-cifti-separate can't do any averaging, that isn't its purpose. Instead, you can use -cifti-stats and the roi of the amygdala to do such an average:
#what you already did, for the purpose of getting the ROI wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz -crop #turn the ROI into cifti wb_command -cifti-create-dense-from-template tfMRI_EMOTION_LR_Atlas.dtseries.nii roi_left_amygdala.dscalar.nii -volume AMYGDALA_LEFT roi_left_amygdala.nii.gz -from-cropped #stats prints a number per column to standard output wb_command -cifti-stats tfMRI_EMOTION_LR_Atlas.dtseries.nii -reduce MEAN -roi roi_left_amygdala.dscalar.nii If you were using a surface structure, you should use -cifti-weighted-stats instead as the last step with -spatial-weights to account for differences in vertex area. Tim On Mon, Aug 31, 2015 at 1:33 PM, Nomi, Jason <[email protected]> wrote: > Dear Experts, > > > I am trying to acquire the averaged volume time series for subcortical > structures in text file form. > > > From this post > http://www.mail-archive.com/[email protected]/msg01184.html , > I assume that doing these commands : > > > wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN > -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi > roi_left_amygdala.nii.gz -crop > > > gives me a nifti file with *all* the voxels from the left amygdala > (output_left_amygdala.nii.gz). > > > Is there a way to get the *averaged* time series for all left amygdala > voxels into a nifti file using the -cifti-separate command? > > > If so, I suppose that I could then use the -nifti-information command to > extract the time series from that averaged nifti file into a text file. > > > Or, is there another way that I should do this? > > > Thanks in advance! > > > Jason > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
