I am trying to run afni_proc on HCP pipeline output in CIFTI space - specifically creating parcellated timeseries for a particular atlas and converting to a 'fake' nifti format using workbench tools. The resulting input files to afni_proc are #ofROIs x 1 x 1 size .nii files. When afni_proc copies the data in the first step to create pb00 files, 3dTcat is automatically turning this into a .1D file and then afni_proc crashes because the next steps can't find the correct input (i.e. 3dToutcount can't open pb00...+tlrc)
Any thoughts on how to remedy or force 3dTcat to output as .nii?
