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January 20, 2019 02:15AM
Hi ,
I have a set of coordinates which correspond to electrode positions and I want to create a circular ROI on each of these positions so that I can visualise them. I can do this using 3dUndump, however I want to view it on the surface and projecting the ROIs onto the surface created by 3dundump distorts them. I therefore need to create the ROIs on the surface. I'm not sure what the best way to do this is, and I can't get it to work with the approach that I'm taking. My approach is to find the closest node that corresponds to each coordinate by using Surf2Volcoord and then creating an ROI on each of those nodes using ROIgrow. after I convert the output from ROIgrow to a surface file to visualize it the whole of the right side of the brain gets masked

I have a file coords.1D which has the 4 coordinates:
66.3985309814671 -1.00058582287324 -15.4765354668334
60.4748253830891 -0.186445728058132 -15.9433046579422
55.5606079666971 0.337490555347936 -16.0875733959558
50.4291732155899 0.829906877934213 -16.2681078444391

I get the corresponding nodes like this:
Surf2VolCoord -i std.60.rh.inflated.asc -i std.60.lh.inflated.asc -sv IR39_mni_SurfVol_Alnd_Exp+orig -qual LR -closest_nodes coords.1D -prefix nodes
the output is a txt file with four node numbers

1986L 16.698700
3263L 11.258648
3231L 6.678189
3230L 2.037704
(im not sure what the number are in the second column. and they should be on the right not left). I then create two files 1D files.

nodelocations.1D:
1986
3263
3231
3230

nodelabels.1D
1
1
1
1

and I use these as inputs in ROIgrow
ROIgrow -overwrite -spec std.60.IR39_mni_lh.spec -surf inflated -roi_nodes nodelocations.1D -roi_labels nodelabels.1D -lim 10 -full_list -prefix SurfCoord

I then convert it to a surface file

ConvertDset -o_niml -add_node_index SurfCoord -prefix SurfCoordRoi

I'm not really sure what I'm doing, It would be really great if someone could help me out!


Subject Author Posted

How to get surface ROIs from coordinates Attachments

ainsley January 20, 2019 02:15AM

Re: How to get surface ROIs from coordinates

ainsley January 28, 2019 07:12AM



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