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  • DIY fix for zeroes near medial wall in rfMRI dtseries data
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A DIY fix of rfMRI time series data with empty vertices (timeseries = 0s) very near the medial wall is available using the command "-cifti-dilate" in wb_command. wb_command is a suite of command line utilities distributed as part of Connectome Workbench, our HCP visualization and analysis platform. The current distribution of Connectome Workbench is available for download at: http://humanconnectome.org/connectome/get-connectome-workbench.html .

Once you have Workbench installed, to get help/syntax for running this command, open a terminal window and type: 

wb_command -cifti-dilate 

 

Use the following settings to fully cover the missing vertices around the medial wall:

<direction> : COLUMN

<surface-distance> : 4

<volume-distance> : 4

 

Assuming you are in the directory with the affected .dtseries.nii file in it,  run the command using the syntax:  

wb_command -cifti-dilate <cifti-in> <direction> <surface-distance> <volume-distance> <cifti-out> -nearest

Example:

wb_command -cifti-dilate rfMRI_REST2_LR_Atlas.dtseries.nii COLUMN 4 4 rfMRI_REST2_LR_Atlas_FIXED.dtseries.nii -nearest

 

 

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