:orphan: .. _ahelp_adjunct_suma_fs_mask_and_qc: *************************** adjunct_suma_fs_mask_and_qc *************************** .. 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 OUTPUTS ======= .. code-block:: none 1) This script creates one new dset in the SUMA/ directory, called fs_parc_wb_mask.nii.gz. This dset is a whole brain mask based on the FS parcellation. Note that this is *different* than the brainmask.nii* dset that FS creates. This mask is created in the following way: + binarize aparc+aseg_REN_all.nii.* + inflate by 2 voxels (3dmask_tool) + infill holes (3dmask_tool) + erode by 2 voxels (3dmask_tool) The final mask seems much more specific to the brain structure than brainmask.nii*. It also removes several small gaps and holes in the parcellation dset. In general, it seems like quite a useful whole brain mask. 2) This script also 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 the fs_parc_wb_mask.nii.gz dset that this script has created (see details just above). qc_02*.jpg : the overlay is a set of tissues, like a segmentation map of 4 classes: red - GM - red blue - WM green - ventricles violet - CSF+other+unknown (from the *REN* files made by AFNI/SUMA). qc_03*.jpg : the GM only qc_04*.jpg : the WM only qc_05*.jpg : the overlay is the "2000" atlas parcellation (from the file: aparc+aseg*REN*all*) EXAMPLE ======= .. code-block:: none adjunct_suma_fs_mask_and_qc \ -sid sub-001 \ -suma_dir group/sub-001/SUMA