Last modified: Tue Sep 28 14:25:54 2004.
NAME:
fMDIO_BlockVolumes
PURPOSE:
Multiple acquisitions of a MDI-Object are blocked to form a "shorter"
series
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fMDIO_BlockVolumes(MDIO, BlockingFactor, Status = Status)
INPUTS:
MDIO : A structure containing the image data. It must be created
by the function fBMT_CreateMDIObject().
BlockingFactor : The number if volumes, which should be grouped (blocked)
OPTIONAL INPUT PARAMETERS:
None
KEYWORD PARAMETERS:
Status : on exit, -1 is returned if an error has occurred, 1 on success
OUTPUTS:
MDI-Object containing the blocked data
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
The data of volumes from 0,..,BlockingFactor-1; BlockingFactor,...,
2*BlockingFactor-1 is averaged.
MODIFICATION HISTORY:
09.01.2001 Function created and tested
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_blockvolumes.pro)
NAME:
fMDIO_CombineInterleaved
PURPOSE:
Combine two scans, which were acquired with an interleaved
geometry.
Scan 1 Slice n -------------------
Scan 2 Slice n -------------------
| | |
Scan 1 Slice 1 -------------------
Scan 2 Slice 1 -------------------
Which scan is assigned to MDIO1 and MDIO2 is irrelevant. The
slices are sorted according to the geomtery parameters.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_CombineInterleaved(MDIO1, MDIO2)
INPUTS:
MDIO1/2: Two scans containing the same number of slices.
OUTPUTS:
MDIO, containing twice the number of slices as MDIO1 or MDIO2
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_combineinterleaved.pro)
NAME:
fMDIO_Create
PURPOSE:
Create a Multi-Dimensional-Image-Object, which is refered as a
scan in the BioMAP philosophy.
This function replaces fBMT_CreateMDIO!!!
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Create()
KEYWORD PARAMETERS:
Vox: Voxelsize in mm
N: Number of MDIOs to be created.
Skeleton: MDIO, from which parameters of the header are taken.
Dimension: Dimension of the scan. If Dimension is provided,
the array to hold the image data will be created.
Type: Type (according the the ANALYZE definition). In the
current version, type can only be 4 or
16. Otherwise, the array must be initialized manually.
OUTPUTS:
The MDIO-structure.
MODIFICATION HISTORY:
Last modification: 18.10.2002
2000/02/14 The Affine transformation matrix is now
initialized to the identity-matrix.
2003/01/22 Parameter1 is initialized as ramp.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_create.pro)
NAME:
fMDIO_Detrend
PURPOSE:
Remove the linear drift of individual voxels. The slope of the
drift is calculated from a series of baseline images either
for each voxel individually or from the global mean.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y =fMDIO_Detrend(MDIO, BaslineRange,Threshold)
INPUTS:
MDIO: MDI-object
BeslineRange: Array of two elements, which contains the index
of the first and last baseline image.
Threshold: Voxels with values below Threshold, will be
removed from analysis.
KEYWORD PARAMETERS:
Overwrite: Overwrite the MDIO, which was passed as the first
argument. This keyword can be used if this MDIO is
not used anymore.
Global: Derive the drift from the global mean of the intensity of
the scan.
Display: Display the global mean of the scan together
with the regression line.
OUTPUTS:
MDIO containing the result of the operation.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_detrend.pro)
NAME:
fMDIO_Divide
PURPOSE:
Divide one scan by another: Result = MDIO1 / MDIO2.
MDIO1 can contain any number of volumes. MDIO2 is allowed to
contain one volume or the same number as MDIO1. The
calculations are carried out according to the array handling
rules of IDL.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Divide(MDIO1, MDIO2)
INPUTS:
MDIO1/2: Scans to be used.
KEYWORD PARAMETERS:
Min1: Minimum of the numerator. Values below Min1 will be
disregarded.
Min2: Minimum of the denominator. Values below Min2 will be
disregarded.
Log: Calculate the natural logarithm of the result. This
option can be used if an attanuation value should be calculated.
OUTPUTS:
A MDIO containing the result of the calculation.
MODIFICATION HISTORY:
2003/01/10: Keyword min1 implemented
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_divide.pro)
NAME:
fMDIO_EditHeader
PURPOSE:
Edit or view the parameters, which are contained in the header
of a MDIO. This procedure can also write the modiefied header
to disk, if the scan was already stored in the database.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_EditHeader(MDIO)
INPUTS:
MDIO to be edited.
OUTPUTS:
If the function will be exited by "Done" and not by "Cancel",
the modified header will be returned. Otherwise the header
will remain unchanged.
MODIFICATION HISTORY:
Last Modification: 17.10.2002
REQUIREMENTS & BUGS
SRK Remove common blocks and rewrite to a procedure.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_editheader.pro)
NAME:
fMDIO_ExtractClusters
PURPOSE:
Extract clusters of pixels, which exceed a minimum value and a
minimum size. First, a threshold is applied to the data and
all remaining voxels are labeled and grouped to
clusters. Secondly, a spatial threshold is applied.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_ExtractClusters(MDIO, MinValue, MinSize)
INPUTS:
MDIO: The scan to be processes.
MinValue: Threshold for voxel values.
MinSize: Threshold for cluster size.
KEYWORD PARAMETERS:
TwoSided: Extract all regions, for which the absolute value
exceeds the given threshold.
OUTPUTS:
Array containing two MDIOs
MDIO, where values of all voxels, which do not belong to the
desired class are set to zero.
ClusterIndex: MDIO with the same dimension as Y,
which contains the index of each cluster, will be returned.
It can be used as a ROI-object.
MODIFICATION HISTORY:
Last Modification:
2003/01/21 Keyword ClusterIndex implemented
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_extractclusters.pro)
NAME:
fMDIO_ExtractVolumes
PURPOSE:
Extract a subset of volumes from a scan
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_ExtractVolumes(MDIO)
INPUTS:
MDIO: A scan, which the operations should be carried out.
KEYWORD PARAMETERS:
Min: First volume to be used. If not specified, all volumes
before max will be returned.
Max: Last volume to be used. If not specified, all volumes
larger than min will be returned.
Odd: Take only volumes with an odd index (0, 2, 4, ...)
representing the first, third, .... volumes.
Even: Take only volumes with an even index (1, 3, 5, ...)
representing the second, fourth, .... volumes.
Index: Extract volumes according to the index list.
Verbose: Print information on the operations.
OUTPUTS:
MDIO, which contains the result of the operation.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_extractvolumes.pro)
NAME:
fMDIO_GlobalMean
PURPOSE:
Calculate the global mean of a data set.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_GlobalMean(MDIO)
INPUTS:
MDIO: MDI-Object
kspace : Calculation is based on calculating the power in the
center of the Fourier space. This approach avoids using a
threshold to eliminate pixels outside of the organ.
Width: Diameter around the center of Fourier space, from
which the mean should be calculated.
OUTPUTS:
Array, which contains the global mean of the MDIO
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_globalmean.pro)
NAME:
fMDIO_HighPass
PURPOSE:
Remove global intensity differences by subtracting the
strongly smoothed version from the data.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_HighPass(MDIO1,S)
INPUTS:
MDIO: Scans to be used.
KEYWORD PARAMETERS:
Sf: Smoothing factor (i.e the width of the boxcar filter)
Global: On exit, the result will contain the smoothed
scan instead of the filtered scan.
OUTPUTS:
A MDIO containing the result of the operation.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_highpass.pro)
NAME:
fMDIO_Integrate
PURPOSE:
Numerical integration of a 4-dimensional data set.
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fBMT_Integrate(MDIO)
INPUTS:
MDIO: Scan data
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
X: N-element vector containing the values of the x-axis, e.g. time.
Range: 2-element array containing the boundaries for integration
BlCorr: Structure containing the parameters for baseline
correction.
RemoveOffset: Subtract the area defined by the interval of
integration and the values at the boundaries
from the result.
Status: Exit status of the function
OUTPUTS:
MDIO containing the result of integration
PROCEDURE:
Numerical integration over the fourth dimension of a MDIO. The boundaried should
be provided by the range - keyword. If no boundaries are given all data is
considered
MODIFICATION HISTORY:
2000/01/16 Input checks added.
2002/10/24 Keyword RemoveOffset implemented.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_integrate.pro)
NAME:
fMDIO_Mean
PURPOSE:
Average data from a slice, a volume or from multiple volumes
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fBMT_Mean(MDIO, [N1, N2], Status=Status)
INPUTS:
MDIO : Data to be averaged.
OPTIONAL INPUT PARAMETERS:
N1 : The first volume considered for volume averaging
N2 : The last volume considered for multiple volume averaging
KEYWORD PARAMETERS:
RemoveOffset : Subtract the area defined by the interval of
integration and the values at the boundaries
from the result.
Status: Exit status of the function
OUTPUTS:
Averaged data
PROCEDURE:
Data from the first argument is averaged, according to the other parameters and
keywords passed to the function. Three modes of operation are implemented:
Y = fBMT_Mean(X, n1, n2)
Average the volumes contained in X starting at n1 and ending at n2. Hence, the function
will return a volume with the same spatial resolution as the input data but with the 4th
dimension set to one.
MODIFICATION HISTORY:
2002/01/09 Error handling implemented
2002/10/25 Keyword RemoveOffset implemented
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_mean.pro)
NAME:
fMDIO_Multiply
PURPOSE:
Multiply voxel values of two scans or multiply the voxel
values of the first scan with a scalar provided in the second argument.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Multiply(MDIO1, MDIO2)
INPUTS:
MDIO1: Two scans of the same matrix size.
MDIO2: Secons scan of the same size or scalar or array of same
dimension as number of volumes contained in the first scan.
