Thank you for the quick reply Tim!
I was wondering if I could simplify things by applying the fsl command "fslmeants" to the output from the first step, on the "output_left_amygdala.nii.gz" file? That should get me the mean of all the voxels included in that file right? If that file contains only the voxels of the left amygdala, then I figure that would get me the averaged time series. If that is not possible, I am unclear where the file in the second step, "tfMRI_EMOTION_LR_Atlas.dtseries.nii roi_left_amygdala.dscalar.nii", comes from. Thanks for the help - Jason ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Monday, August 31, 2015 6:45 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file -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 <jxn...@miami.edu<mailto:jxn...@miami.edu>> 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/hcp-users@humanconnectome.org/msg01184.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg01184.html&d=BQMFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=ZJUDSwWP05vEvMBUQZ8FbQ&m=BmKcM4Yzl6xcnzSTeNcIEuHvRFAqTKTTeOiGiMbb7UQ&s=rMIzyQLLAXu4Qo1sXKKB9Rx2BEZhsmIRPFso5N-9d_0&e=> > , 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 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=BQMFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=ZJUDSwWP05vEvMBUQZ8FbQ&m=BmKcM4Yzl6xcnzSTeNcIEuHvRFAqTKTTeOiGiMbb7UQ&s=eIqQcGiHAP8KDaMKQ5LBktP1HatoITSdGPtrXN1YFqs&e=> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
