Resting State Individual Extraction

AFNI Message Board
1

Hi,

I ran between group resting state functional analyses between two groups of participants. I created three seeds for my regions of interest (left and right M1, left and right IFG, and left and right pSTS).

I started by using this script for pre-processing:
afni_proc.py -subj_id s01.REST
-dsets s01_rest_EPI.nii
-copy_anat s01_anat.nii
-blocks despike tshift align tlrc volreg blur mask regress
-tcat_remove_first_trs 3
-volreg_align_e2a
-volreg_tlrc_warp
-regress_anaticor
-regress_censor_motion 0.2
-regress_censor_outliers 0.1
-regress_bandpass 0.01 0.1
-regress_apply_mot_types demean deriv
-regress_run_clustsim no
-regress_est_blur_epits
-regress_est_blur_errts

I then followed the steps to extract mean time series within each ROI, generated pearson correlation between mean time series an voxels, and then converted a r score to a z score for use in group analyses.

I now want to extract a single mean value of connectivity for each of my subjects between each seed region and the results of the between group analyses. Can somebody please help me?

Thanks so much!!!

2

Hello,

Note that for a handful of ROIs, one can use 3dGroupInCorr
to go from the collection of errts time series and a
2-sample t-test, which can be very convenient to script.

For the single mean value of connectivity, do you mean
that given an ROI, you would want to output the average
correlation with that ROI time series across the brain?

If so, your proc script might already be doing something
like that. Either way, you can look at how it is done
from Example 11 of the help. Here is the resulting proc
script, s17.proc.FT.rest.11
https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/FT_analysis/s17.proc.FT.rest.11

Search for “create correlation volume corr_af_FSvent”,
where it does exactly this for those ROIs requested
via the -regress_make_corr_vols option.

That is how the GCOR value is computed, too. Though
for GCOR, the ROI of interest is the whole brain.

Is that what you want to do?

  • rick