Back to PLS HelpPosted on 10/16/14 05:53:20
Number of posts: 13
Dear PLS experts,
I am interested to compute the average intensity response of voxels within a mask. Task PLS was carried out on fMRI data, and I am now interested to check the mean intensity response of all voxels within a ROI. Is there any easy solution for this? I also noticed that multiple voxel extraction only works for a voxel, but not for a mask.
My second question is whether it is possible to subtract one of LVs from the preprocessèd data and rerun task PLS?
Thanks in advance for your help!
/Kami
Replies:
Posted on 10/17/14 10:15:32
Number of posts: 394
Hi Kami,
Unfortunately we do not have tools in PLSgui to do the averages within an ROI. If you are facile in MATLAB, its fairly easy to write a script to do that.
As for your second question, yes it is possible, but if you are running a regular task PLS (as opposed to non-rotated) the LV as mutually orthogonal so you will get the same result if you 'subtract' one LV out and rerun the analysis. If you want to do this for other purposes, there is a function 'residualize' that is distributed with the code. You would use the designLV for the input vector on the original datamat and then run the followup analysis on the residualized datamat.
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Posted on 10/17/14 10:55:10
Number of posts: 229
kari..
while we do not support ROIs per se, you can extract the average of voxels in the surrounding area, thresholded by the current bootstrap ratio setting.
To see how this looks, and to get a sense of how many voxels would be included in your average data, use the response function plot window. You have an option there to increase the neighborhood size - the number of voxels in the neighborhood are displayed.. eg, if you choose a neighborhood of one, you can extract the mean of a maximum of 27 voxels, etc.
Once you know the size of the neighborhood you want, use the multiple voxel extraction option and indicate the neighborhood size you have chosen.
your output will be the average of voxels in the neighborhood that surpass the bootstrap ratio for each voxel in your list.
nancy
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