OUTPUTS:
MDIO, containing the resilt of the operation
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_multiply.pro)
NAME:
fMDIO_Realign
PURPOSE:
Realign volumes of a scan. This function uses AIR-functions for
realignment. Temporary data will be stored in the /tmp
directory.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Realign(MDIO)
INPUTS:
MDIO: Scan to be realigned
KEYWORD PARAMETERS:
Mode: Index of the model to be used for realignment.
3-D models:
6. rigid body 6 parameter model
7. global rescale 7 parameter model
9. traditional 9 parameter model (std must be on AC-PC line)
12. affine 12 parameter model
15. perspective 15 parameter model
2-D models (constrained to in-plane, no interpolation):
23. 2-D rigid body 3 parameter model
24. 2-D global rescale 4 parameter model
25. 2-D affine/fixed determinant 5 parameter model
26. 2-D affine 6 parameter model
28. 2-D perspective 8 parameter model
Model 6 will be used as default.
CostFunction: Cost function. Can be 1, 2 or 3. See AIR
documentation for details.
Target: A MDIO, which contains one volume to be used as
target. If this keyword is not supplied, the first
volume of the scan will be used as reference.
Threshold: Voxels haven a value below threshold will be
disregared during realign.
OUTPUTS:
MDIO containing the result of the operation.
RESTRICTIONS:
BioMAP must have been started before using this function.
MODIFICATION HISTORY:
__________________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_realign.pro)
NAME:
fMDIO_Reciproce
PURPOSE:
Calculate 1/VoxelValue of a scan.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Reciproce(MDIO1)
KEYWORD PARAMETERS:
Min: Minimum value to be considered.
Max: Minimum value to be considered.
INPUTS:
MDIO1/2: Two scans of the same matrix size.
OUTPUTS:
MDIO, containing the resilt of the operation
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_reciproce.pro)
NAME:
fMDIO_Regrid
PURPOSE:
Compose the data matrix of a scan at a different spatial
resolution. The geometry parameters of the header will be
changed accordingly.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Regrid(MDIO, Resolution)
INPUTS:
MDIO: Scan to be processed.
Resolution: Array containing three elements defining the new matrix
size.
KEYWORD PARAMETERS:
Interp: Interpolate between voxels.
OUTPUTS:
Regridded MDIO
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
SRK1 Clarify interpolation scheme (Interp)
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_regrid.pro)
NAME:
fMDIO_Reorder
PURPOSE:
Create multiple volumes from a stack of slices. Background:
Scans, which were imported from another source, are not
structured in a logical sense. E.g. in a
multi-slice-multi-echo experiment all images could be arranged
in a single volume. With fMDIO_Reorder one can rearange them
to a multi-slice-multi-volume scan.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Reorder(MDIO, Repetitions, Order)
INPUTS:
MDIO: Scan to be reordered
Repetitions: Number of repetitions (number of values for the parameter)
Order: 0: Blocked (All slices belonging to the same
parameter-value were stored consecutively)
1: Interleaved (All parameter-values for the n'th
slice are stored conscutively)
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Slice2Ev: Exchange the slice/evolution index (3th<->4th
index) prior to reordering.
OUTPUTS:
The reordered MDIO.
MODIFICATION HISTORY:
Last Modification: 2002/11/29
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_reorder.pro)
NAME:
fMDIO_Reslice
PURPOSE:
Reslice a object scan according to its geomtrical parameters
to the geomtrical space defined by the target scan. This
function can be used after coregistration of two scans.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_Reslice(Object, Target)
INPUTS:
Object: MDIO containing the object, which has to be resliced to match the geometry of the target.
MDIO: MDIO defining the space.
KEYWORD PARAMETERS:
Cubic: Use Cubic interpolation.
OUTPUTS:
Resliced MDIO
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
The geometry parameters are taken from the two MDIO. They are used to transfer each voxel
of the ROI to the correct position in world space.
MODIFICATION HISTORY:
2000/02/14 If Roi has only one slice, then translation in third direction is inhibited. Additionally,
the ceil(.)-function is applied to the volume indices.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_reslice.pro)
NAME:
fMDIO_ReverseVolumeOrder
PURPOSE:
Reverse the order by which volumes are aranged in a scan.
CATEGORY:
MDIO
CALLING SEQUENCE:
Y = fMDIO_ReverseVolumeOrder(MDIO)
INPUTS:
MDIO: A scan to be reordered
OUTPUTS:
MDIO containing the reordered volumes.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_reversevolumeorder.pro)
NAME:
fMDIO_ScanMean
PURPOSE:
Averaging of scans. Two modes of input are implemented: You
can provide scans of same size as multiple arguments. Up to 16 scans
are allowed. Or scans can be passed to the function as an
array containing multiple MDIO. However, the data-field must
have the same size for all elements.
This function is comparable to fMDIO_Mean but provides the
option to pass several scans as argument.
CALLING SEQUENCE:
Y = fMDIO_Mean(MDIO)
or
Y = fMDIO_Mean(MDIO1, MDIO2, ...)
INPUTS:
MDI-objects
OUTPUTS:
The mean value is returned and if the second input mode was
used, the standard-deviation is returned by the keyword s.
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_scanmean.pro)
NAME:
fMDIO_Stdev
PURPOSE:
Calculate the standard deviation along the 4th dimension of a scan.
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fMDIO_Stdev(MDIO, [N1, N2], Status=Status)
INPUTS:
MDIO : Scan, for which the standard deviation
should be calculated.
OPTIONAL INPUT PARAMETERS:
N1 : The first volume considered. N1 can also be an
array of indices for volumes to be used for calculation.
N2 : The last volume considered
OUTPUTS:
Averaged data
PROCEDURE:
Y = fMDIO_Stdev(X, n1, n2)
Average the volumes contained in X starting at n1 and ending at n2. Hence, the function
will return a volume with the same spatial resolution as the input data but with the 4th
dimension set to one.
MODIFICATION HISTORY:
09.01.2001 Error handling implemented
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_stdev.pro)
NAME:
fMDIO_Subtract
PURPOSE:
Subtract two scans. If the 4th dimensions of both scans are not equal, the first volume of
MDIO2 is used for subtraction.
CATEGORY:
__________________________________
CALLING SEQUENCE:
Y = fMDIO_Subtract(MDIO1, MDIO2, min2=min2)
INPUTS:
MDIO1 and MDIO2 are two scan objects, which should have the same spatial dimensions.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Min2: Threshold applied to MDIO2. Only those voxel, which have a larger value
are considered.
OUTPUTS:
Scan object, containing the result of the subtraction
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_subtract.pro)
NAME:
fMDIO_SVD
PURPOSE:
Single value decomposition for 3D+Time image data
CATEGORY:
Image analysis
CALLING SEQUENCE:
Y = fMDIO_SVD(MDIO, Eigenimage, TempProfile, Singular, Thres = x , SeriesRange = [x,y]
INPUTS:
MDIO: Scan to be decomposed
OPTIONAL INPUT PARAMETERS:
Profile: Named variable that will hold the temporal profile with
which the eigenimage contributes to the time series. The
first index of the matrix contains the index of the
eigenimage.
Singular: Named variable that will hold the singular values
(eigenvalues) on exit. The singular values are a
monotonically decreasing array.
KEYWORD PARAMETERS:
Thres: Threshold parameter that gives the minimum value in the
data which should be considered
OUTPUTS:
See optional input parameters
MODIFICATION HISTORY:
Created on 05.05.2000
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_svd.pro)
NAME:
fMDIO_TensorAnalysis
PURPOSE:
Calculate Eigenvalues, Direction, Trace and Anisotropy of a
data set. Volumes of the scan should comprise direction
(diffusion) sensitization for the following six directions:
xx, yy, zz, xy, xz, yz.
CATEGORY:
MDIO (WIP)
CALLING SEQUENCE:
Y = fMDIO_TensorAnalysis(MDIO)
INPUTS:
MDIO containing 6 volumes representing the 6 encoding directions.
KEYWORD PARAMETERS:
Min: Minimum signal value considered.
OUTPUTS:
An array of 4 MDIOs will be returned (not one scan containing
4 volumes). This array contains the following parameter maps:
1) Eigenvalues
2) Direction of the principal axis of the 3-dimensional
elipsoid.
3) Trace
4) Anisotropy
; MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_tensoranalysis.pro)
NAME:
fMDIO_Total
PURPOSE:
Average data from a slice, a volume or from multiple volumes
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fBMT_Total(MDIO, [N1, N2], Status=Status)
INPUTS:
MDIO : Data to be processed.
OPTIONAL INPUT PARAMETERS:
N1 : The first volume considered for volume averaging
N2 : The last volume considered for multiple volume averaging
KEYWORD PARAMETERS:
Status: Exit status of the function
OUTPUTS:
total of data
PROCEDURE:
Data from the first argument is averaged, according to the other parameters and
keywords passed to the function. Three modes of operation are implemented:
Y = fBMT_Total(X, n1, n2)
Average the volumes contained in X starting at n1 and ending at n2. Hence, the function
will return a volume with the same spatial resolution as the input data but with the 4th
dimension set to one.
MODIFICATION HISTORY:
2002/01/09 Error handling implemented
2002/10/25 Keyword RemoveOffset implemented
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fmdio_total.pro)
NAME:
pMDIO_Destroy
PURPOSE:
Release memory allocated for data of the MDIO.
CATEGORY:
MDIO
CALLING SEQUENCE:
pMDIO_Destroy, MDIO1, MDIO2, ....
INPUTS:
MDIO1,...,MDIO8
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_destroy.pro)
NAME:
pMDIO_EditEvents
PURPOSE:
Interface to create, delete and edit event entries for a given
MDIO. Events consist of a name and a time. The time must be
specified in units of Parameter1.Events will be shown if their
name is not "".
