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

_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMF-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4&m=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54&s=VlpGPeejrRi73VM-uLx85SXITabqd6-wTiQRi2j3Dc4&e=>

________________________________
The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Reply via email to