The original cifti file has an internal ROI of where it has data, which excludes the medial wall. Use the -roi suboption of the -metric option to recover this ROI. As Matt suggests, you can do smoothing on the original cifti file, which will use that ROI internally. You can also smooth it while it is a metric file, providing that recovered ROI - the metric files will have zeros in the medial wall, which is normal and intentional. You will want to also specify that ROI to -cifti-create-* commands to avoid including the zeros.
Tim On Fri, Oct 10, 2014 at 9:32 AM, Glasser, Matthew <[email protected]> wrote: > What is it that you are trying to do? I’m not sure why the > -cifti-separate and -cifti-create-dense-timeseries commands are in there, > but you won’t have zeros if you simply run -cifti-smoothing on the cleaned > dense timeseries. > > Peace, > > Matt. > > From: Long <[email protected]> > Date: Friday, October 10, 2014 at 4:30 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Zeros found in the surface space resting-state fMRI > data. > > Dear all, > > I'm using workbench to extract resting-state fMRI data and smoothing, > the data is from HCP_S500, the version of workbench is v1.0: > > 1) wb_command -cifti-separate > rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii \ > COLUMN \ > -metric CORTEX_LEFT \ > rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.left_metric.gii > > 2) wb_command -cifti-create-dense-timeseries \ > rfMRI_REST1_RL_left.dtseries.nii \ > -leftmetric \ > rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.left_metric.gii > > 3) wb_command -cifti-smoothing \ > rfMRI_REST1_RL_left.dtseries.nii \ > 2 2 COLUMN \ > rfMRI_REST1_RL_left_smoothed.dtseries.nii \ > -left-surface 100307.L.very_inflated.32k_fs_LR.surf.gii > > Then I load the data 'rfMRI_REST1_RL_left_smoothed.dtseries.nii' to > Matlab7: > > fid = fopen('rfMRI_REST1_RL_left_smoothed.dtseries.nii', 'r'); > tseries = fread(fid,[32492 32492], 'float32'); > > I found that the tseries has lots of zero value, is it normal? Could you > please check which step is wrong? Thank you for your time. > > Best, > Xiangyu > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