CATEGORY:
MDIO
CALLING SEQUENCE:
pMDIO_EditEvents, MDIO
INPUTS:
MDIO to be processed
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_editevents.pro)
NAME:
pMDIO_SetGeo
PURPOSE:
Set the affine transformation matrix, which defines the
transformation from index- to world- (physical-) space. The
matrix is generated from the three direction cosines and the
center-parameter. These are taken from the header of the
MDIO.
MDIO.row, MDIO.col, MDIO.normal and MDIO.center are stored in
the associated dat-file, while MDIO.Geo is just as a variable
in memory. Note that this function generates the
transformation matrix by the standard scheme. If one of the
vectors MDIO.row, MDIO.col or MDIO.normal is not complient to
the standard coordinate system, pMDIO_Geo might not lead to
the correct result.
CATEGORY:
MDIO
CALLING SEQUENCE:
pMDIO_SetGeo, MDIO
INPUTS:
MDIO: Scan to be processed.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_setgeo.pro)
NAME:
pMDIO_SetMinMax
PURPOSE:
Set the minimum and maximum parameter in a MDIO. Thsi
procedure must be used if a scan was modified by a
calculation. The min and max parameter are used in displaying
routines and must be set correctly.
CATEGORY:
MDIO
CALLING SEQUENCE:
pMDIO_SetMinMax, MDIO
INPUTS:
MDIO: Scan to be processed.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_setminmax.pro)
NAME:
pMDIO_SpikeCrop
PURPOSE:
Set voxel values that exceed a given range to the given minimum
or maximum value. In addition, infinite elements will be set
to zero.
CATEGORY:
MDIO
CALLING SEQUENCE:
pro pMDIO_SpikeCrop, MDIO, min, max
INPUTS:
MDIO: Scan to be processed
Min: Allowed minimum.
Max: Allowed maximum.
MODIFICATION HISTORY:
Last Modification: 18.10.2002
18.10.2002: Infinite elements will be removed from the scan
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_spikecrop.pro)
NAME:
pMDIO_TypeConvert
PURPOSE:
Convert the data type of an MDIO. This types are related to
the possible storage formats of ANALYZE. Posible types are:
2: byte (1 byte)
4: signed integer (2 byte)
8: signed long (4 byte)
16: float (4 byte)
Type conversion is carried out irespective of the values
contained in the data set. E.g. a -1 is converted to 255 if
type 2 was selected. However, scaling is applied using the
maximum of the MDIO. Problems will occur, if the absolute of
the minimum is larger than the maximum. Voxels, with these
values will be projected outside the range of the variable.
CATEGORY:
MDIO
CALLING SEQUENCE:
pMDIO_TypeConvert, MDIO, Type
INPUTS:
MDIO: The dataset stored as a MDIO, which should be converted
Type: The type to which the dataset should be converted.
MODIFICATION HISTORY:
2002/10/02 First implementation
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pmdio_typeconvert.pro)
NAME:
fWIN_CoordConv
PURPOSE:
Convert the pixel position of an image, which is displayed in one of the Biomap-windows,
to the 3-dimensional index within the volume.
CATEGORY:
BMT
CALLING SEQUENCE:
Y=fWIN_CoordConv(Winx,Winy)
INPUTS:
x: Position in x-direction. Can be an array or a scalar.
y: Position in x-direction. Can be an array or a scalar.
Mode: Optional parameter, which defines the Mode of conversion. If Mode is one,
interpolation is performed, otherwise an image coordinate is directly selected
from the Index-array.
OUTPUTS:
__________________________________
MODIFICATION HISTORY:
2001/02/22 If the index is out of range, it will be set to 0
2001/07/19 If the index is out of range, it will be set to the boundaries
(See /usr/people/ivm/rauscma1/programs/biomap/source/fwin_coordconv.pro)
NAME:
fWIN_GetMDIO
PURPOSE:
Retrieve the scan, which is stored in a BioMAP-window
CATEGORY:
WIN
CALLING SEQUENCE:
Y = fWIN_GetMDIO([WinIndex], /copy, Status=Status)
OPTIONAL INPUT PARAMETERS:
WinIndex: Index of BioMAP-window (0,...)
KEYWORD PARAMETERS:
Copy: Return a copy of the scan. Otherwise the MDIO itself is
returned, which means that the pointers are the same. As a
consequence, destroying Y, would also erase the data of the window.
OUTPUTS:
MDIO
COMMON BLOCKS:
None.
SIDE EFFECTS:
Window data can be erased.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fwin_getmdio.pro)
NAME:
fWIN_ImageCreate
PURPOSE:
Uses the paramters defined in structure win(.) and creates a true color image,
which can be displayed. It passes all parameters of the currently active window to
fBMT_PrepareImage. It just requires the output size as input parameter.
Optionally, the slice to be shown can be passed as a keyword parameter. This
can be helpful, if all slices of a volume should be displayed with the same
overlay, roi, etc..
CATEGORY:
Image display
CALLING SEQUENCE:
Image = fBMT_ImageCreate(OutputSize)
INPUTS:
Outputsize: Basic size of image in pixel
OPTIONAL INPUT PARAMETERS:
KEYWORD PARAMETERS:
Slice: Slice orientation, otherwise Win(.).slice is
used.
OvlEv: Index to volume in overlay associated with the
window.
No_Overlay: Do not calculate the overlays (like Roi or
overlays)
Restore: Use the image, which was calculated in the
last run of the the function.
OUTPUTS:
True color image
COMMON BLOCKS:
Uses inf.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2001/03/15 Keyword No_Overlay implemented.
2003/01/20 Keyword OvlEv implemented.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fwin_imagecreate.pro)
NAME:
pWIN_Clear
PURPOSE:
Remove data from a BioMap window
CATEGORY:
WIN
CALLING SEQUENCE:
pWIN_Clear, Index
INPUTS:
Index: Index of the window ranging from 0 to NumberOfWindows
KEYWORD PARAMETERS:
All: Erase all windows
OUTPUTS:
None
COMMON BLOCKS:
Inf
RESTRICTIONS:
BioMAP must have been started
(See /usr/people/ivm/rauscma1/programs/biomap/source/pwin_clear.pro)
NAME:
pBMT_Cell_ui
PURPOSE:
Automatically segment a T2-weighted brain
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_Cell_ui
OUTPUTS:
The result is stored in the selected window.
COMMON BLOCKS:
Inf
MODIFICATION HISTORY:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_cell_ui.pro)
NAME:
fBMT_ClusterAnalysis
PURPOSE:
Read a set of parameter files and perform a cluster analysis on the data.
The routine is at the moment designed for the analysis of Gamma-Variate data
but could be generalized for the analysis of other parameter sets.
CATEGORY:
Data analysis
CALLING SEQUENCE:
Result = fBMT_ClusterAnalysis(MDIO)
INPUTS:
The directory from which the Gpdf-files should be used is given by the
scan filename defined by the MDIO.
OPTIONAL INPUT PARAMETERS:
None
KEYWORD PARAMETERS:
NClusters: Number of clusters, which will be created
ParRange: Parameter range used for inclusion of pixels. It is a 3 by 2 matrix
Chi2Max: Maximal chi^2 allowed for a pixel to be included into CA. This will
exclude all pixels for which the fit was not very well.
VarWeights: Parameter passed to CA. It is a 3-element vector, which describes
The importance of a parameter.
Slice: Consider only one slice given by its slice number.
Verbose: Plot some information about the analysis.
OUTPUTS:
An array of same dimensionality as the source volume is returned which contains
the index of cluster a pixel was assigned to.
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK1 Function should be moved to MDIO-library
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_clusteranalysis.pro)
NAME:
fBMT_CompScans
PURPOSE:
Verify if to scans have equal properties.
CATEGORY:
Matrix operation
CALLING SEQUENCE:
Result = fBMT_CompScans(MDIO11, MDIO2)
INPUTS:
MDIO1/2 are two MDI-Objects
KEYWORD PARAMETERS:
DIMENSION: Compare spatial dimensions
REPETITIONS: Compare number of repetitions
GEOMETRY: Compare orientation
OUTPUTS:
1 if equal, -1 else
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
Perform comparisons and return the result
MODIFICATION HISTORY:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_compscans.pro)
NAME:
fBMT_CoordConv
PURPOSE:
Convert from the index to the worl coordinate system or backwords.
CATEGORY:
__________________________________
CALLING SEQUENCE:
__________________________________
INPUTS:
Header: MDIO-Header
Coord: Array of the form [N, 3] providing the coordinates.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Affine: Affine is used as a second affine transformation, which can modify the physical
orientation of the volume.
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_coordconv.pro)
NAME:
fBMT_CreateView2D
PURPOSE:
Create a structure, which contains the parameter to extract a 2D slice
from a MDIO
CATEGORY:
Brainmap basic functions
CALLING SEQUENCE:
Y = fBMT_CreateView2D(Origin, ax, ay, az, ev)
INPUTS:
Origin: Array of three elements containing the origin of the slice
AX, AY, AZ: Angle of the slice
EV: Volume from which the slice should be extracted
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
Zoom: Zoom factor
OUTPUTS:
Structure, which contains the above mentioned parameters.
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
MODIFICATION HISTORY:
2000/02/13 Keyword Zoom added.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_createview2d.pro)
NAME:
fBMT_ExtractSlice
PURPOSE:
Extracting a slice from a three dimensional volume. Indices are stored in VolInd(NP,4).
CATEGORY:
BMT
CALLING SEQUENCE:
Image = fBMT_ExtractSlice(Header, Volume, x_size, y_size, x_center, y_center, z_center,
x_rot, y_rot, z_rot)
INPUTS:
Header: Structure containing the header information
Volume: three dimensional matrix containing the data
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Spacing : Resolution used for interpolation. It can be used to create a larger
output image, e.g. to fit the image to the window.
