tilt(1)                                                                tilt(1)



NAME
       tilt - calculates 3-D tomographic reconstruction from a tilt series

SYNOPSIS
       tilt [options] [input_file] [output_file]

DESCRIPTION
       Tilt is a program for reconstructing a three-dimensional object from a
       series of two-dimensional projections.  The projections are assumed to
       arise from rotation about a fixed tilt axis, subject to minor varia-
       tions from this scheme.

       The program uses a number of different numerical strategies depending
       on the complexity of the alignments needed to reconstruct the volume
       and on whether the computation is being done by the central processing
       unit (CPU) or the graphical processing unit (GPU).  If there are no
       local alignments being applied, then for processing on the CPU, the
       program will do a preliminary stretching of each input line by the
       cosine of the tilt angle.  This stretching speeds up the direct back-
       projection because each stretched input line is in register with the
       lines of the output planes.  The stretching will not be used if the
       maximum tilt angle is over 80 degrees, if the option "COSINTERP 0" is
       entered, or in the unlikely event that there is insufficient memory for
       the stretched data.  When computing on the GPU, the program does not
       use cosine stretching, thus avoiding the consequences of interpolating
       the data twice.

       If there is no X-axis tilt being imposed, then each output plane is
       derived from one line of the input data; i.e., data all at one Y value
       in the input images.  With a fixed tilt around the X axis, each output
       slice derives from several lines of input data.  However, as long as
       there are no "Z-factors", it is still possible to compute a slice prior
       to the tilting from a single line of input.  Thus, the program will
       compute such untilted slices, one per input line, and interpolate an
       output slice from the relevant untilted slices.  If the option "XTILT-
       INTERP 0" is entered, or in the unlikely event that there is insuffi-
       cient memory for this approach, the program reverts to "old-style" X-
       axis tilting, in which the output slice is computed directly from the
       various input slices.

       With output of perpendicular slices, the header of the output file will
       set up a coordinate system congruent with that of the original views.
       This represents a 90 degree rotation about X but no change in handed-
       ness.  With parallel slice output using "PARALLEL", the handedness is
       inverted; whereas parallel slice output with the "RotateBy90" option
       retains the handedness.

       The program can do two different kinds of reprojections.  First, it can
       compute each tomogram slice as usual then, instead of writing the slice
       to the output file, it outputs a reprojection of that slice at selected
       angles.  This reprojection should match what xyzproj would produce
       by reprojecting from the tomogram, but it will not match the input
       images if the reconstruction is computed with a fixed or variable X
       axis tilt, Z factors, or local alignments.  Getting a reprojection that
       matches input images in any of these cases requires multiple slices of
       reconstruction to get one line of reprojection.  Thus, these reprojec-
       tions are obtained by first computing the full reconstruction, then
       providing this file as input to the program on a second run.  On that
       run, the program needs to know about all the parameters used to make
       the reconstruction, as well as about the original projection file.

       The scaling of data by the backprojection is somewhat unpredictable.
       If the radial filter were scaled to go from 0 at zero frequency to 1 at
       0.5 cycle/pixel, then the backprojection would produce numbers that
       correspond approximately to the underlying densities; i.e., their
       reprojection by summation would give numbers comparable to those in the
       input projections.  Unfortunately, the radial filter goes from 0 to NX
       / 2, where NX is the X dimension of the input data.  This means that in
       order to get output that would reproject to give values comparable to
       the input, you would need to: a) not take the log of the data; and b)
       set the scaling factor in the SCALE entry to 2/NX.

       The scaling of data in the reprojection from a tomogram takes the back-
       projection scaling into account.  Specifically, the program first
       undoes the output scaling that was specified by the SCALE entry, then
       it multiplies by 2.2 / NX.  The reprojection is computed by summing
       these unscaled values.  If the log was not being taken in the backpro-
       jection, these sums are then divided by the weighting factors entered
       with WeightFile, if any, and output.  If the log was taken, the sums
       are adjusted by adding an amount that should give a constant mean
       level, then the exponential is taken.

       The program can use the GPU of an NVIDIA graphics card for all kinds of
       reconstructions and reprojections from an existing reconstruction file.
       The card must be capable of supporting computations with CUDA, and you
       must have a version of NVIDIA graphics drivers installed that supports
       the particular version of CUDA against which your version of Tilt was
       compiled.  Typically this will be CUDA 2.1, supported by drivers 180.22
       and higher in Linux, or 181.20 and higher in Windows.  Not all IMOD
       packages can be used with a GPU; ones that do will have cudart and
       cufft libraries in either IMOD/bin, IMOD/lib or IMOD/qtlib.

