:orphan: .. _ahelp_adjunct_suma_fs_qc.tcsh: *********************** adjunct_suma_fs_qc.tcsh *********************** .. contents:: :local: | OVERVIEW ======== .. code-block:: none In brief, this script is for quickly making some QC images for the SUMA/ directory created by @SUMA_Make_Spec_FS after running FreeSurfer's recon-all. Phew, we made it. 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 -no_clean :(opt) do not remove temporary working subdirectory (def: remove it) -help :(opt) show help -hview :(opt) show help in text editor -ver :(opt) show version OUTPUT ====== .. code-block:: none This script makes three *.jpg files in the specified SUMA/ directory. The underlay in each is the *SurfVol.nii* dset. Each JPG is row of axial, sagittal and coronal montages around the volumes defined by the brainmask.nii*: qc_00*.jpg : the overlay is the brainmask.nii* volume in red, and the subset of that volume that was parcellated by FS (in either the "2000" or "2009" atlases) is outlined in black. The idea for this formatting is that we do want to see the official FS brainmask, but we might also want to note its differences with the the binarized aparc+aseg file. We might prefer using one or the other dsets as a mask for other work. qc_01*.jpg : the overlay is a set of tissues, like a segmentation map of 4 classes: GM, WM, ventricles, and then CSF+other+unknown (from the *REN* files made by AFNI/SUMA). qc_02*.jpg : the overlay is the "2000" atlas parcellation (from the file: aparc+aseg*REN*all*) EXAMPLE ======= .. code-block:: none adjunct_suma_fs_qc.tcsh \ -sid sub-001 \ -suma_dir group/sub-001/SUMA