/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
#include "mrilib.h"
static char * helpstring =
"EDITING OPTIONS APPLIED TO EACH INPUT DATASET:\n"
" -1thtoin = Copy threshold data over intensity data.\n"
" This is only valid for datasets with some\n"
" thresholding statistic attached. All\n"
" subsequent operations apply to this\n"
" substituted data.\n"
" -2thtoin = The same as -1thtoin, but do NOT scale the\n"
" threshold values from shorts to floats when\n"
" processing. This option is only provided\n"
" for compatibility with the earlier versions\n"
" of the AFNI package '3d*' programs.\n"
" -1noneg = Zero out voxels with negative intensities\n"
" -1abs = Take absolute values of intensities\n"
" -1clip val = Clip intensities in range (-val,val) to zero\n"
" -2clip v1 v2 = Clip intensities in range (v1,v2) to zero\n"
" -1uclip val = These options are like the above, but do not apply\n"
" -2uclip v1 v2 any automatic scaling factor that may be attached\n"
" to the data. These are for use only in special\n"
" circumstances. (The 'u' means 'unscaled'. Program\n"
" '3dinfo' can be used to find the scaling factors.)\n"
" N.B.: Only one of these 'clip' options can be used; you cannot\n"
" combine them to have multiple clipping executed.\n"
" -1thresh thr = Use the threshold data to censor the intensities\n"
" (only valid for 'fith', 'fico', or 'fitt' datasets).\n"
" N.B.: The value 'thr' is floating point, in the range\n"
" 0.0 < thr < 1.0 for 'fith' and 'fico' datasets,\n"
" and 0.0 < thr < 32.7 for 'fitt' datasets.\n"
" -1blur_sigma bmm = Gaussian blur with sigma = bmm (in mm)\n"
" -1blur_rms bmm = Gaussian blur with rms deviation = bmm\n"
" -1blur_fwhm bmm = Gaussian blur with FWHM = bmm\n"
" -t1blur_sigma bmm= Gaussian blur of threshold with sigma = bmm(in mm)\n"
" -t1blur_rms bmm = Gaussian blur of threshold with rms deviation = bmm\n"
" -t1blur_fwhm bmm = Gaussian blur of threshold with FWHM = bmm\n"
" -1zvol x1 x2 y1 y2 z1 z2\n"
" = Zero out entries inside the 3D volume defined\n"
" by x1 <= x <= x2, y1 <= y <= y2, z1 <= z <= z2 ;\n"
" N.B.: The ranges of x,y,z in a dataset can be found\n"
" using the '3dinfo' program. Dimensions are in mm.\n"
" N.B.: This option may not work correctly at this time, but\n"
" I've not figured out why!\n"
"\n"
" CLUSTERING\n"
" -dxyz=1 = In the cluster editing options, the spatial clusters\n"
" are defined by connectivity in true 3D distance, using\n"
" the voxel dimensions recorded in the dataset header.\n"
" This option forces the cluster editing to behave as if\n"
" all 3 voxel dimensions were set to 1 mm. In this case,\n"
" 'rmm' is then the max number of grid cells apart voxels\n"
" can be to be considered directly connected, and 'vmul'\n"
" is the min number of voxels to keep in the cluster.\n"
" N.B.: The '=1' is part of the option string, and can't be\n"
" replaced by some other value. If you MUST have some\n"
" other value for voxel dimensions, use program 3drefit.\n"
" \n"
" The following cluster options are mutually exclusive: \n"
" -1clust rmm vmul = Form clusters with connection distance rmm\n"
" and clip off data not in clusters of\n"
" volume at least vmul microliters\n"
" -1clust_mean rmm vmul = Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the average\n"
" intensity of the cluster. \n"
" -1clust_max rmm vmul = Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the maximum\n"
" intensity of the cluster. \n"
" -1clust_amax rmm vmul = Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the maximum\n"
" absolute intensity of the cluster. \n"
" -1clust_smax rmm vmul = Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the maximum\n"
" signed intensity of the cluster. \n"
" -1clust_size rmm vmul = Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the size \n"
" of the cluster (in multiples of vmul). \n"