       The program can compute multiple iterations of the Simultaneous Itera-
       tive Reconstruction Technique (SIRT) internally for the situation where
       a reconstruction slice backprojects from, and reprojects to, a single
       set of lines in the projection images.  This option is thus not avail-
       able when the reconstruction involves the Z factors produced when solv-
       ing for linear stretch in Tiltalign, a variable X-axis tilt produced
       when correcting for beam tilt, or local alignments.  It also requires
       that the reconstruction be the same size as the aligned stack in X and
       Y (i.e., no SLICE or WIDTH entries) and that the tilt axis be in the
       center of the aligned images.  The procedure starts with a slice com-
       puted with no or reduced R-weighting, or read in from prevous itera-
       tions.  The slice is reprojected, the difference is formed between the
       reprojections and the original projections, and this difference is
       backprojected with a weighting that distributes the error in difference
       among the pixels along a projection ray.  The backprojected difference
       is then subtracted from the starting slice, and the procedure is ready
       to be iterated.  The program carries each slice through the full set of
       iterations before writing it out and going on to the next slice.  Fur-
       ther details are given under the SIRTIterations options.

       Backprojection works with angles up to and beyond 90 degrees on both
       the CPU and GPU.  Both reprojection and internal SIRT should work for
       such data sets provided that local alignments are not used.

OPTIONS
       Tilt uses the PIP package for input (see the manual page for pip)
       but it has several special features to maintain compatibility with the
       old input method and old command files.  1) Options are case-insensi-
       tive and can be entered in upper, lower, or mixed case.  2) If the pro-
       gram is started with no command line arguments, it behaves as if -Stan-
       dardInput were given and takes lines from standard input.  3) The first
       two lines taken from standard input can be the input and output file-
       names, without their respective keywords.  This will not work if the
       filenames match a subset of any of the option strings.

       The following options can be specified either as command line arguments
       (with the -) or one per line in a command file or parameter file (with-
       out the -).  Options can be abbreviated to unique letters; the cur-
       rently valid abbreviations for short names are shown in parentheses.


       -input (-inp) OR -InputProjections       File name
              Input image file with aligned projections.  If this option is
              not entered, the first non-option argument is taken as the input
              name.

       -output (-o) OR -OutputFile    File name
              Output file for reconstruction or reprojection.  If this option
              is not entered, the second non-option argument is taken as the
              output name.

       -recfile (-r) OR -RecFileToReproject     File name
              Reconstruction file to reproject or run SIRT with.  When using
              this option, all of the entries to the program used when build-
              ing this reconstruction should be included as well.

       -ProjectModel   File name
              Model file with point positions to reproject onto the projection
              images.  The output file will be a model.  All of the other
              parameter entries should be the same as were used for generating
              the tomogram upon which the model was built.  Points will be
              output only for the views included in that tomogram.  The model
              header will be set so that the model will display properly on
              both the aligned stack used to generate the tomogram and on
              aligned stacks at other binnings.

       -BaseRecFile    File name
              Previous reconstruction file to add views to or subtract views
              from.  One use for this option is to compute a series recon-
              structions quickly with different views left out.  The
              BaseNumViews option must also be entered in order for the right
              scaling to be set up when reading in the existing reconstruction
              and writing out the new one (unless -1 is entered for Subtract-
              FromBase).  If the WeightAngleFile option is also used, then
              incremental reconstructions computed in this way should match
              reconstructions computed de novo very closely.  If the input
              projection file contains only the views being added or sub-
              tracted, then you should also use the MinMaxMean option to keep
              fill values constant.

       -ActionIfGPUFails    Two integers
              The action to take when the GPU cannot be used after being
              requested: 0 to no action, 1 to issue a warning prefixed with
              MESSAGE:, and 2 to exit with an error.  Enter 2 numbers: the
              first for the action when the GPU is requested by the UseGPU
              option; the second for the action when the GPU is requested only
              by the environment variable IMOD_USE_GPU, or by the variable
              IMOD_USE_GPU2.

       -AdjustOrigin
              Adjust origin for shifts with the SHIFT option and size changes
              with WIDTH and SLICES, and base the origin on that of the
              aligned stack.  With this option, reconstructions in PERPENDICU-
              LAR mode of different size and location will have congruent
              coordinate systems and will load models interchangeably.  In
              addition, reconstructions from different sized projection stacks
              will have congruent coordinates provided that the origin was
              adjusted when making the projection stack (e.g., with the -ori-
              gin option to Newstack).  The default is to produce legacy
              origin values that are not adjusted for these operations, with
              the origin in X and Y in the center of the volume.

