Hello Bruce,
Thanks for the quick reply. I tried to follow your suggestions, there
still seems to be some errors. Hence I am sending you the subject
directory, at:
http://www.ensc.sfu.ca/~mfbeg/outgoing/topologyCorrectionProblem_PradeepFromSFU.tar.gz
When trying to visualize the defect locations
Dear Nick
Is it possible to refer the "faces" I got with the command below to the
labels from an annotation file?
[Macintosh-10:subjects/fsaverage_fineparc_uniformareas/surf] diana%
mris_make_face_parcellation rh.inflated
/Applications/freesurfer/lib/bem/ic4.tri rh.ic4.annot
I would like t
Hi Martin,
so you think the current segmentation is worse than it used to be? Can
you send us a dataset where this appears to be true? I wasn't sure from
the images you sent which were old and which new, but they looked more
like topology problems than segmentation ones (although the two are
Dear Freesurfers,
I have a question on manual white matter edits:
I have cases where a considerable amount of gray matter is classified
as white in my wm.mgz and therefore the original surface (green) is
not accurate but then that is fixed in the next steps and the wm
surface (yellow) is a
Hi Freesurfers,
More questions about this analysis.
1) Referring to the documentation, we used the following command:
tksurfer fsaverage lh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2
-curv -gray
The documentation says we should see an image as shown in Figure 1
(attached). But what we s
Hi Nasim,
1-Will I get accurate results if I do the edits (erasing misclassified
white
matter in wm.mgz) to my white matter mask only in those 10% areas that
the wm
surface is not accurate or should I correct the wm.mgz 'every where' no
matter what?
You can just make edits in the problem
What is displayed if you turn off the annotation display?
The threshold in the simulation is used to determine whether clusters
are found or not. A threshold of 2 indicates a p-value of 0.01
(1/(10^2), 3 is 0.001, etc. The threshold referred to in the tksurfer
display is just for color threshold
