00001 /*****************************************************************************
00002    Major portions of this software are copyrighted by the Medical College
00003    of Wisconsin, 1994-2000, and are released under the Gnu General Public
00004    License, Version 2.  See the file README.Copyright for details.
00005 ******************************************************************************/
00006 
00007 #include "mrilib.h"
00008 
00009 static char * helpstring =
00010     "EDITING OPTIONS APPLIED TO EACH INPUT DATASET:\n"
00011     "  -1thtoin         = Copy threshold data over intensity data.\n"
00012     "                       This is only valid for datasets with some\n"
00013     "                       thresholding statistic attached.  All\n"
00014     "                       subsequent operations apply to this\n"
00015     "                       substituted data.\n"
00016     "  -2thtoin         = The same as -1thtoin, but do NOT scale the\n"
00017     "                       threshold values from shorts to floats when\n"
00018     "                       processing.  This option is only provided\n"
00019     "                       for compatibility with the earlier versions\n"
00020     "                       of the AFNI package '3d*' programs.\n"
00021     "  -1noneg          = Zero out voxels with negative intensities\n"
00022     "  -1abs            = Take absolute values of intensities\n"
00023     "  -1clip val       = Clip intensities in range (-val,val) to zero\n"
00024     "  -2clip v1 v2     = Clip intensities in range (v1,v2) to zero\n"
00025     "  -1uclip val      = These options are like the above, but do not apply\n"
00026     "  -2uclip v1 v2        any automatic scaling factor that may be attached\n"
00027     "                       to the data.  These are for use only in special\n"
00028     "                       circumstances.  (The 'u' means 'unscaled'.  Program\n"
00029     "                       '3dinfo' can be used to find the scaling factors.)\n"
00030     "               N.B.: Only one of these 'clip' options can be used; you cannot\n"
00031     "                       combine them to have multiple clipping executed.\n"
00032     "  -1thresh thr     = Use the threshold data to censor the intensities\n"
00033     "                       (only valid for 'fith', 'fico', or 'fitt' datasets).\n"
00034     "               N.B.: The value 'thr' is floating point, in the range\n"
00035     "                           0.0 < thr < 1.0  for 'fith' and 'fico' datasets,\n"
00036     "                       and 0.0 < thr < 32.7 for 'fitt' datasets.\n"
00037     "  -1blur_sigma bmm = Gaussian blur with sigma = bmm (in mm)\n"
00038     "  -1blur_rms bmm   = Gaussian blur with rms deviation = bmm\n"
00039     "  -1blur_fwhm bmm  = Gaussian blur with FWHM = bmm\n"
00040     "  -t1blur_sigma bmm= Gaussian blur of threshold with sigma = bmm(in mm)\n"
00041     "  -t1blur_rms bmm  = Gaussian blur of threshold with rms deviation = bmm\n"
00042     "  -t1blur_fwhm bmm = Gaussian blur of threshold with FWHM = bmm\n"
00043     "  -1zvol x1 x2 y1 y2 z1 z2\n"
00044     "                   = Zero out entries inside the 3D volume defined\n"
00045     "                       by x1 <= x <= x2, y1 <= y <= y2, z1 <= z <= z2 ;\n"
00046     "               N.B.: The ranges of x,y,z in a dataset can be found\n"
00047     "                       using the '3dinfo' program. Dimensions are in mm.\n"
00048     "               N.B.: This option may not work correctly at this time, but\n"
00049     "                       I've not figured out why!\n"
00050     "\n"
00051     " CLUSTERING\n"
00052     "  -dxyz=1  = In the cluster editing options, the spatial clusters\n"
00053     "             are defined by connectivity in true 3D distance, using\n"
00054     "             the voxel dimensions recorded in the dataset header.\n"
00055     "             This option forces the cluster editing to behave as if\n"
00056     "             all 3 voxel dimensions were set to 1 mm.  In this case,\n"
00057     "             'rmm' is then the max number of grid cells apart voxels\n"
00058     "             can be to be considered directly connected, and 'vmul'\n"
00059     "             is the min number of voxels to keep in the cluster.\n"
00060     "       N.B.: The '=1' is part of the option string, and can't be\n"
00061     "             replaced by some other value.  If you MUST have some\n"
00062     "             other value for voxel dimensions, use program 3drefit.\n"
00063     " \n"
00064     "  The following cluster options are mutually exclusive: \n"
00065     "  -1clust rmm vmul = Form clusters with connection distance rmm\n"
00066     "                       and clip off data not in clusters of\n"
00067     "                       volume at least vmul microliters\n"
00068     "  -1clust_mean rmm vmul = Same as -1clust, but all voxel intensities \n"
00069     "                            within a cluster are replaced by the average\n"
00070     "                            intensity of the cluster. \n"
00071     "  -1clust_max rmm vmul  = Same as -1clust, but all voxel intensities \n"
00072     "                            within a cluster are replaced by the maximum\n"
00073     "                            intensity of the cluster. \n"
00074     "  -1clust_amax rmm vmul = Same as -1clust, but all voxel intensities \n"
00075     "                            within a cluster are replaced by the maximum\n"
00076     "                            absolute intensity of the cluster. \n"
00077     "  -1clust_smax rmm vmul = Same as -1clust, but all voxel intensities \n"