Voxel : If keyword is set, congrid(.) is used for interpolation. Moreover, just
the center point is used for extractration and all angles are ignored.
OUTPUTS:
Image
EXAMPLE:
tvscl, (fBMT_ExtractSlice(Header(0),reform((*scan_ptr(0))(*,*,*,0)),128,128,64,64,0,0,0,0)).image
MODIFICATION HISTORY:
2001/02/14 Ceil(.)-function applied to indices, which where calculated in BaseImage-mode
2001/02/14 Procedure "Voxel display mode" was changed. Now applying ceil(.)-function to volume
indices.
2001/02/15 Ceil(.) -> Round(.)
2001/02/16 If slices are parallel, Z is used directly from BaseImage.
2001/03/19 Keyword "Missing" removed from interpolate(.) if all rotation parameters = 0
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_extractslice.pro)
NAME:
fBMT_FitForFun
PURPOSE:
Least square fit of gamma variate function to a 1D perfusion curve
CATEGORY:
brain imaging anlysis
CALLING SEQUENCE:
Y = fBMT_FitForFun(X, Y, FunctionName)
INPUTS:
X: Independent variable
Y: Dependent variable
FunctionName: Model function, which should be fitted to the data. It can be:
"fit_exp": f = a[0] * exp(a[1] * x)
"fit_exp3": F = A[0] * bx + A[2]; bx = EXP(A[1] * X)
"fit_gausstb": Gauss with tilted baseline.
The difference between the two models is, that fit_exp3 can also
account for an offset.
OPTIONAL INPUT PARAMETERS:
NONE
KEYWORD PARAMETERS:
Init: Starting values for the fit can be provided by this keyword.
CHISQ: The CHI^2 value of the fit is hold by this parameter
STATUS: A "1" indicates convergence, a "-1" failure of the least square fit
Weights: Array of weights used for the leasr square fit. It must have the same
number of elements as the data array
VERBOSE: Some comments during the run of the function are displayed in teh IDL window
DISPLAY : Graphical display of the data and the fit
OUTPUTS:
The parameters of the fit are returned if the fit was successful
Otherwise [0,0,0] is returned.
COMMON BLOCKS:
None.
SIDE EFFECTS:
If DISPLAY is set, window DISPLAY is used for output
RESTRICTIONS:
NONE
PROCEDURE:
Least square fit of a gamma probability density function to a concentration time curve
of contrast agent.
MODIFICATION HISTORY:
15/09/99 Version 1.0 shows stable results for the fit in a case of cerebral infarction
21/09/99 /TSEARCH is doing now 10 iterations
23/09/99 The option /TWCUT was introduced
24/09/99 The complex search procedure was removed from wcut; the temporal cut-off
is now defined by twcut.
Search of maximum for definition of start values is now restricted to weights>0
22/09/99 Cleaning up some badly arranged functions.
2001/02/16 Model function fit_exp3 added, which uses three parameters.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_fitforfun.pro)
NAME:
fBMT_FunctionFit
PURPOSE:
Fit a model curve to each pixel of a MDIO.
CATEGORY:
__________________________________
CALLING SEQUENCE:
Y = fBMT_FunctionFit(MDIO, X, Func)
INPUTS:
MDIO: MDIO, for which the fit should be performed. The 4th dimension should be large than 2.
X: An independent variable, which matches the 4th dimension of the MDIO.
Func: The model function. Currently 3 models have been implemented:
"T2": Calculation of the Proton- and T2-map of a multi echo sequence.
"ADC": Calculation of the apparent diffusion coefficient.
"Exp-": Calculation of the S0 and exponential decay map of a multi echo or diffusion
sequence
"Epx3P": Fit of the function: Y = P1 * exp(P2 * V) + P3 to the data. This model can be used
to model exponential signal increase.
"Epx4P": Fit of the function: Y = P1 * exp(P2 * (V-P4)) + P3 to the data. This model can be used
to model exponential signal increase in case of leakage. The data should contain reletive
concentrations (i.e. scaled from 0.0 to 1.0)
Thres: Intensity-threshold. Voxels, whos value exceeds this threshold in at least one volume are considered for analysis.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Thres: The smallest pixel value to be considered.
Weights: Array containing the individual weighting for each point along the 4th dimension.
ChiSq: Maximimum Chi² to be considered as useful fit.
OUTPUTS:
MDIO containing a volume for each parameter of the model function.
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
None.
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2001/02/19 Keyword ChiSq added.
2001/02/20 Model "fit_exp4" added.
2001/03/22 Infinite elements set to 0.0
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_functionfit.pro)
NAME:
fBMT_GetVoxelSize
PURPOSE:
Calculate the size of one window-pixel. The size will be returned in mm or in voxel-dimensions.
CATEGORY:
BMT
CALLING SEQUENCE:
Y = fBMT_GetVoxelSize()
INPUTS:
__________________________________
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_getvoxelsize.pro)
NAME:
fBMT_ImageCombine
PURPOSE:
Create an image of a MDIO using the parameters passed to this function. Usually a true color
image is generated, which can be displayed by
tv, Y, true = 3.
Overlays and Rois can be passed by keyword parameters optionally.
CATEGORY:
Image processing
CALLING SEQUENCE:
Y
INPUTS:
MDIO: The MDI-Object
Orientation: A structure (generated by fBMT_CreateView2D()) containing the information about the slice
which should be displayed.
ImageRange: Array of 2 elements, containing the minimum and maximum values used for scaling.
OutputSize: Scalar giving the size of the final image.
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
Native8Bit: The slice of the MDIO is returned as a scaled image. No overlays or rois are added.
DisplayMethod: If this keyword is set, the specified display method is used:
0: Interpolation giving smooth images
1: Regridding giving images that allow to identify individual voxels.
TransparentRoi: The ROI-Object passed with this keyword is added to the image as transparent overlay.
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2000/02/14 NoSpatialTransformation is not used anymore for overlaying. It is only used for
ROIs, because they have been already transformed during loading.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_imagecombine.pro)
NAME:
fBMT_ImageProcess
PURPOSE:
This function is used to extract a slice from a 3D or 4D volume.
CATEGORY:
BrainMap
CALLING SEQUENCE:
Y = fBMT_ImageProcess(MDIO, Orientation, WindowSize)
INPUTS:
MDIO : MDIO-structure, containing the scan data
orientation : Structure containing the information about the slice orientation and the volume from
a N-Volume scan
WindowSize : The size of a window with equal length in x and y direction
KEYWORDS:
VERBOSE : Displays information about input parameters
BaseImage : Header of the scan on which Volume will be overlayed
DisplayMethod : How the image is resized. Possible values are 'bilinear' (0) and 'cubic' (1)
OUTPUTS:
The image extracted from the volume
MODIFICATION HISTORY:
Written by: MR, February 1999.
2001/03/15 Keyword Affine removed.
2001/03/22 Function derived from bm_image_process.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_imageprocess.pro)
NAME:
fBMT_ImportPixMap_ui
PURPOSE:
Import any pixmap (image) as a MDIO.
CATEGORY:
BMT
CALLING SEQUENCE:
__________________________________
INPUTS:
None.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2001/03/13 Calibration function implemented.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_loadpixmap_ui.pro)
NAME:
fBMT_Mean
PURPOSE:
Average data from a slice, a volume or from multiple volumes
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fBMT_Mean(Scan, [N1, N2], MeanOfScan = MeanOfScan, MeanOfVolume = MeanofVolume)
INPUTS:
Scan : Data to be averaged. Currently, this is not a MDI-Object
OPTIONAL INPUT PARAMETERS:
N1 : The first volume considered at multiple volume averaging
N2 : The last volume considered at multiple volume averaging
KEYWORD PARAMETERS:
MeanOfScan : Return the average of all data as a scalar
MeanOfVolume : Return the average of the volume denoted by number passed by the keyword.
Status : On exit, -1 is returned if an error has occurred, 1 on success
OUTPUTS:
Averaged data
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
Data from the first argument is averaged, according to the other parameters and
keywords passed to the function. Three modes od operation are implemented:
(1) Y = fBMT_Mean(X, n1, n2)
Average the volumes contained in X starting at n1 and ending at n2. Hence, the function
will return a volume with the same spatial resolution as the input data but with the 4th
dimension set to one.
(2) Y = fBMT(X, /MeanOfScan)
Simply return the mean of the whole data as a scalar value.
(3) Y = fBMT(X, MeanOfVolume = N)
Return the mean of volume N as a scalar value.
MODIFICATION HISTORY:
09.01.2001 Error handling implemented
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_mean.pro)
NAME:
fBMT_RoiStat
PURPOSE:
Calculate statistics of Rois defined for a scan
CATEGORY:
Analysis
CALLING SEQUENCE:
Y = fBMT_RoiStat(MDIO, Roi))
INPUTS:
MDIO: Scan-object
ROI: Roi-Object
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
Histogram: Histograms of the values of each Roi.
Range: Range of values considered for calculation.
ExcludeZero: Exclude all points whos values are zero from analysis.
OUTPUTS:
Array of structure, which containe the calculated values: It is defined as
{Region:"", Population:0, Mean:0.0, Median: 0.0, Stdev:0.0, Min:0.0, Max:0.0}
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
Calculations are performed using standard functions.
MODIFICATION HISTORY:
2001/01/23 Function derived from bm_roi_stat-function.
2001/02/13 Keyword SaveData added in order to store the generated tables on disc.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_roistat.pro)
NAME:
fBMT_ROITrace
PURPOSE:
Extract the longitudinal ROI-data from a scan. The scan should
contain more than one volume.
