:orphan: .. _ahelp_adjunct_suma_fs_rois.tcsh: ************************* adjunct_suma_fs_rois.tcsh ************************* .. contents:: :local: | OVERVIEW ======== .. code-block:: none In brief, this script is for quickly making some ROI stats (counts) for the SUMA/ directory created by @SUMA_Make_Spec_FS after running FreeSurfer's recon-all. written by PA Taylor. # -------------------------------------------------------------------- USAGE ===== .. code-block:: none This program has the following options: -sid SUBJ_ID :(req) subject ID -suma_dir SUMA_DIR :(req) SUMA/ directory output by AFNI's @SUMA_Make_Spec_FS -help :(opt) show help -hview :(opt) show help in text editor -ver :(opt) show version OUTPUT ====== .. code-block:: none This script makes four *.1D files in the specified SUMA/ directory. Column labels are present in each file. Note that the ROI string labels are provided for each ROI, but behind a comment symbol in each line (so you can use them as regular *.1D files, with 1dcat, 1dtranspose, etc.): stats_fs_rois_2000_FT.1D : voxel counts of the "2000" parcellation (from the file: aparc+aseg_REN_all.nii*) stats_fs_rois_2009_FT.1D : voxel counts of the "2009" parcellation (from the file: aparc+aseg_REN_all.nii*) stats_fs_segs_2000_FT.1D : voxel counts of the "2000" parc brain mask and tissue/segmentations (from the brainmask.nii* and aparc+aseg_REN_* files) stats_fs_segs_2009_FT.1D : voxel counts of the "2009" parc brain mask and tissue/segmentations (from the brainmask.nii* and aparc.a2009s+aseg_REN_* files) EXAMPLE ======= .. code-block:: none adjunct_suma_fs_rois.tcsh \ -sid sub-001 \ -suma_dir group/sub-001/SUMA