2016_longitudinal.pd... I still need to find time to clean up the code and put it up on FreeSurfer. For the time being, you can run the subfield module on the longitudinally analyzed recons (method “L-INIT” in the paper). Cheers, Eugenio
Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 15 Jul 2016, at 09:00, Mojmír Vinkler <mojmir.vinkler@gmail.commailto:mojmir.vinkler@gmail.com> wrote:
Hi Juan,
Thanks! You're right, they really are tightly correlated (although their absolute values differ by 30%). We tried it on couple of subjects, but didn't find subfields to be significantly better than aseg stats though. By the way, is Freesurfer capable of using multiple scans from the same subject (longitudinal study, same modality) to make more precise measurements? For example by using T1 from the same subject / different time instead of T2 in subfields?
Thanks! Mojmir
On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote: Hi Mojmir, ASEG typically gives a larger estimate of the volume, though highly correlated with that from the subfield package. We have found the measurements from the subfield package to be a bit more reliable, though. Cheers, Eugenio
Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/
On 13 Jul 2016, at 16:07, Mojmír Vinkler <mojmir.vinkler@gmail.commailto:mojmir.vinkler@gmail.com> wrote:
Hi experts,
I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields segmentation. I only need to measure total hippocampus volume, but measurements from basic `recon-all` were too volatile and I was hoping that using subfields with T2 modality would reduce variance. However, volume measured by hippocampal subfields is significantly different from volume in aseg.stats.
Here are volumes for right hippocampus from various methods: aseg.stats - 3312.8 rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8 rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97 rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation) - 2596.09
I checked labeling visually and there were no obvious problems. Is such a large difference common? Am I missing something? What number should be most trusted?
Thanks for any hints! Mojmir _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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