Hello,
I would like to report the coordinates of the regions found in my clusters.
This is what I did so far.
1- TBSS, followed by randomize (All is well till here).
2- I got my clusters using the autoaq command and the results are 4 clusters. Each cluster has several regions in it.
I have the voxel# of the clusters and the coordinates of the clusters.
I want to get the coordinate and voxel number of each of the sub clusters.
So to get the coordinates I wrote the cluster command with --olmax.
Now to name the clusters, I went to atlasquery and used -c for each of the coordinates.
Until now I have all the sub cluster coordinates and names, however I don’t know the cluster size of each sub cluster region.
Can someone help me know the cluster size of each of the sub cluster region?
Also, I have another question.
Since in one of my clusters, for e.g., I saw that the superior longitudinal fasciculus (SLF), exists twice. Each having separate coordinates.
Also the SLF not only exists twice in the same cluster, but also is a sub region in other clusters
Example
Cluster 1
1-SLF coordinates
2- Some region coordinates
3- SLF coordinates
Cluster 2
1- Some region
2- SLF
3-Some regions coordinates
Is it proper to make a ROI (SLF) and try to check how many significant voxels are in that ROI instead of what I did above?
If that is okay, how can I do that?
E.g. SLF is the ROI
To get the # voxels in ROI
-Go to FSL view, load the JHU tact atlas SLF, save it as make and binarize it, then how do I get the # of voxels inside that ROI?
For coordinates of this ROI, should I just report the local max of SLF itself? If not, how do I get that as well
Sorry for asking several Qs..
Thank you in advance,
WY
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