       -ANGLES    Multiple floats
              Use this entry to specify the tilt angles of the views if they
              are not in a separate file.  You must enter one tilt angle for
              each view.  Use more than one ANGLES entry if necessary.  This
              information will override tilt angles specified in the file
              header.  If you enter angles in this way, the file header need
              not contain tilt information.  (Successive entries accumulate)

       -BaseNumViews   Integer
              When adding or subtracting views from a base reconstruction,
              this option must be entered with the number of views in the pre-
              vious reconstruction.  However, if the SubtractFromBase option
              is entered with a -1 to indicate that a reconstruction is to be
              subtracted from a base file for SIRT, this option should not be
              entered.

       -BoundaryInfoFile    File name
              File with information about boundary locations and files when
              directly writing in parallel to a single output file.

       -COMPFRACTION   Floating point
              If the compression measured by TILTALIGN occurred over only a
              fraction of the distance between the fiducials, enter the frac-
              tion with this option.

       -COMPRESS       Multiple floats
              With this entry, the program will assume that the section has
              compressed in Z by the amount given by the amount given for each
              view.  The compressions would be taken directly from the  output
              of TILTALIGN for incremental compression.  A value must be
              entered for each view.  (Successive entries accumulate)

       -ConstrainSign       Integer
              Enter -1 or 1 to constrain the result to negative or positive
              when subtracting a reconstruction from a base reconstruction, or
              when subtracting an error reconstruction from the current slice
              with SIRT internally.

       -COSINTERP      Multiple integers
              Interpolation order and sampling factor for cosine stretching of
              the input data.  The order can be 1 for linear, 2 for quadratic,
              3 for cubic, or 0 to disable cosine stretching.  The default is
              linear to provide some smoothing of the data; higher orders are
              appropriate if data are relatively noise-free.  The factor is
              optional; the default is 2, which prevents further smoothing
              when the stretched data are linearly interpolated during back-
              projection.

       -DENSWEIGHT     Multiple floats
              Use this entry to control the weighting of each view propor-
              tional to the local average tilt increment between views.  The
              first value specifies the number of intervals on EACH side of a
              view to consider; the default is 2, and a value of 0 disables
              weighting.  Optionally, this value may be followed by that num-
              ber of weights to be applied in averaging the adjacent incre-
              ments (the default is equal weighting).

       -DONE  The entry is equivalent to EndInput, and lines of input follow-
              ing it will be ignored.  This option is provided for compatibil-
              ity with old command files, but eTomo does not handle it prop-
              erly, so it should not be used.

       -EXCLUDELIST2   List of integer ranges
              List of views to be excluded from the reconstruction, numbered
              from 1.  The list can consist of individual view numbers, or of
              ranges (e.g., 1-4), separated by commas or spaces.  The EXCLUDE
              and EXCLUDELIST entries available in old versions of the program
              are treated as this option.  You may have any number of entries
              with exclude lists, but they cannot be combined with INCLUDE
              entries.  (Successive entries accumulate)

       -FlatFilterFraction       Floating point
              With a value entered between 0 and 1, the radial filter will be
              set up as a linear combination of the standard R-weighting fil-
              ter and a flat filter, which will greatly overemphasize low fre-
              quencies.  The entered value is the fraction for the flat fil-
              ter.  The flat filter is scaled to give output densities roughly
              comparable to those obtained with the R-weighting filter.  The
              zero-frequency component of each filter is 0.2 times the compo-
              nent at the lowest non-zero frequency.  If the value is greater
              than one, a filter suitable for Simultaneous Iterative Recon-
              struction (SIRT) is set up, scaled so as to distribute input
              values equally along each ray.  The zero-frequency component is
              the same as the other components in this case.

       -FBPINTERP      Integer
              This option was discontinued in IMOD 4.0.20

       -FULLIMAGE      Two integers
              Use this entry to specify the full size in X and Y of the origi-
              nal stack of tilted views, so that a subset of the aligned stack
              can be handled properly when using a global X-axis tilt or local
              alignments.

       -IMAGEBINNED    Integer
              If the input images have been binned, this entry can be entered
              to specify the binning and have various other dimensions scaled
              down by this factor.  Values entered with SHIFT, OFFSET, THICK-
              NESS, WIDTH, FULLIMAGESIZE, SLICE, and SUBSETSTART will be
              scaled.  These entries thus do not need to be changed when the
              input binning is changed.