CATEGORY:
BMT
CALLING SEQUENCE:
Y = fBMT_RoiTrace(MDIO, ROI, Id)
INPUTS:
MDIO: Image data
ROI : ROI data (must have the same dimension as the image data
but may contain not more than one volume)
Id : Id of the region. It can be the number (e.g. 1, 2, ...)
or the name (e.g. "R1", which is defined by the
variable ROI.parameter1).
KEYWORD PARAMETERS:
Error: Contains the stdev of each data point if the region
contains more than two voxels.
Status: Exit status (1: ok, -1: error)
Exclude: value, which should be exluded from calculation of
the average.
OUTPUTS:
Array (length is number of volumes contained in MDIO)
containing the mean image data values of the region.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_roitrace.pro)
NAME:
fBMT_RoiTransfer
PURPOSE:
Transform a ROI, which was set for a scan to another. Scans can have different geometries and
orientations.
CATEGORY:
__________________________________
CALLING SEQUENCE:
__________________________________
INPUTS:
ROI: MDIO containing the ROI, which was loaded from disk or taken
from a different window.
MDIO: MDIO, to which the ROI should be transferred.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
Affine: Multiply a affine transformation matrix with the Geo-Matrix of the MDIO
Range: Truncate all ROIS, where pixel values of the scan, to which it is transferred
are not in the disered range.
RegridFactor: A factor, which allows to increase the
resolution of the scan. Values should be below 1.
OUTPUTS:
Volume containing the rois
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
The geometry parameters are taken from the two MDIO. They are used to transfer each voxel
of the ROI to the correct position in world space.
MODIFICATION HISTORY:
2000/02/13 Keyword "Range" added
2000/02/14 If Roi has only one slice, then translation in
third direction is inhibited. Additionally,
the ceil(.)-function is applied to the volume indices.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_roitransfer.pro)
NAME:
fBMT_ScanAlgebra
PURPOSE:
Perform basic calculations on a MDI-Object
CATEGORY:
Scan processing
CALLING SEQUENCE:
Y = fBMT_ScanAlgebra(MDIO, [Parameter1])
INPUTS:
MDIO: The scan object, on which calculations should be performed
OPTIONAL INPUT PARAMETERS:
Parameter1: An optional parameter, which is required for some operations
KEYWORD PARAMETERS:
LinearScaling: Every volume of the scan is devided by its mean and
therefore the global mean becomes 1.
SubractVolume: A volume (defined by Parameter1) is subracted from every
other volume.
SubtractSpecific: Subtract a specific volume from any of the others. Parameter1
should contain an array of indices of same length as the scan contains
volumes. If an entry of Parameter1 is -1, then no subtraction is
performed.
Magnitude: The magnitude of every volume is calculated.
Baseline: Subtract a global baseline value from each volume.
Invert: Invert the values of a scan.
Status: The exit status of the function.
OUTPUTS:
MDI-Object
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
Calculations are performed according to the keyword passed to the function.
MODIFICATION HISTORY:
2001/01/23 Parameters are not passed by the keyword; instead Parameter1 is used.
Imprint added.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_scanalgebra.pro)
NAME:
fBMT_SolidOvl
PURPOSE:
Create an overlay image of Image1 and Image2. Pixels that are visible from
Image2 completely hide the underlying pixels of Image1. Scaling of Image2
can be defined by using the keyword "Range". Image1 and 2 must be of same size.
CATEGORY:
Image display
CALLING SEQUENCE:
Y = fBMT_SolidOvl(Image1, Image2)
INPUTS:
__________________________________
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2000/02/15 Keyword "Thres" replaced by "Range". Scaling of Image1 was
replaced, since it should already be scaled. Scaling of
Image2 is performed only once.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_solidovl.pro)
NAME:
fBMT_SvdCompose
PURPOSE:
Use the spatial modes, temporal profiles and the singular vector
to restore the original time series data. The singular vector can
be modified by the keyword SMod in order to remove confounding
contributions to the data such as noise or other spectral
components.
CATEGORY:
Image processing
CALLING SEQUENCE:
Y = fBMT_SvdCompose(MDIO, [SMod = ....])
INPUTS:
WinIndex: Index to BRAINMAP window
OPTIONAL INPUT PARAMETERS:
None
KEYWORD PARAMETERS:
SMod: Array, with number of entries equal to the number of
spatial modes calculated.
OUTPUTS:
The restored (and modiefied) time series data.
COMMON BLOCKS:
None
SIDE EFFECTS:
None
RESTRICTIONS:
Can only be used if Brainmap was started. No parameter consistency
checks are performed.
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_svdcompose.pro)
NAME:
fBMT_TransparentOvl
PURPOSE:
Use two indexed images an combine them as an rgb image
CATEGORY:
Imaging
CALLING SEQUENCE:
__________________________________
INPUTS:
Image1/2: Two images which have to scaled from 0 to 256
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fbmt_transparentovl.pro)
NAME:
pBMT_CopyScanToWindow
PURPOSE:
Copy data from source window or file to a target window.
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_CopyScanToWindow, MyMDIO, Source, WinIndex
INPUTS:
Scan : MDIO, which contains the source data
Source : Index of window, from where the scan is copied (-1=no
source)
WinIndex: Index of window, to which the scan should be copied
(-1=copy to file). The filename must be defined in
MDIO.ScanFilename. If the keyword LABEL is
specified, it is used as the filename, while the
path is taken from MDIO.ScanFilename.
KEYWORD PARAMETERS:
__________________________________
COMMON BLOCKS:
inf
MODIFICATION HISTORY:
2001/03/26 Keyword "OverwritePointer" implemented
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_copyscantowindow.pro)
NAME:
PBMT_CREATEHELP
PURPOSE:
Given a list of IDL procedure files (.PRO), VMS text library
files (.TLB), or directories that contain such files, this procedure
generates a file in the HTML format that contains the documentation
for those routines that contain a DOC_LIBRARY style documentation
template. The output file is compatible with World Wide Web browsers.
CATEGORY:
Help, documentation.
CALLING SEQUENCE:
PLIB_CREATEHELP, Sources, Outfile
INPUTS:
Sources: A string or string array containing the name(s) of the
.pro or .tlb files (or the names of directories containing
such files) for which help is desired. If a source file is
a VMS text library, it must include the .TLB file extension.
If a source file is an IDL procedure, it must include the .PRO
file extension. All other source files are assumed to be
directories.
Outfile: The name of the output file which will be generated.
KEYWORDS:
TITLE: If present, a string which supplies the name that
should appear as the Document Title for the help.
VERBOSE: Normally, PLIB_CREATEHELP does its work silently.
Setting this keyword to a non-zero value causes the procedure
to issue informational messages that indicate what it
is currently doing. !QUIET must be 0 for these messages
to appear.
STRICT: If this keyword is set to a non-zero value, PLIB_CREATEHELP will
adhere strictly to the HTML format by scanning the
the document headers for characters that are reserved in
HTML (<,>,&,"). These are then converted to the appropriate
HTML syntax in the output file. By default, this keyword
is set to zero (to allow for faster processing).
COMMON BLOCKS:
None.
SIDE EFFECTS:
A help file with the name given by the Outfile argument is
created.
RESTRICTIONS:
The following rules must be followed in formatting the .pro
files that are to be searched.
(a) The first line of the documentation block contains
only the characters ";+", starting in column 1.
(b) There must be a line which contains the string "NAME:",
which is immediately followed by a line containing the
name of the procedure or function being described in
that documentation block. If this NAME field is not
present, the name of the source file will be used.
(c) The last line of the documentation block contains
only the characters ";-", starting in column 1.
(d) Every other line in the documentation block contains
a ";" in column 1.
Note that a single .pro file can contain multiple procedures and/or
functions, each with their own documentation blocks. If it is desired
to have "invisible" routines in a file, i.e. routines which are only
for internal use and should not appear in the help file, simply leave
out the ";+" and ";-" lines in the documentation block for those
routines.
No reformatting of the documentation is done.
MODIFICATION HISTORY:
July 5, 1995, DD, RSI. Original version.
July 13, 1995, Mark Rivers, University of Chicago. Added support for
multiple source directories and multiple documentation
headers per .pro file.
July 17, 1995, DD, RSI. Added code to alphabetize the subjects;
At the end of each description block in the HTML file,
added a reference to the source .pro file.
July 18, 1995, DD, RSI. Added STRICT keyword to handle angle brackets.
July 19, 1995, DD, RSI. Updated STRICT to handle & and ".
Changed calling sequence to accept .pro filenames, .tlb
text librarie names, and/or directory names.
Added code to set default subject to name of file if NAME
field is not present in the doc header.
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_createhelp.pro)
NAME:
pBMT_MTR_ui
PURPOSE:
Calculate the magnetization transfer ratio from a scan with an
scan without MTS-preperation. Input data is selected from the
common BioMAP data pool.
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_MTR_ui
OUTPUTS:
The result is stored in the selected window.
COMMON BLOCKS:
Inf
MODIFICATION HISTORY:
2002/12/11 Values lower than 0 will be removed.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_mtr_ui.pro)
NAME:
pBMT_Plot_ui
PURPOSE:
Plot profiles, spects, ACFs, etc. of a point or ROI and provide a graphical interface.
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_Plot_ui, Data
INPUTS:
Data: Structure of the form
{x:fltarr(n), y: fltarr(n,m), err:fltarr(n,m)}
MODIFICATION HISTORY:
2001/02/16 Psym-Keyword removed from pBMT_Plotxy. Symbols are now generated
within the function. XY coordinates will be displayed.
2001/02/19 wDraw is directly used for printing. Before it was event.top+1
2001/02/26 An option is provided, that allows to select the evolution by a click
with the left mouse button.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_plot_ui.pro)
NAME:
pBMT_ReadParameter
PURPOSE:
Read values of a given structure from a file. The file has
a name that is derived from the name of the structure or the
filame supplied as a keyword.
