resting-state fmri analysis

AFNI Message Board
1

Hello
is there any tutorial or example to do resting-state fMRI analysis for 25 subject dataset. actually i do not know how to get start, there is many tutorials and documents over the internet which i did not understand.
dataset link ( NYU_TRT_session1 ):
https://www.nitrc.org/frs/?group_id=274

2

Sure, we would recommend using afni_proc.py to set up your analysis. I would start by looking at examples 11 and 11b here in the afni_proc.py help:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/afni_proc.py_sphx.html#example-11-resting-state-analysis-now-even-more-modern

There is the APMULTI demo, for afni_proc.py processing of multi-echo FMRI (resting state) data, which also contains a script for single-echo (= “standard acquisition”) FMRI processing that would be useful to you; run the following to download+unpack it:
@Install_APMULTI_Demo
The README* files there provide more information. There are scripts_desktop/ and scripts_biowulf/ versions of the scripts, for whether you aim to process on a desktop computer or a cluster, respectively. The do_*tcsh scripts have the single subject processing commands, and the corresponding run_tcsh scripts contain the pieces to loop over everything. You could organize your starting data similarly to how the data_00 tree looks (with more subjects, in your case), and then apply the scripts pretty directly. You would likely want to use the do_ssw.tcsh script to skullstrip your anatomical and align it to standard space; perhaps the do_fs.tcsh script would be of interest for running FreeSurfer’s recon-all for parcellating the data and if you want tissue-based regressors; and the do_20_ap_se.tcsh contains the single-echo afni_proc.py processing suggestion, as a starting point for creating your own analysis.

You have to decide a bit about what kind of processing choices you want: are you going to do ROI-based processing (in which case, pick an appropriate template and atlas for that, and don’t blur during processing), or voxelwise (in which case, likely still pick an appropriate template, but then decide how much blurring you want). Do you want to use tissue-based regressors (like fast anaticor)? Do you want to bandpass (lots of resting state studies do, but it might be better not to, to preserve degrees of freedom and higher-frequency useful info)?

Some papers about resting state processing:

Some papers about why you likely wouldn’t want to include global signal regression:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/published/citations.html#re-global-signal-regression-noooo

Please feel free to ping back with more questions/comments here, too.

–pt

3

Also, there are a lot of video tutorials on features of processing here on the AFNI Academy channel:
https://www.youtube.com/c/afnibootcamp
… and more here (recordings of a Bootcamp set of lectures at MIT a few years ago):
https://cbmm.mit.edu/afni

–pt

4

thank you ptaylor for your useful information.
actually i want to do the resting-state fMRI analysis over mentioned data by seed-based correlation analysis.may i know what should i do first and what is the steps.
thank you so much…

5

Hi-

That typically means processing all of your data with steps including alignment to a standard template (so the final EPI time series of each subject have approximate spatial correspondence), and blurring (to increase each voxel’s SNR at the cost of spatial specificity). Once that is complete—and you have verified each subject’s data analysis streams and QC’ed the results—then calculating the seedbased correlation in each subject’s processed data is a relatively small step.

So, the resting state processing example in afni_proc.py’s help 11 and 11b
file:///home/ptaylor/afni_doc/_build/html/programs/afni_proc.py_sphx.html#example-11-resting-state-analysis-now-even-more-modern
file:///home/ptaylor/afni_doc/_build/html/programs/afni_proc.py_sphx.html#example-11b-similar-to-11-but-without-freesurfer
… would be good places to start.

–pt