" -1clust_order rmm vmul= Same as -1clust, but all voxel intensities \n"
" within a cluster are replaced by the cluster\n"
" size index (largest cluster=1, next=2, ...).\n"
" * If rmm is given as 0, this means to use the 6 nearest neighbors to\n"
" form clusters of nonzero voxels.\n"
" * If vmul is given as zero, then all cluster sizes will be accepted\n"
" (probably not very useful!).\n"
" * If vmul is given as negative, then abs(vmul) is the minimum number\n"
" of voxels to keep.\n"
" \n"
" The following commands produce erosion and dilation of 3D clusters. \n"
" These commands assume that one of the -1clust commands has been used.\n"
" The purpose is to avoid forming strange clusters with 2 (or more) \n"
" main bodies connected by thin 'necks'. Erosion can cut off the neck.\n"
" Dilation will minimize erosion of the main bodies. \n"
" Note: Manipulation of values inside a cluster (-1clust commands) \n"
" occurs AFTER the following two commands have been executed. \n"
" -1erode pv For each voxel, set the intensity to zero unless pv % \n"
" of the voxels within radius rmm are nonzero. \n"
" -1dilate Restore voxels that were removed by the previous \n"
" command if there remains a nonzero voxel within rmm. \n"
" \n"
" The following filter options are mutually exclusive: \n"
" -1filter_mean rmm = Set each voxel to the average intensity of the \n"
" voxels within a radius of rmm. \n"
" -1filter_nzmean rmm = Set each voxel to the average intensity of the \n"
" non-zero voxels within a radius of rmm. \n"
" -1filter_max rmm = Set each voxel to the maximum intensity of the \n"
" voxels within a radius of rmm. \n"
" -1filter_amax rmm = Set each voxel to the maximum absolute intensity\n"
" of the voxels within a radius of rmm. \n"
" -1filter_smax rmm = Set each voxel to the maximum signed intensity \n"
" of the voxels within a radius of rmm. \n"
" -1filter_aver rmm = Same idea as '_mean', but implemented using a\n"
" new code that should be faster.\n"
" \n"
" The following threshold filter options are mutually exclusive: \n"
" -t1filter_mean rmm = Set each correlation or threshold voxel to the \n"
" average of the voxels within a radius of rmm. \n"
" -t1filter_nzmean rmm = Set each correlation or threshold voxel to the \n"
" average of the non-zero voxels within \n"
" a radius of rmm. \n"
" -t1filter_max rmm = Set each correlation or threshold voxel to the \n"
" maximum of the voxels within a radius of rmm. \n"
" -t1filter_amax rmm = Set each correlation or threshold voxel to the \n"
" maximum absolute intensity of the voxels \n"
" within a radius of rmm. \n"
" -t1filter_smax rmm = Set each correlation or threshold voxel to the \n"
" maximum signed intensity of the voxels \n"
" within a radius of rmm. \n"
" -t1filter_aver rmm = Same idea as '_mean', but implemented using a\n"
" new code that should be faster.\n"
" \n"
#ifdef ALLOW_SCALE_TO_MAX
" -1scale = Linearly scale intensities so that max is 10000\n"
#endif
" -1mult factor = Multiply intensities by the given factor\n"
" -1zscore = If the sub-brick is labeled as a statistic from\n"
" a known distribution, it will be converted to\n"
" an equivalent N(0,1) deviate (or 'z score').\n"
" If the sub-brick is not so labeled, nothing will\n"
" be done.\n"
"\n"
"The above '-1' options are carried out in the order given above,\n"
"regardless of the order in which they are entered on the command line.\n"
"\n"
"N.B.: The 3 '-1blur' options just provide different ways of\n"
" specifying the radius used for the blurring function.\n"
" The relationships among these specifications are\n"
" sigma = 0.57735027 * rms = 0.42466090 * fwhm\n"
" The requisite convolutions are done using FFTs; this is by\n"
" far the slowest operation among the editing options.\n"
;
char * EDIT_options_help(void)
{
return helpstring ;
}