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_ReadParameter, StructName
INPUTS:
StructName: Name of the structure
KEYWORD PARAMETERS:
File: Name of file to be read.
MODIFICATION HISTORY:
2003/01/07 Function fBMT_ProcessTracing() replaced by keyword
"Verbose". The procedure can now be called independently from BioMAP.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_readparameter.pro)
NAME:
pBMT_RoiLoad
PURPOSE:
Provide a file dialog box and load a ROI-Volume from disk.
CATEGORY:
ROI Analysis
CALLING SEQUENCE:
pBMT_RoiLoad
INPUTS:
None.
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
None.
OUTPUTS:
None
COMMON BLOCKS:
Inf
SIDE EFFECTS:
None.
RESTRICTIONS:
Brainmap must be initialized.
PROCEDURE:
A ROI-volume is loaded from disk and stored in the current window. If the geomtery
of the stored ROI and the scan in the current window is different, spatial transformations
are applied.
MODIFICATION HISTORY:
2001/02/16 The DIM-field of the ROI is modiefied to have the same dimensions as the scan.
2001/03/02 Geometry parameters will be copied from the
scan to the Roi.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_roiload.pro)
NAME:
pBMT_WriteParameter
PURPOSE:
Write values from a given structure to a file. The file has
a name that is derived from the name of the structure, which
is STRUCTURENAMErc. The procedure writes the file to the
directory of the scan. Note that only arrys with a length of
less than 512 elements will be written to the file.
CATEGORY:
BMT
CALLING SEQUENCE:
pBMT_WriteParameter, StructName
INPUTS:
StructName: Structure containing the data.
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
File: Write data to file with the name "file".
Stdout: Write to the console (for debugging purposes)
NoPointer: Do not write contents of pointer variables.
OUTPUTS:
__________________________________
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pbmt_writeparameter.pro)
NAME:
fLIB_ColorTranslate
PURPOSE:
Create a true color image from an indexed image and a color table;
the third index is corresponding to one of the RGB-channels.
CATEGORY:
__________________________________
CALLING SEQUENCE:
__________________________________
INPUTS:
IMAGE: Image data scaled from 0 to 255
OPTIONAL INPUT PARAMETERS:
CT : Index of a colortable
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
True color image
COMMON BLOCKS:
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/flib_colortranslate.pro)
NAME:
CURVEFIT
PURPOSE:
Non-linear least squares fit to a function of an arbitrary
number of parameters. The function may be any non-linear
function. If available, partial derivatives can be calculated by
the user function, else this routine will estimate partial derivatives
with a forward difference approximation.
CATEGORY:
E2 - Curve and Surface Fitting.
CALLING SEQUENCE:
Result = CURVEFIT(X, Y, Weights, A, SIGMA, FUNCTION_NAME = name, $
ITMAX=ITMAX, ITER=ITER, TOL=TOL, /NODERIVATIVE)
INPUTS:
X: A row vector of independent variables. This routine does
not manipulate or use values in X, it simply passes X
to the user-written function.
Y: A row vector containing the dependent variable.
Weights: A row vector of weights, the same length as Y.
For no weighting,
Weights(i) = 1.0.
For instrumental (Gaussian) weighting,
Weights(i)=1.0/sigma(i)^2
For statistical (Poisson) weighting,
Weights(i) = 1.0/y(i), etc.
A: A vector, with as many elements as the number of terms, that
contains the initial estimate for each parameter. IF A is double-
precision, calculations are performed in double precision,
otherwise they are performed in single precision. Fitted parameters
are returned in A.
KEYWORDS:
FUNCTION_NAME: The name of the function (actually, a procedure) to
fit. IF omitted, "FUNCT" is used. The procedure must be written as
described under RESTRICTIONS, below.
ITMAX: Maximum number of iterations. Default = 20.
ITER: The actual number of iterations which were performed
TOL: The convergence tolerance. The routine returns when the
relative decrease in chi-squared is less than TOL in an
interation. Default = 1.e-3.
CHI2: The value of chi-squared on exit (obselete)
CHISQ: The value of reduced chi-squared on exit
NODERIVATIVE: IF this keyword is set THEN the user procedure will not
be requested to provide partial derivatives. The partial
derivatives will be estimated in CURVEFIT using forward
differences. IF analytical derivatives are available they
should always be used.
STATUS: Is 1 if estimation converged and -1 else
SILENT: Do not send messages
OUTPUTS:
Returns a vector of calculated values.
A: A vector of parameters containing fit.
OPTIONAL OUTPUT PARAMETERS:
Sigma: A vector of standard deviations for the parameters in A.
COMMON BLOCKS:
NONE.
SIDE EFFECTS:
None.
RESTRICTIONS:
The function to be fit must be defined and called FUNCT,
unless the FUNCTION_NAME keyword is supplied. This function,
(actually written as a procedure) must accept values of
X (the independent variable), and A (the fitted function's
parameter values), and return F (the function's value at
X), and PDER (a 2D array of partial derivatives).
For an example, see FUNCT in the IDL User's Libaray.
A call to FUNCT is entered as:
FUNCT, X, A, F, PDER
where:
X = Variable passed into CURVEFIT. It is the job of the user-written
function to interpret this variable.
A = Vector of NTERMS function parameters, input.
F = Vector of NPOINT values of function, y(i) = funct(x), output.
PDER = Array, (NPOINT, NTERMS), of partial derivatives of funct.
PDER(I,J) = DErivative of function at ith point with
respect to jth parameter. Optional output parameter.
PDER should not be calculated IF the parameter is not
supplied in call. IF the /NODERIVATIVE keyword is set in the
call to CURVEFIT THEN the user routine will never need to
calculate PDER.
PROCEDURE:
Copied from "CURFIT", least squares fit to a non-linear
function, pages 237-239, Bevington, Data Reduction and Error
Analysis for the Physical Sciences. This is adapted from:
Marquardt, "An Algorithm for Least-Squares Estimation of Nonlinear
Parameters", J. Soc. Ind. Appl. Math., Vol 11, no. 2, pp. 431-441,
June, 1963.
"This method is the Gradient-expansion algorithm which
combines the best features of the gradient search with
the method of linearizing the fitting function."
Iterations are performed until the chi square changes by
only TOL or until ITMAX iterations have been performed.
The initial guess of the parameter values should be
as close to the actual values as possible or the solution
may not converge.
EXAMPLE: Fit a function of the form f(x) = a * exp(b*x) + c to
sample pairs contained in x and y.
In this example, a=a(0), b=a(1) and c=a(2).
The partials are easily computed symbolicaly:
df/da = exp(b*x), df/db = a * x * exp(b*x), and df/dc = 1.0
Here is the user-written procedure to return F(x) and
the partials, given x:
pro gfunct, x, a, f, pder ; Function + partials
bx = exp(a(1) * x)
f= a(0) * bx + a(2) ;Evaluate the function
IF N_PARAMS() ge 4 THEN $ ;Return partials?
pder= [[bx], [a(0) * x * bx], [replicate(1.0, N_ELEMENTS(f))]]
end
x=findgen(10) ;Define indep & dep variables.
y=[12.0, 11.0,10.2,9.4,8.7,8.1,7.5,6.9,6.5,6.1]
Weights=1.0/y ;Weights
a=[10.0,-0.1,2.0] ;Initial guess
yfit=curvefit(x,y,Weights,a,sigma,function_name='gfunct')
print, 'Function parameters: ', a
print, yfit
end
MODIFICATION HISTORY:
Written, DMS, RSI, September, 1982.
Does not iterate IF the first guess is good. DMS, Oct, 1990.
Added CALL_PROCEDURE to make the function's name a parameter.
(Nov 1990)
12/14/92 - modified to reflect the changes in the 1991
edition of Bevington (eq. II-27) (jiy-suggested by CreaSo)
Mark Rivers, U of Chicago, Feb. 12, 1995
- Added following keywords: ITMAX, ITER, TOL, CHI2, NODERIVATIVE
These make the routine much more generally useful.
- Removed Oct. 1990 modification so the routine does one iteration
even IF first guess is good. Required to get meaningful output
for errors.
- Added forward difference derivative calculations required for
NODERIVATIVE keyword.
- Fixed a bug: PDER was passed to user's procedure on first call,
but was not defined. Thus, user's procedure might not calculate
it, but the result was THEN used.
Steve Penton, RSI, June 1996.
- Changed SIGMAA to SIGMA to be consistant with other fitting
routines.
- Changed CHI2 to CHISQ to be consistant with other fitting
routines.
- Changed W to Weights to be consistant with other fitting
routines.
_ Updated docs regarding weighing.
Martin Rausch, 1999
- status keyword added
- silent keyword added
(See /usr/people/ivm/rauscma1/programs/biomap/source/flib_curvefit.pro)
NAME:
fLIB_Gauss
PURPOSE:
Calculate a values of gauss-function.
CATEGORY:
LIB
CALLING SEQUENCE:
Y=fLIB_Gauss(x, Center, FWHM)
INPUTS:
x : Scalar or array containing the x-values.
Center: Center of the curve
FWHM : Full width half maximum
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/flib_gauss.pro)
NAME:
fLIB_ReadAffineTrans
PURPOSE:
Read an affine transformation matrix from disk. If opening
fails an unit matrix is returned.
CATEGORY:
File I/O
CALLING SEQUENCE:
Affine = fLIB_ReadAffine(filename)
INPUTS:
Filename: The name of the scan. This is used
to generate the name of the output file.