       -INCLUDE   List of integer ranges
              A subset of views to be used for the reconstruction, numbered
              from 1.  The values can be individual view numbers or ranges,
              separated by spaces or commas.  Use more than one INCLUDE entry
              if the numbers do not all fit on one line.  (Successive entries
              accumulate)

       -LOCALFILE      File name
              File containing local tilt alignment information.

       -LOCALSCALE     Floating point
              If local tilt alignments were obtained from unreduced data, but
              the aligned stack was reduced by binning or transforming, use
              this entry to specify the factor by which the data were scaled,
              so that the local alignment information can be adjusted.  With-
              out this entry, the program will use the ratio of the pixel size
              at which local alignments were computed to the pixel size of the
              aligned images, which should be correct if data were binned.

       -LOG       Floating point
              This entry allows one to generate a reconstruction using the
              logarithm of the densities in the input file, with the entered
              value added before taking the logarithm.

       -MASK      Integer
              This entry allows a mask to be applied so as to exclude from the
              reconstructed volume those parts which lie outside the volume
              for which the projection data are complete.  This volume is a
              cylinder whose axis lies along the tilt axis.  The entered value
              specifies the number of extra pixels to mask out in this way; a
              negative value can be used to set the mask farther out.  Inside
              the masked area, densities are smoothly tapered from the value
              of a pixel at the edge of the area down to the mean value at the
              edge.  This masking is needed to prevent artifacts from building
              up at the edges of the slice during iterations with SIRT.

       -MinMaxMean     Three integers
              Min, max, and mean densities to use instead of values in the
              input projection file.  Use this entry to keep the fill value
              used for back projecting from outside the data constant when
              doing incremental reconstruction with a projection file that
              contains only the views being added or subtracted.

       -MODE      Integer
              This entry allows one to specify the data mode of the output
              file, which is 2 by default.  Be sure to use an appropriate
              SCALE entry so that data will be scaled to the proper range.

       -OFFSET    Multiple floats
              This entry can contain two numbers, DELANG and DELXX.  An offset
              of DELANG degrees will be applied to all tilt angles.  DELANG
              positive rotates reconstructed sections anticlockwise.  A DELXX
              entry indicates that the tilt axis would be offset in a stack of
              full-sized projection images, cutting the X-axis at  NX/2. +
              DELXX instead of NX/2.  The DELXX entry is optional and defaults
              to 0 when omitted.  If the tilt axis is offset from the center
              because the projection images are a non-centered subset of the
              full images, use the SUBSETSTART entry instead.  If the projec-
              tion images are a non-centered subset with the tilt axis cen-
              tered in them, then using this entry together with SUBSETSTART
              and FULLIMAGE should produce a correct result.

       -PARALLEL
              Output slices parallel to the plane of the zero tilt projection.
              This option cannot be used with direct writing of data to a sin-
              gle output file from parallelized Tilt runs.  It inverts the
              handedness of the reconstruction.

       -PERPENDICULAR
              Output slices perpendicular to the plane of the specimen.  This
              output is the default since it corresponds to the way in which
              slices are computed and allows efficient computation of chunks
              in parallel.

       -RADIAL    Two floats
              This entry controls low-pass filtering with the radial weighting
              function.  The radial weighting function is linear away from the
              origin out to the distance in reciprocal space specified by the
              first value, followed by a Gaussian fall-off with a s.d. (sigma)
              given by the second value.  If the cutoff is great than 1 the
              distances are interpreted as pixels in Fourier space; otherwise
              they are treated as frequencies in cycles/pixel, which range
              from 0 to 0.5.

       -REPLICATE      Two floats
              This option was discontinued in IMOD 4.0.21 (Successive entries
              accumulate)

       -REPROJECT      Multiple floats
              With this entry, the program will output one or more reprojec-
              tions of the reconstructed slices at the given angles.  If Rec-
              FileToReproject is entered, then the reprojections should match
              the input projections; otherwise the reprojections will be of
              the computed slices and should match what Xyzproj would pro-
              duce.  (Successive entries accumulate)

       -RotateBy90
              Output slices parallel to the plane of the zero tilt projection,
              but in the proper order to avoid inverting handedness.  This
              option cannot be used with direct writing of data to a single
              output file from parallelized Tilt runs.

