Re: [Freesurfer] Re: Multiple Comparison - Clusterwise Correction

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

Re: [Freesurfer] wm edits

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

[Freesurfer] Multiple Comparison - Clusterwise Correction

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

[Freesurfer] wm edits

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

Re: [Freesurfer] Version differences

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

Re: [Freesurfer] microparcellation

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

Re: [Freesurfer] Problem while fixing the Surface Topology

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