Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
________________________________
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin....@mssm.edu<mailto:benjamin....@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg04403.html&d=DwMF-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4&m=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54&s=XOJJuzw82VOhaCYWwXk5uBoLsl8E7AyfiW_3Uz35EJo&e=>.
Since my ROIs are fairly small, I'd like to calculate the correlation between
the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging
within the ROI) and the subject's smoothed cifti data. However, the wb_command
-cifti-average-roi-correlation function only generates correlations from an ROI
within the same cifti file, and none of the other functions seem appropriate
(possibly -cifti-cross-correlation where one input is a cifti containing a
single row with the mean unsmoothed timeseries, but I couldn't get this to
work). Is there a straightforward way to generate these correlations using
workbench, or will I need to e.g. write a matlab script? My ROIs are
subcortical (voxel-based), if that matters.
Thank you!
-Ely
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