Hello, Sir and Madam
I’m beginner of AFNI.
I want to make correlation matrix from functional MRI data, then want to extract the results as some style (i.e.: text file or csv file), and depict the result.
I have a datasets of a normal subject(named Sub1001.T1.nii and Sub1001.fun.nii), and have done IntraCorr procedure.
Then I want to know how to generate their correlation matrix. Can I do this by AFNI software?
What command should I use? 3dROCorr?, @ROI_Corr_Mat?
Can I do that from GUI? If I have to do that from command line, please teach me how to describe the script.
I’m very sorry for interrupting your work, but I am looking for your reply.
Best regards
Tsuyoshi Hashimoto, PhD (JAPAN)
Mail:ytm.workspace@gmail.com
Hi, Tsuyoshi–
Well, welcome to AFNI, then.
3dNetCorr would be my suggestion. An example of using the command is given in this recent post:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,153670,153673#msg-153673
… and you can also check out the helpfile and see if it provides what you want… Basically, you can put in a time series data set and a map of ROIs, and then the function calculates the mean time series of each region and plops out the correlation matrix results in a couple different formats, one of which is a text file that can be plotted most easily with fat_mat_sel.py.
Feel free to take those for a test drive, and to ask questions as you go. I note that there is also an example script in the FATCAT Demo, as described here, which you can download:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/FATCAT/FATCAT_All.html#demo-data-sets-and-scripts
the 3dNetCorr example script is currently: Do_12_RUNrsfc_netw_corr.tcsh.
–pt