OUTPUTS:
Affine : A 12-parameter set from which an affine transformation
matrix can be created: [tx,ty,tz, ax,ay,az, sx,sy,sy, a1,a2,a3]
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2001/03/22 Length of input vector corrected to 9 elements.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/flib_readaffinetrans.pro)
NAME:
SEARCH3D
PURPOSE:
This function finds "objects" or regions of similar data
values within a 3-D array of data. Given a starting location
and a range of values to search for, SEARCH3D will find all
the cells within the volume that are within the specified range
of values, and have some path of connectivity through these cells
to the starting location. In addition to searching for cells
within a global range of data values, SEARCH3D can also search
for adjacent cells whose values deviate from their neighbors within
specified tolerances. See the procedure "SEARCH2D" for the
two dimensional case.
This function returns a list of the array subscripts that define
the selected object or region.
CATEGORY:
Data subsetting.
Volume manipulation.
CALLING SEQUENCE:
Region = SEARCH3D(Array, Xpos, Ypos, Zpos, Min_val, Max_val)
INPUTS:
Array: The 3-D volume of data to search.
Data type : Any 3-D array except string or structure.
Xpos: The X coordinate (first subscript into the 3-D Array)
of the starting cell for the search.
Data type : Long.
Ypos: The Y coordinate (second subscript into the 3-D Array)
of the starting cell for the search.
Data type : Long.
Zpos: The Z coordinate (third subscript into the 3-D Array)
of the starting cell for the search.
Data type : Long.
Min_val: The minimum data value to search for. All cells that
are connected to the starting cell, and have a value
greater than or equal to Min_val and less that or equal
to Max_val, will be considered part of the "object".
Max_val: The maximum data value to search for.
KEYWORD PARAMETERS:
DECREASE: If the DECREASE or INCREASE keywords are specified,
then SEARCH3D creates an internal copy of Array.
This internal copy is then processed to enhance the
object edges by using an algorithm similar to the
"SOBEL" edge enhancement process (in 3-D). Any
adjacent cells will be found if their corresponding
data value in the edge enhanced array is greater
than DECREASE and less than INCREASE. In any case,
the adjacent cells will NEVER be selected if their
data value is not between Min_val and Max_val.
The default is 0.0 if INCREASE is specified.
Otherwise, the default is no edge checking.
Data type : Int or Float (usually less than zero).
INCREASE: The maximum value in the edge enhanced array for
a cell to be considered part of the selected object.
Some savings in execution time and memory usage result
when DECREASE and INCREASE are omitted.
See DECREASE above.
The default is 0.0 if DECREASE is specified.
Otherwise, the default is no edge checking.
Data type : Int or Float (usually greater than zero).
LPF_BAND: This keyword indicates what (if any) Low Pass Filtering
is performed on the edge enhanced array before the
search begins. If LPF_BAND is set to 3 or higher
then the edge enhanced array will be smoothed using
LPF_BAND as the width of the smoothing window.
If LPF_BAND is less than 3 then no smoothing is
performed. This keyword only has effect when the
DECREASE or INCREASE keywords are supplied.
See DECREASE above.
The default is zero (no smoothing).
Data type : Int.
DIAGONAL: Normally, cells are considered adjacent only when
cubes surrounding the cells share a common face.
If a non-zero value is passed to DIAGONAL then
SEARCH3D will also locate cells meeting the search
criteria whose surrounding cubes share a common
edge or corner. Specifying diagonal search mode
requires more memory and execution time.
The default is no diagonal searching.
Data type : int
OUTPUTS:
This function returns a list of the indices into the 3-D array
that are part of the located object or region. This list is
returned as a LONARR(n) where n is the number of cells found.
If the returned array of indices is called Region, and the
size of the 3-D volume of data is size_x by size_y by size_z,
then the actual X, Y, and Z indices can be obtained by using
the following algorithm :
index_z = Region / (size_x * size_y)
index_y = (Region - (index_z * size_x * size_y)) / size_x
index_x = (Region - (index_z * size_x * size_y)) - (index_y * size_x)
The object within the 3-D Array could then be subscripted as :
Array(Region)
OR
Array(index_x, index_y, index_z)
EXAMPLE:
Find all the indices corresponding to an object contained in a
3-D volume of data.
; Create some data.
vol = RANDOMU(s, 40, 40, 40)
vol(3:13, 1:15, 17:33) = 1.3
vol(15:25, 5:25, 15:25) = 0.2
vol(5:30,17:38,7:28) = 1.3
vol(9:23, 16:27, 7:33) = 1.5
; Search for an object starting at (6, 22, 16) whose data values
; are between (1.2) and (1.4)..
Region = SEARCH3D(vol, 6, 22, 16, 1.2, 1.4, /DIAGONAL)
; Scale the background cells into the range 0 to 127.
vol = BYTSCL(vol, TOP=127B)
; Highlight the object region by setting it to 255.
vol(Region) = 255B
; Set up a 3-D view.
Window, 0, Xsize=640, Ysize=512, Retain=2
Create_View, Xmax=39, Ymax=39, Zmax=39, ax=(-30), az=30, zoom=0.8
; Display the volume with the highlighted object in it.
TVSCL, PROJECT_VOL(vol, 64, 64, 40, Depth_Q=0.4)
MODIFICATION HISTORY:
Written by: Daniel Carr. Thu Sep 3 17:36:04 MDT 1992
(See /usr/people/ivm/rauscma1/programs/biomap/source/flib_search3d.pro)
NAME: PLIB_IMAGECONT PURPOSE: Overlay an image and a contour plot. CATEGORY: General graphics. CALLING SEQUENCE: PLIB_IMAGECONT, A, B INPUTS: A: The two-dimensional array to display as a contour B: The two-dimensional array to display as a image KEYWORD PARAMETERS: WINDOW_SCALE: Set this keyword to scale the window size to the image size. Otherwise, the image size is scaled to the window size. This keyword is ignored when outputting to devices with scalable pixels (e.g., PostScript). ASPECT: Set this keyword to retain the image's aspect ratio. Square pixels are assumed. If WINDOW_SCALE is set, the aspect ratio is automatically retained. INTERP: If this keyword is set, bilinear interpolation is used if the image is resized. OUTPUTS: No explicit outputs. COMMON BLOCKS: None. SIDE EFFECTS: The currently selected display is affected. RESTRICTIONS: None. PROCEDURE: If the device has scalable pixels, then the image is written over the plot window. MODIFICATION HISTORY: DMS, May, 1988.
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_imagecont.pro)
NAME:
pLIB_ImagePlot
PURPOSE:
Overlay an image and a contour plot.
CATEGORY:
General graphics.
CALLING SEQUENCE:
IMAGE_CONT, A
INPUTS:
A: The two-dimensional array to display.
KEYWORD PARAMETERS:
WINDOW_SCALE: Set this keyword to scale the window size to the image size.
Otherwise, the image size is scaled to the window size.
This keyword is ignored when outputting to devices with
scalable pixels (e.g., PostScript).
ASPECT: Set this keyword to retain the image's aspect ratio.
Square pixels are assumed. If WINDOW_SCALE is set, the
aspect ratio is automatically retained.
INTERPolate: If this keyword is set, bilinear interpolation is used if
the image is resized.
BACKGROUND: Background color
Color: Color of text
XRANGE: A two-element-vector, which defines the _Annotation_ on the x-axis.
It does not affect the output
of the image.
POSITION: [x0, y0, x1, y1]
OUTPUTS:
No explicit outputs.
COMMON BLOCKS:
None.
SIDE EFFECTS:
The currently selected display is affected.
RESTRICTIONS:
None.
PROCEDURE:
If the device has scalable pixels, then the image is written over
the plot window.
MODIFICATION HISTORY:
DMS, May, 1988.
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_imageplot.pro)
NAME:
pLIB_MatrixSize
PURPOSE:
Obtain size, dimension and type from an array with maximum of 4 dimensions
CATEGORY:
Standard Library
CALLING SEQUENCE:
pLIB_MatrixSize, M, xs, ys, zs, n, dim = dim, type = type
INPUTS:
M: Matrix
OPTIONAL INPUT PARAMETERS:
xs, ys, zs, n
KEYWORD PARAMETERS:
Dim: Dimensionality of the scan
Type: Type of the scan
0 Undefined
1 Byte
2 Integer
3 Longword integer
4 Floating point
5 Double-precision floating
6 Complex floating
7 String
8 Structure
9 Double-precision complex
10 Pointer
11 Object reference
12 Unsigned Integer
13 Unsigned Longword Integer
14 64-bit Integer
15 Unsigned 64-bit Integer
OUTPUTS:
None.
COMMON BLOCKS:
None.
SIDE EFFECTS:
None
RESTRICTIONS:
Dimensions larger then 4 are not considered
PROCEDURE:
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_matrixsize.pro)
NAME:
PLIB_OPLOTERR
PURPOSE:
Overplot data points with accompanying error bars.
CATEGORY:
Plotting, 2-dimensional.
CALLING SEQUENCE:
PLIB_OPLOTERR, [ X ,] Y , Err [, Psym ], Color = Color
INPUTS:
Y: The array of Y values.
Err: The array of error bar values.
OPTIONAL INPUT PARAMETERS:
X: An optional array of X values. The procedure checks whether
or not the third parameter passed is a vector to decide if X
was passed.
If X is not passed, then INDGEN(N_ELEMENTS(Y)) is assumed for
the X values.
PSYM: The plotting symbol to use (default = +7).
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
Arrays cannot be of type string. There must be enough points to
plot.
PROCEDURE:
A plot of X versus Y with error bars drawn from Y - ERR to Y + ERR
is written to the output device over any plot already there.
MODIFICATION HISTORY:
William Thompson Applied Research Corporation
July, 1986 8201 Corporate Drive
Landover, MD 20785
kdb, March, 1997 - Fixed a problem if 1 element arrays where used.
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_oploterr.pro)
NAME:
pLIB_WriteAffine
PURPOSE:
Write a affine transformation matrix to disk
CATEGORY:
File I/O
CALLING SEQUENCE:
pLIB_WriteAffine, filename
INPUTS:
Filename: The name of the scan. This is used
to generate the name of the output file.