       -SCALE     Two floats
              With this entry, the values in the reconstruction will be scaled
              by adding the first value then multiplying by the second one.
              The default is 0,1.  After the reconstruction is complete, the
              program will output the scale values that would make the data
              range from 10 to 245.

       -SHIFT     Multiple floats
              This entry allows one to shift the reconstructed slice in X or Z
              before it is output.  If the X shift is positive, the slice will
              be shifted to the right, and the output will contain the left
              part of the whole potentially reconstructable area.  If the Z
              shift is positive, the slice is shifted upward.  The Z entry is
              optional and defaults to 0 when omitted.

       -SIRTIterations      Integer
              This entry directs the program to compute a SIRT reconstruction
              internally for the given number of iterations, as described
              above.  If the RecFileToReproject option is given, then the pro-
              gram will read in slices from the existing reconstruction,
              interpolating between them to make vertical slices if there is a
              fixed X-axis tilt.  Each read-in slice or vertical slice is then
              used for reprojection and modified by a backprojection of the
              difference between the reprojection and the original projection
              image.  In this case, the FlatFilterFraction option is not
              needed, as the appropriate filter is used automatically.  If no
              existing reconstruction is given, then the program generates an
              initial reconstruction with a flat filter fraction of 1.0 unless
              a value is supplied with the FlatFilterFraction option.

       -SIRTSubtraction
              Subtract reprojections from original projections to produce a
              reprojection difference for SIRT.  The width of the reprojection
              must match the width of the input data.

       -SLICE     Multiple integers
              Starting and ending slice number to reconstruct, and interval
              between slices.  The numbers refer to slices in the X/Z plane
              and correspond to Y coordinates in the projection images.
              Slices are numbered from 0.  The interval entry is optional,
              must be positive, and defaults to 1 when omitted.

       -StartingIteration   Integer
              Starting SIRT iteration number, in order to obtain reports of
              the mean and standard deviation of a difference reconstruction
              in a SIRT procedure.  These values are computed for slices in
              the middle 80% of the slice range, in the middle 80% of the
              width in X, and in the middle half of the height in Y.  When
              running SIRT internally, the statistics are computed as each
              difference slice is computed.  Otherwise, they are computed just
              before subtracting the difference reconstruction from read-in
              slices.  A summary is printed when the program finishes.

       -SUBSETSTART    Two integers
              If the aligned stack contains a subset of the area in the origi-
              nal images, and this area is not centered in X or a global X-
              axis tilt or local alignments are being used, use this entry to
              enter the X and Y index coordinates (numbered from 0) of the
              lower left corner of the subset within the original images.  A
              FULLIMAGE entry must also be included.  If the aligned stack is
              larger than the original images, use negative values.

       -SubtractFromBase    List of integer ranges
              Views to subtract from the previous reconstruction specified by
              BaseRecFile.  Without this entry, all views are added.  Enter
              the list of specific views to subtract, 0 to have all included
              views subtracted, or -1 to have all views subtracted for a SIRT
              reconstruction.

       -THICKNESS      Integer
              Thickness in Z of reconstructed volume, in pixels

       -TILTFILE       File name
              Use this entry to specify a file containing a list of all tilt
              angles.  The angles may be one per line or many per line.

       -TITLE     Text string
              An alphanumeric string giving the title for the job, which will
              be added to the output map.  Limit 50 characters.  This entry is
              optional; the default is "Tomographic reconstruction".

       -TOTALSLICES    Two integers
              This entry is used to allow multiple runs of Tilt to compute a
              subset of slices and place them into the same output file.  The
              values specify the first and last slice to be reconstructed in
              the whole volume, numbered from 0.  When this entry is present,
              the behavior of the program depends on the SLICE entry (or the
              ZMinAndMax entry when reprojecting from a tomogram).  The pro-
              gram should be run initially with SLICE -1 -1 (or ZMinAndMax -1
              -1 when reprojecting), which will cause it to create the output
              file and write its header.  On successive runs with SLICE or
              ZMinAndMax indicating a real range of slices, the program will
              open the existing file, write only those slices, and not write
              the header when it is done.

       -UseGPU    Integer
              Use the GPU (graphical processing unit) for computations if pos-
              sible; enter 0 to use the best GPU on the system, or the number
              of a specific GPU (numbered from 1).  The GPU can be used for
              all types of operations as long as there is sufficient memory.

       -ViewsToReproject    List of integer ranges
              List of views to reproject from a reconstruction file, numbered
              from 1.  The default is to project just the views that were
              included in the reconstruction.  To project all views in the
              input projection file, enter 0.

