:orphan: .. _ahelp_@SUMA_Make_Spec_FS: ****************** @SUMA_Make_Spec_FS ****************** .. contents:: :local: | ++ Running @SUMA_Make_Spec_FS version: 2.2.4 OVERVIEW ======== .. code-block:: none @SUMA_Make_Spec_FS - prepare for surface viewing in SUMA This script goes through the following steps: + verify existence of necessary programs (afni, to3d, suma, mris_convert) + determine the location of surface and COR files + creation of ascii surface files via 'mris_convert' + creation of left and right hemisphere SUMA spec files + creation of an AFNI dataset from the COR files via 'to3d' + creation of AFNI datasets from various .mgz volumes created by FreeSurfer. The segmentation volumes with aseg in the name are best viewed in AFNI with the FreeSurfer_Seg_255 colormap. See bottom of @SUMA_FSvolToBRIK -help for more info. + renumbered data sets output, to replace old '*rank*' file data sets. Also new tissue maps based on FS functions and labels. Collectively, these are the '*REN*' dsets in the output directory. (Rank dsets are no longer output by default, from Nov, 2019; instead, use -make_rank_dsets if really needed.) + convenience dsets for afni_proc.py processing with tissue-based regressors (fs_ap_* files: subset of ventricle and WM maps) + all created files are stored in a new SUMA directory USAGE ===== .. code-block:: none @SUMA_Make_Spec_FS [options] -sid SUBJECT_ID examples ('-NIFTI' is really useful-- see below!): @SUMA_Make_Spec_FS -help @SUMA_Make_Spec_FS -NIFTI -sid subject1 @SUMA_Make_Spec_FS -NIFTI -fspath subject1/surface_stuff -sid subject1 @SUMA_Make_Spec_FS -NIFTI -sid 3.14159265 -debug 1 OPTIONS ======= .. code-block:: none -help : show this help information -debug LEVEL : print debug information along the way e.g. -debug 1 the default level is 0, max is 2 A debug level of 2 will "set echo", so one can follow the actual commands executed in the script. -fs_setup : source $FREESURFER_HOME/SetUpFreeSurfer.csh This might be useful on OS X, as FreeSurfer uses DYLD_LIBRARY_PATH, which does not propagate to child shells. Then this program would require them to source SetUpFreeSurfer.csh from .cshrc, which might happen too often and could be irrirating. With -fs_setup, that will happen from within this script, so it is not necessary to do from the .cshrc file. -fspath PATH : path to 'surf' and 'orig' directories e.g. -fspath subject1/surface_info the default PATH value is './', the current directory This is generally the location of the 'surf' directory, though having PATH end in surf is OK. The mri/orig directory should also be located here. Note: when this option is provided, all file/path messages will be with respect to this directory. -extra_annot_labels L1 L2 ... : convert extra annot files into ROI dsets e.g. -extra_annot_labels aparc FS typically outputs annotation files: lh.aparc.a2005s.annot rh.aparc.a2005s.annot lh.aparc.a2009s.annot rh.aparc.a2009s.annot from each of which Make_Spec extracts a colormap, ROI and a displayable surface dataset. Use this option to specify other labels to extract. If LABEL is specified, then expected annotation files will be: lh.LABEL.annot rh.LABEL.annot -extra_fs_dsets AA BB CC ... : FS calculates many types of data on the surface, listed in their surf/ output directory. By default, this program brings the following ones into the SUMA surface realm: thickness curv sulc which get turned into 'std.141.{l,r}h.curv.niml.dset' and '{l,r}h.curv.gii.dset' files, for example. This option allows the user to list *other* dsets to include, as well. Ones that users have selected are, for example: volume area area.pial curv.pial -make_rank_dsets : before Nov 14, 2019, *rank* dsets used to be created by this command by default; these dsets mapped the FreeSurfer ROI numbering to a 1..N set of labels, where N was the number of ROIs. Because this number might *not* be constant across a group (though, the ROI string labels in each would be), we don't recommend using these; the *REN* dsets are renumbered in a consistent, mapped way, and so those are more useful. The present option is purely for backward compatability, for Zome Special Scientists out there who might still use these dsets. -use_mgz : use MGZ volumes even if COR volumes are there -neuro : use neurological orientation e.g. -neuro the default is radiological orientation In the default radiological orientation, the subject's right is on the left side of the image. In the neurological orientation, left is really left. * This is not compatible with -NIFTI. -nocor: This option is no longer supported because it created GIFTI surfaces with coordinates in RAI, rather