Ah that makes sense, thanks! The effect of the z transformation is quite subtle (as expected since the correlation distributions are close to gaussian before transformation). ________________________________ From: Harms, Michael [mha...@wustl.edu] Sent: Thursday, May 04, 2017 10:21 AM To: Ely, Benjamin; Glasser, Matthew; HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
I would probably z transform before averaging across runs, so that you are averaging something with at least an approximately gaussian distribution. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu 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 11:46 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation 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<mailto:glass...@wustl.edu>] Sent: Wednesday, May 03, 2017 11:32 PM To: Ely, Benjamin; HCP-Users@humanconnectome.org<mailto: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. 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