Hi Doug,
Sorry to bother again and I hope I'm not becoming too annoying with my questions. I will be very grateful if you can advise what to do for the following:
1) I am still struggling to find a way to localize my clusters in other words to get the nearest cortical label(annotation) if I know the MNI coordinates on the MNI space.
As a reminder I was trying to get a the nearest cortical label(annotation) on the CVS space since this data was registered on the CVS space but can I get their
location on the MNI space if I have their coordinates without doing another registration to MNI? Can I use fsaverage or what should I do?
2) Can you please advise me what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study:
Should I use the:
mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite
But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one.
3) For a paper to be published what is the recommended threshold (what people use in general) for the voxel-wise threshold of the clusters when running the perm or grf. Is a threshold of 3 acceptable (P<0.001) or in general I should use 2 (p<0.01)?
Many thanks. AK
Hi Antonella, sorry for the delay. I have actually been working on your first question, but I don't have a good answer for you. One way to get this would be to load aparc+aseg.mgz when viewing fsaverage, ie,
tkmedit fsaverage orig.mgz -aparc+aseg
Then put the MNI coordinate into the GUI and see where the cursor lands (or just navigate to a point that is close), then see what the closest label is.
Antonella Kis wrote:
Hi Doug,
Sorry to bother again and I hope I'm not becoming too annoying with my questions. I will be very grateful if you can advise what to do for the following:
- I am still struggling to find a way to localize my clusters in
other words to get the nearest cortical label(annotation) if I know the MNI coordinates on the MNI space.
As a reminder I was trying to get a the nearest cortical label(annotation) on the CVS space since this data was registered on the CVS space but can I get their
location on the MNI space if I have their coordinates without doing another registration to MNI? Can I use fsaverage or what should I do?
- Can you please advise me what is the best way in catching the
uncorrected clusters results from the sig.mgh for a structural study:
Should I use the:
mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite
But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one.
That command should do what you are asking. How many clusters are missing?
- For a paper to be published what is the recommended threshold (what
people use in general) for the voxel-wise threshold of the clusters when running the perm or grf. Is a threshold of 3 acceptable (P<0.001) or in general I should use 2 (p<0.01)?
Either one of those is fine with the higher one being preferable.
doug
Many thanks. AK
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Douglas N Greve