than LPI which is the GIFTI standard. While using RAI surfaces within AFNI/SUMA is not problematic, the resultant GIFTI surfaces do not port well to other software. The replacement option for -nocor is -GNIFTI but the surfaces will have negated coordinates along the x and y compared to those with -nocor. GIFTI surfaces produced with SUMA programs compiled before August 1st 2013 will have their X and Y coordinates negated and will no longer line up with the anatomy. Correcting such surfaces can be done with ConvertSurface with the following command: ConvertSurface \ -i lh.smoothwm.gii \ -o_gii lh.smoothwm \ -overwrite \ -xmat_1D NegXY or for an entire SUMA directory: cd SUMA tcsh foreach ss (*.gii) ConvertSurface \ -i $ss \ -o_gii $ss \ -overwrite \ -xmat_1D NegXY end -GNIFTI/-GIFTI/-IFTI: same as -NIFTI -NIFTI :Produce files in exchangeable formats. With this option :COR volumes are no longer used and output volumes :and surfaces are in alignment with the original :volume used to create the surface. All volumes are written out NIFTI format, and all surfaces are in GIFTI format. This option is incompatible with -neuro or -use_mgz ** Note: from 22 Feb 2013 through 20 Mar 2017, use of -NIFTI would distort standard mesh surfaces. To evaluate effects of this, consider: MapIcosahedron -write_dist. * If you are seeing this message, that problem was fixed years ago. -inflate INF: Create modereately inflated surfaces using SurfSmooth. INF controls the amount of smoothness in the final image. It is the number of iterations in the command such as: SurfSmooth \ -i lh.white.asc \ -met NN_geom \ -Niter 200 \ -o_gii \ -surf_out lh.inf_200 \ -match_vol 0.01 You can use multiple instances of -inflate to create inflations of various levels. -set_space SPACE: Set the space flag of all volumes to SPACE (orig, MNI, TLRC, MNIa). The default is orig space. You should only use this option when the volume you passed to FreeSurfer was not in 'orig' space. Use '3dinfo -space YOUR_DATASET' to find the space of a certain dataset. -sid SUBJECT_ID : required subject ID for file naming -ld LD : Create standard mesh surfaces with mesh density linear depth (see MapIcosahedron -help, option -ld) set to LD. You can use multiple -ld options. By default the script will run ld values of 141 and 60. -ldpref LDpref: Supply what ends up being the -prefix option for MapIcosahedron. By default it is std.LD. You need as many -ldpref as you have -ld -no_ld: Do not run MapIcosahedron. NOTES ===== .. code-block:: none Making use of FreeSurfer's -contrasurfreg output with MapIcosahedron: This script will create SUMA versions of lh.rh.sphere.reg and rh.lh.sphere.reg but in this current state, MapIcosahedron does not attempt to use them for backward compatibility. Should you want to create standard mesh surfaces with node index correspondence across the hemispheres you will need to run MapIcosahedron manually in the output SUMA/ directory. For example: MapIcosahedron \ -spec SUBJ_rh.spec -ld 60 \ -dset_map rh.thickness.gii.dset \ -dset_map rh.curv.gii.dset \ -dset_map rh.sulc.gii.dset \ -morph rh.lh.sphere.reg.gii \ -prefix std.60.lhreg. This command is very similar to the one use to create the default output spec file std.60.SUBJ_rh.spec (look at the top of the spec file for a record of the command that created it), except for the last two options -morph and -prefix. By using -morph rh.lh.sphere.reg.gii the resultant standard-mesh right hemispheres (std.60.lhreg.rh.*.gii) will have node index correspondence with std.60.lh.*.gii surfaces. To verify visually the correspondence, run the following: count -column 0 36001 > std.60.lh.rh.nodeindex.1D.dset suma -noniml -spec std.60.SUBJ_lh.spec & suma -noniml -spec std.60.SUBJ_rh.spec & suma -noniml -spec std.60.lhreg.SUBJ_rh.spec & Then load std.60.lh.rh.nodeindex.1D.dset into each of the three SUMA windows. Note how the color pattern (node indices) matches between SUBJ_lh and lhreg.SUBJ_rh surfaces, but NOT between SUBJ_lh and SUBJ_rh surfaces. COMMENTS ======== .. code-block:: none 0. More help may be found at: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/SUMA/main_toc.html 1. Surface file names should look like 'lh.smoothwm'. 2. Patches of surfaces need the word patch in their name, in order to use the correct option for 'mris_convert'. 3. Flat surfaces must have .flat in their name. 4. You can tailor the script to your needs. Just make sure you rename it or risk having your modifications overwritten with the next SUMA version you install. Authors to pester: R. Reynolds (reynoldr@mail.nih.gov) Z. Saad (saadz@mail.nih.gov) M. Beauchamp (michael.beauchamp@bcm.edu)