00078     "                            within a cluster are replaced by the maximum\n"
00079     "                            signed intensity of the cluster. \n"
00080     "  -1clust_size rmm vmul = Same as -1clust, but all voxel intensities \n"
00081     "                            within a cluster are replaced by the size \n"
00082     "                            of the cluster (in multiples of vmul).   \n"
00083     "  -1clust_order rmm vmul= Same as -1clust, but all voxel intensities \n"
00084     "                            within a cluster are replaced by the cluster\n"
00085     "                            size index (largest cluster=1, next=2, ...).\n"
00086     " * If rmm is given as 0, this means to use the 6 nearest neighbors to\n"
00087     "     form clusters of nonzero voxels.\n"
00088     " * If vmul is given as zero, then all cluster sizes will be accepted\n"
00089     "     (probably not very useful!).\n"
00090     " * If vmul is given as negative, then abs(vmul) is the minimum number\n"
00091     "     of voxels to keep.\n"
00092     " \n"
00093     "  The following commands produce erosion and dilation of 3D clusters.  \n"
00094     "  These commands assume that one of the -1clust commands has been used.\n"
00095     "  The purpose is to avoid forming strange clusters with 2 (or more)    \n"
00096     "  main bodies connected by thin 'necks'.  Erosion can cut off the neck.\n"
00097     "  Dilation will minimize erosion of the main bodies.                   \n"
00098     "  Note:  Manipulation of values inside a cluster (-1clust commands)    \n"
00099     "         occurs AFTER the following two commands have been executed.   \n"
00100     "  -1erode pv    For each voxel, set the intensity to zero unless pv %  \n"
00101     "                of the voxels within radius rmm are nonzero.           \n"
00102     "  -1dilate      Restore voxels that were removed by the previous       \n"
00103     "                command if there remains a nonzero voxel within rmm.   \n"
00104     " \n"
00105     "  The following filter options are mutually exclusive: \n"
00106     "  -1filter_mean rmm   = Set each voxel to the average intensity of the \n"
00107     "                          voxels within a radius of rmm. \n"
00108     "  -1filter_nzmean rmm = Set each voxel to the average intensity of the \n"
00109     "                          non-zero voxels within a radius of rmm. \n"
00110     "  -1filter_max rmm    = Set each voxel to the maximum intensity of the \n"
00111     "                          voxels within a radius of rmm. \n"
00112     "  -1filter_amax rmm   = Set each voxel to the maximum absolute intensity\n"
00113     "                          of the voxels within a radius of rmm. \n"
00114     "  -1filter_smax rmm   = Set each voxel to the maximum signed intensity \n"
00115     "                          of the voxels within a radius of rmm. \n"
00116     "  -1filter_aver rmm   = Same idea as '_mean', but implemented using a\n"
00117     "                          new code that should be faster.\n"
00118     " \n"
00119     "  The following threshold filter options are mutually exclusive: \n"
00120     "  -t1filter_mean rmm   = Set each correlation or threshold voxel to the \n"
00121     "                          average of the voxels within a radius of rmm. \n"
00122     "  -t1filter_nzmean rmm = Set each correlation or threshold voxel to the \n"
00123     "                          average of the non-zero voxels within \n"
00124     "                          a radius of rmm. \n"
00125     "  -t1filter_max rmm    = Set each correlation or threshold voxel to the \n"
00126     "                          maximum of the voxels within a radius of rmm. \n"
00127     "  -t1filter_amax rmm   = Set each correlation or threshold voxel to the \n"
00128     "                          maximum absolute intensity of the voxels \n"
00129     "                          within a radius of rmm. \n"
00130     "  -t1filter_smax rmm   = Set each correlation or threshold voxel to the \n"
00131     "                          maximum signed intensity of the voxels \n"
00132     "                          within a radius of rmm. \n"
00133     "  -t1filter_aver rmm   = Same idea as '_mean', but implemented using a\n"
00134     "                          new code that should be faster.\n"
00135     " \n"
00136 #ifdef ALLOW_SCALE_TO_MAX
00137     "  -1scale          = Linearly scale intensities so that max is 10000\n"
00138 #endif
00139     "  -1mult factor    = Multiply intensities by the given factor\n"
00140     "  -1zscore         = If the sub-brick is labeled as a statistic from\n"
00141     "                     a known distribution, it will be converted to\n"
00142     "                     an equivalent N(0,1) deviate (or 'z score').\n"
00143     "                     If the sub-brick is not so labeled, nothing will\n"
00144     "                     be done.\n"
00145     "\n"
00146     "The above '-1' options are carried out in the order given above,\n"
00147     "regardless of the order in which they are entered on the command line.\n"
00148     "\n"
00149     "N.B.: The 3 '-1blur' options just provide different ways of\n"
00150     "      specifying the radius used for the blurring function.\n"
00151     "      The relationships among these specifications are\n"
00152     "         sigma = 0.57735027 * rms = 0.42466090 * fwhm\n"
00153     "      The requisite convolutions are done using FFTs; this is by\n"
00154     "      far the slowest operation among the editing options.\n"
00155 ;
00156 
00157 char * EDIT_options_help(void)
00158 {
00159    return helpstring ;
00160 }