       -VertBoundaryFile    File name
              File with information about boundaries and temporary files when
              writing a vertical slice output file and running multiple chunks
              in parallel.

       -VertSliceOutputFile      File name
              File for saving internally produced vertical slices at the last
              iteration when running SIRT internally.  When such a file is
              saved, SIRT can be resumed with it and the vertical slices will
              not be degraded by being interpolated on output and input.

       -VertForSIRTInput
              The file to be reprojected when resuming internal SIRT is a ver-
              tical slice file, specified by VertSliceOutputFile on the previ-
              ous run.  When such a file is provided, the program will use its
              slices directly instead of having to interpolate from the slices
              of the reconstruction file.

       -WeightAngleFile     File name
              File with a list of tilt angles to be used for computing the
              relative weighting of the views.  Use this entry to keep the
              weightings applied to each view constant across reconstructions
              from subsets of views, regardless of which views are actually
              included in a particular reconstruction.  For example, when
              leaving one view out, the two adjacent views would receive
              higher weights without this entry, but with this entry they
              would have the same weights as with the view included.

       -WeightFile     File name
              Name of a file containing a list of weighting factors to be
              applied to the views, such as for mass normalization.  The fac-
              tors may be one per line or many per line.  These weights are
              ignored if the log is being taken of the data.

       -WIDTH     Integer
              The width of the output image; the default is the width of the
              input image.

       -XAXISTILT      Floating point
              This entry allows one to rotate the reconstruction around the X
              axis, so that a section that appears to be tilted around the X
              axis can be made flat to fit into a smaller volume.  The angle
              should be the tilt of the section relative to the X-Y plane in
              an unrotated reconstruction.  For example, if the reconstruction
              extends 500 slices, and the section is 5 pixels below the middle
              in the first slice and 5 pixels above the middle in the last
              slice, the angle should be 1.1 (the arc sine of 10/500).

       -xminmax (-x) OR -XMinAndMaxReproj       Two integers
              Starting and ending X index coordinates of region to reproject
              from a reconstruction file (numbered from 0).  The default is
              the whole extent in X.

       -XTILTFILE      File name
              Use this entry to specify a file containing a list of tilts to
              be applied around the X axis for the individual views.  A global
              tilt specified by the XAXISTILT entry, if any, will be sub-
              tracted from these tilts.  If this file contains all zeros, the
              program runs the same as if the file was not entered.

       -XTILTINTERP    Integer
              This entry controls the order for interpolating an output slice
              tilted around the X axis from vertical, untilted slices each
              computed from a single line of input data.  Set the order to 1
              for linear, 2 for quadratic, 3 for cubic, or 0 to disable this
              method of X-axis tilting and revert to computing the output
              slice directly from input data.  The default is 1; higher orders
              are appropriate if data are particularly noise-free.

       -yminmax (-y) OR -YMinAndMaxReproj       Two integers
              Starting and ending Y index coordinates of region to reproject
              from a reconstruction file (numbered from 0).  Y is the thick-
              ness dimension.  The default is the whole extent in Y.

       -ZFACTORFILE    File name
              Use this entry to specify a file containing factors for adjust-
              ing the backprojection position in each image as a function of Z
              height in the output slice.  These factors are necessary when
              input images have been transformed to correct for an apparent
              specimen stretch.  If this entry is absent, Z factors in a local
              alignment file will not be applied.

       -zminmax (-z) OR -ZMinAndMaxReproj       Two integers
              Starting and ending Z index coordinates of region to reproject
              from a reconstruction file (numbered from 0).  Z is the the
              dimension along the tilt axis.  The default is the whole extent
              in Z.

       -debug (-d) OR -DebugOutput
              Print output for debugging

       -internal (-int) OR -InternalSIRTSlices       Two integers
              Output reprojections or reconstruction slices held internally on
              the last iteration of SIRT.  The first value is the type of
              reprojection: 0 for none, 1 for actual reprojection, or 2 for
              difference between reprojection and input data.  The second
              value is for type of slice: 0 for none, 1 for backprojection of
              difference lines, 2 for final vertical slice, 3 for slice pro-
              duced on iteration 0, and 4 for vertical slice decomposed from
              input.  Output files are sirttst.prj and sirttst.drec, respec-
              tively.

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter
              file.

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.


HISTORY
       The program was originally written by Mike Lawrence and has been modified
       vastly and repeatedly by David Mastronarde.

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                             tilt(1)