That file contains all the voxels of the structure, plus zero voxels out to the bounding box of the structure, so you probably also need the ROI volume to get it to do the right thing. I'm not all that familiar with fsl tools.
The tfMRI_EMOTION_LR_Atlas.dtseries.nii file is the same as the input in the first step. The roi_left_amygdala.dscalar.nii file is written out by the second step, for use in the third step. Tim On Mon, Aug 31, 2015 at 7:07 PM, Nomi, Jason <[email protected]> wrote: > 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 <[email protected]> > *Sent:* Monday, August 31, 2015 6:45 PM > *To:* Nomi, Jason > *Cc:* [email protected] > *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 <[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 >> <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 >> [email protected] >> 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
