freesurfer ROI and ROI-ROI correlation

AFNI Message Board
1

Hello，

I have both T1 data and resting fmri data. The resting fmri data is processed with afni_proc.py My T1 data is processed with Freesurfer. I have created an atlas for each subject with 68 cortical regions and 8 subcortical regions. How can I use this subject specific atlas to calculate the ROI-to-ROI correlation and then create an 82*82 matrix? and the mean timecourse of each ROIs?

Thank you so much!

Best,

Jinsong

2

Hi-

Assuming you have mapped your Freesurfer-created ROIs into the space of the FMRI data, then I think 3dNetCorr will do what you want. You can calculate the correlation matrix (default), as well as output the average time series (“-ts_out”) of each region. If you want, you can also make whole brain correlation maps from each ROI’s average time series- in your case, that would make a lot of files, I suppose.

-pt

3

Thank you so much!

Hi-

Assuming you have mapped your Freesurfer-created
ROIs into the space of the FMRI data, then I think
3dNetCorr will do what you want. You can
calculate the correlation matrix (default), as
well as output the average time series (“-ts_out”)
of each region. If you want, you can also make
whole brain correlation maps from each ROI’s
average time series- in your case, that would make
a lot of files, I suppose.

-pt

4

Hi pt~

I’m also doing the similar analysis as in this post. I just have a question:
how to map the FreeSurfer-created ROIs into the space of the fMRI data?

I tried 3dNetCorr and it tells me that
Data sets of -inset' and in_rois’ have different numbers of voxels per brik!
I guess the reason is that I didn’t map the FreeSurfer-created ROIs into the space of the fMRI.

Could you please give me some hints? Thank you very much

  • Tracy
5

Hi Tracy,

Exactly what have you done to process the data so far?
Initially, there is FreeSurfer anatomical space, say, and
original subject anat/EPI spaces.

  1. Is the SurfVol from FreeSurfer in the exact same location
    as the subject anat applied in the FMRI analysis?

  2. What exact steps were taken in the FMRI analysis so far?
    Was it done with afni_proc.py?

  • rick
6

Hi Rick,

Thanks for your reply!

For now, I have preprocessed the resting state fMRI data using afni_proc.py. SurfVol works well.
And now I want to use the FreeSurfer-created atlas to get the time series signals and generate correlation matrix in AFNI.

Since I have tried 3dNetCorr directly and get error before. I guess I should do the following steps:

  1. create a mask using FreeSurfer atlas with 3dcal since the atlas has labels in it. (But do I need to use 3dmaskave? I’m not sure)
  2. resample the mask into the fMRI data space using 3dresample
  3. get the matrix using 3dNetCorr

Are these steps correct? Thank you.

-Tracy