jasonlerch
commented
6 years ago Neat!
Also check out how to do it in RMINC, if you’re curious:
https://mouse-imaging-centre.github.io/blog/post/2018-02-08_peaks-intro/
Jason
On Apr 5, 2018, 11:44 AM -0400, Eduardo Garza-Villarreal notifications@github.com, wrote:
Dear all,
After I finish the vertexLm and get the t-value thresholds with vertexFDR, I needed to go to minc Display and get the MNI coordinates of each significant PEAK by hand. I could not find a better way to get all the information I needed in one place (significant peak brain area, MNI coordinate, vertex and t-value).
So I made a small function with some of my students that solved my particular problem, called Vertex Coordinate Atlas: vertex_coordatlashttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_egarza_scripts&d=DwMCaQ&c=Sj806OTFwmuG2UO1EEDr-2uZRzm2EPz39TfVBG2Km-o&r=HeHbjTJnvHS1LfU-oVbj4xp56MzXc8SwpgPYe318jo0&m=YZHHs2TWZm1hTu0A3eeVnUSepYFCNXXXGzMDFJ8hxvE&s=Kk-2W7DoucvEyl3ZKdGCER_sT7RUecj7lNbtIYgrt7Y&e=.
The output is a table that one can export to Word or use ztable or whatever.
I would like to share this function and get feedback for it, and perhaps someone can improve it. It has some issues, for example, it uses the AAL labels as factors, and from there it finds the MAX t-value, and uses that particular row. So if you have 2 clusters in the same AAL label, you only get the MAX t-value MNI coordinate.
For now it needs some files I created based on the AAL atlas with 4,0962 vertices.
Thanks in advance,
Eduardo
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egarza
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gdevenyi
Dear all,
After I finish the vertexLm and get the t-value thresholds with vertexFDR, I needed to go to minc Display and get the MNI coordinates of each significant PEAK by hand. I could not find a better way to get all the information I needed in one place (significant peak brain area, MNI coordinate, vertex and t-value).
So I made a small function with some of my students that solved my particular problem, called Vertex Coordinate Atlas: vertex_coordatlas.
The output is a table that one can export to Word or use ztable or whatever.
I would like to share this function and get feedback for it, and perhaps someone can improve it. It has some issues, for example, it uses the AAL labels as factors, and from there it finds the MAX t-value, and uses that particular row. So if you have 2 clusters in the same AAL label, you only get the MAX t-value MNI coordinate.
For now it needs some files I created based on the AAL atlas with 4,0962 vertices.
Thanks in advance,
Eduardo