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?
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.
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.
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
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:
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)
resample the mask into the fMRI data space using 3dresample
get the matrix using 3dNetCorr
Are these steps correct? Thank you.
-Tracy
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.