Back to PLS HelpPosted on 02/15/18 06:11:03
Number of posts: 3
Dear all,
I ran PLS from the command line on cortical thickness data extracted from .gii files.
I was wondering now how to visualize the results in a way similar as the gui, namely the identified LV. I know where to find it in my result file but I don't know how to plot it on a standard template.
Thank you.
Giuliano
Replies:
I'm Online
Posted on 02/15/18 08:51:59
Number of posts: 229
Hi.. you have a couple of options.
1) the plotroi code could be useful to display your results on a user-defined template - instructions are in the plotroi directory in the plscmd directory. This would allow you to have simple template plots of the data, and the gui allows you to threshold the results. Note: coordinates for each "roi" (vertex) are with respect to the image (jpg,tiff) not to MRI space.
2) If you are able to display the mesh coordinates in your favourite viewer (freesurfer?), you could take a gii image and replace those data with the bootstrap ratios in the results structure. If you want to get fancy, you could also threshold those results by zeroing out the non-stable BSRs
nancy
Posted on 02/20/18 07:41:53
Number of posts: 3
Thank you for the answer.
I tried the second option you mentioned but I guess I did something wrong.
I opened the .gii files in matlab with this tool https://www.artefact.tk/software/matlab/gifti/ . Then I substitued the values with those in my result file and saved the new gifti object. However when I open it in freeview as an overlay to my original .gii file I see only another exact copy of it and not my covariance pattern, which instead I can see if I plot the gifti object in matlab.
I don't know now if the problem is in how I save the .gii file (see the script below) or is in freesurfer visualization. Any help would be appreciated.
Best,
Giuliano
surf = gifti('s15.mesh.thickness.resampled_32k.5-001-02-MRIT1-PT-001-T00-avg.gii');
surf.cdata(:,1) = result.boot_result.compare_u(:,1);
save(surf','lv.gii','Base64Binary');
I'm Online
Posted on 02/20/18 09:08:40
Number of posts: 229
Hi.. I'm not familiar with that file format, so probably can't help too much.
I would first check that the vectors are the same length. Can you see the mesh if you don't load it as an overlay (the range of values may be too small to see it overtop of the mesh values??)
If you applied any "thresholding" to mask the input data - which may have happened depending on how you read the data in- you may need to expand back to the full vector using rri_coord2xyz - but doubt that is the issue b/c you did not read in *.nii files, right? (check your results mat-files to see if "coords" is populated)
cheers,nancy
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