B) You can't partial-volume correct the DICE, but you
can compare the volumes after partial-volume corrections.
C) There are references in our Neuron paper on the definition of
the hippocampus (Caviness, Makris, Kennedy papers)
cheers
Bruce
On Tue, 11 Nov 2014, Bernd Merkel wrote:
Dear all !
I know, this has been discussed a lot in the forum, however, I
am still not
sure, whether my analysis pipeline is correct.
I simply want to compare volumes of FS vs. manual segmentation
in the
hippocampus and calculate the dice coefficient. So these are my
steps:
1. mri_convert T1.mgz T1.nii
2. Register (e.g. with FLIRT) T1.nii to original_mprage.nii
(where the
manual segmentation was done), output: registration.matrix
3. mri_extract_label aseg.mgz 17 left_FreeSurfer_HC.nii
mri_extract_label 53 right_FreeSurfer_HC.nii
4. Register left_ & right_FreeSurfer_HC.nii to
original_mprage.nii by using
registration.matrix
5. mri_compute_overlap left_Freesurfer_ HC left_manual_HC
Now here are my questions:
A) I've read that I should use mri_label2vol instead of
mri_convert
Is that correct and how would I process that afterwards ?
B) The volumes form aseg.mgz are different (in my case: bigger)
to the
aseg.stats because of partial volume correction. Can I use
partial volume
corrected hippocampal masks ?
C) Where can I find information about the segmentation method of
the
hippocampus, used in FreeSurfer, especially regarding the HC
borders ?
Because otherwise it might be difficult to calculate and
interpret dice
coefficients.
Best regards and thanks for any help,
Bernd
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