Affine : 4x4 affine transformation matrix, which can
be created with fLIB_CreateAffine()
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
A file with the name .afn
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_writeaffine.pro)
NAME:
pLIB_WriteAffineTrans
PURPOSE:
Write a affine transformation matrix to disk
CATEGORY:
File I/O
CALLING SEQUENCE:
pLIB_WriteAffine, filename
INPUTS:
Filename: The name of the scan. This is used
to generate the name of the output file.
Affine : 12-parameter set to create an affine transformation
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
A file with the name .aft
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2000/02/13 Dialog for overwriting added, if keyword is selected.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_writeaffinetrans.pro)
NAME:
pLIB_WriteList.StructArray, Filename
PURPOSE:
Write data from a structure to a file.
CATEGORY:
LIB
CALLING SEQUENCE:
__________________________________
INPUTS:
Array of structures
KEYWORD PARAMETERS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/plib_writelist.pro)
NAME:
fFTB_BaselineCorrection
PURPOSE:
Perform a baseline correction on a given vector of non-complex numbers.
CATEGORY:
Filter Tool Box
CALLING SEQUENCE:
Y = fFTB_BaselineCorrection(Y, BlCorr)
INPUTS:
Y : Vector of real numbers.
BlCorr : Structure providing the parameters to be used.
OUTPUTS:
Array of baseline corrected values
PROCEDURE:
The baseline will be determined by a procedure (selected by
the mode tag of the structure BlCorr, which can be created by the
function fFTB_CreateBlCorrCls()
Mode 1: The 1st derivative of Y is calculated. Each point,
where the derivative is less then BlCorr.DerivThres
is used as basepoint for interpolation.
Mode11: This method uses the same approach as mode
1. Additionally, a potential basepoint is removed if
the derivative exceeds BlCorr.DerivThres within an
intervall given by BlCorr.MinFlatPoints.
Mode12: Linear ramp going from the value at BlCorr.DisplayMin
to the value at BlCorr.DisplayMax
Mode13: Exactly as 1, but points are considered, for which the
1st derivative is larger than BlCorr.DerivThres,
This mode can detect ramps.
Mode 2: The 2nd derivative of Y is calculated. Each point,
where the 2nd derivative is less then BlCorr.Deriv2Thres
is used as basepoint for interpolation.
Mode 3: This mode is a combination of Mode 1 and Mode 2. The
second derivative of a valid point must be larger than
a given threshold (maximums of peaks have to be
excluded) and the absolute value of the first
derivative must be less than a given
threshold. Additionally, the minimum distance of two
basepoints is BlCorr.MinRasterDistance $
and points which are too near will be
removed. Finally, points will be inserted for
interpolation if the distance between two
points is too large, as defined by
BlCorr.MaxRasterDistance (if MaxRasterDistance not
equal 0). Below an example is for a typical parameter
setting is shown:
MODE = 3
ACTIVE = 0
LOWPASS = 0.00200000
DERIVTHRES = 0.0200000
DERIV2THRES = 0.00200000
MINFLATPOINTS = 5
MAXRASTERDISTANCE = 0
DISPLAYFLAG = 0
DISPLAYMIN = 0
DISPLAYMAX = 9517
OFFSET = 0
The baseline detection creates a vector of pairs of (x1, y1). The baseline will be interpolated at these points.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fftb_baselinecorrection.pro)
NAME:
fFTB_Close
PURPOSE:
Performs a morphological closing operation on a set of
images. Morphological closing is performed on each slice
seperately.
CATEGORY:
FTB
CALLING SEQUENCE:
Y = fFTB_Close(Image, [/Gray])
INPUTS:
An image data with up to 4 dimensions. The first two
dimensions are expected to encode the slice.
KEYWORD PARAMETERS:
Gray: Perform closing on a gray scale image
SrtuctSize: Size of the area, which will "closed". The default
is three.
Status: Set this keyword to a named variable that will
contain -1 or 1 dependent on the success of the operation.
OUTPUTS:
Array of the same dimension as the input data.
COMMON BLOCKS:
None.
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fftb_close.pro)
NAME:
fFTB_Convol
PURPOSE:
Apply a digital filter to a 1-dimensional array. The filter is
a structure defined by fFTB_CreateFilter(). The input array
and the filter kernel are convolved using the built in function.
If the filter is not defined, then the signal is returned.
CATEGORY:
Filter Tool Box
CALLING SEQUENCE:
Y = fFTB_Convol(X, Filter, Status)
INPUTS:
X : A 1-dimensional array
Filter : structure containing the information about the filter
defined by fFTB_CreateFilter()
OPTIONAL INPUT PARAMETERS:
Status : Exit status of the function (1 = success, -1 = error)
KEYWORD PARAMETERS:
None
OUTPUTS:
Filtered arry
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fftb_convol.pro)
NAME:
fFTB_CreateFilter
PURPOSE:
Create a structur, which defines a digital filter
CATEGORY:
Signal processing
CALLING SEQUENCE:
sFilter = fFTB_CreateFilter()
INPUTS:
None.
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
Type: Defines the method used for filtering; 1 means fft-type, 0 means convol-type
fLOW: Lowest frequency, which will pass the filter
fHigh: Highest frequency, which will pass the filter
active: The filter can be made active by setting this keyword to 1
fSize: The size of the filter kernel. Only applicable to
filters of convol-type.
Res: Relative resolution of the image to be filtered. Res
is an array containing three elements.
For 2D-inplane isotropic filtering it is
[1,1,0]
For 2D-inplane anisotropic filtering it is
[res_x,res_y,0] / max ([res_x,res_y,0])
For 3D-filtering it is
[res_x,res_y,res_z] / max([res_x,res_y,res_z])
OUTPUTS:
Structure, containing the filter parameters.
COMMON BLOCKS:
None.
SIDE EFFECTS:
None
RESTRICTIONS:
None.
MODIFICATION HISTORY:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fftb_createfilter.pro)
NAME:
fASL_AddSuffix
PURPOSE:
Add a suffix the the filename of a scan.
CATEGORY:
ASL
CALLING SEQUENCE:
Y = fASL_AddSuffix(Filename, Suffix)
INPUTS:
Filename: Filename of the scan (e.g. MDIO.ScanFilename)
Suffix: The Suffix to be added (e.g. _dtr.img). The
extension ".img" will be added if not supplied.
OUTPUTS:
The new filename
(See /usr/people/ivm/rauscma1/programs/biomap/source/fasl_addsuffix.pro)
NAME:
fASL_CheckResultSubject
PURPOSE:
Check if a folder with the name "Result" exists for a
data set, which was stored under the name "Filename". The
filename must be conform to the folder structure of BioMAP's
ANALYZE+-database. The "Result"-Subject can be created and
used for specific projects as a container for results from
multi-subject-analysis.
CATEGORY:
ASL
CALLING SEQUENCE:
Y = fASL_CheckResultSubject(Filename)
INPUTS:
Filename: Filename of a MDIO, which was already stored in the database.
KEYWORD PARAMETERS:
Create: Create the folder, in case that it does not exist.
ResultFolder: On exit, this variable will contain the name of
the result folder.
OUTPUTS:
The function will return 1, if the folder exists or was
created and -1, if it does not exist or if the filename was
not valid.
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fasl_checkresultsubject.pro)
NAME:
fASL_GetLabel
PURPOSE:
Extract the basic scan name of the filename of a MDIO.
CATEGORY:
ASL
CALLING SEQUENCE:
Y = fASL_GetLabel(ScanFilename)
INPUTS:
ScanFilename: String containing the name of the img-file.
OUTPUTS:
Scanfilename without path, suffix or index
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fasl_getlabel.pro)
NAME:
fASL_ReadAnalyze_ui
PURPOSE:
Provide a file dialog box and load an ANALYZE volume from disk.
CATEGORY:
__________________________________
CALLING SEQUENCE:
__________________________________
INPUTS:
__________________________________
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2001/02/16 The dialog box appears centered on the brainmap window.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fasl_readanalyze_ui.pro)
NAME:
fASL_CreateSubject
PURPOSE:
Create folder for a new subject.
CATEGORY:
ASL
CALLING SEQUENCE:
pASL_CreateSubject, ProjectName, [FolderName]
INPUTS:
FolderName: If ommited a name will be generate from the system
time.
KEYWORD PARAMETERS:
Folderpath: On exit, this variable will contain the name of
the result folder.
MODIFICATION HISTORY:
__________________________________
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pasl_createsubject.pro)
NAME:
pASL_DataManager
PURPOSE:
Load, store and manager all data sets and associated data.
CATEGORY:
ASL
CALLING SEQUENCE:
pASL_DataManager, RootFolder
INPUTS:
RootFolder: Name of folder, which contains project folders
COMMON BLOCKS:
None.
MODIFICATION HISTORY:
2001/02/14 After saving, the source-field of the MDIO is set to ANALYZE. This
will indicate that the scan now a copy of the scan exists in ANALYZE
format, which allows further processing.
2001/03/23 A check for session and project definition is performed before saving
(See /usr/people/ivm/rauscma1/programs/biomap/source/pasl_datamanager.pro)
NAME:
pASL_ReadDat
PURPOSE:
Read a dat-file, which is associated to an ANALYZE-scan from disk.
CATEGORY:
ASL
CALLING SEQUENCE:
pASL_ReadDat, Filename, Header, verbose = Verbose, KeepSuffix
= KeepSuffix, Status = Status
INPUTS:
__________________________________
OPTIONAL INPUT PARAMETERS:
__________________________________
KEYWORD PARAMETERS:
__________________________________
OUTPUTS:
__________________________________
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
if Vox(2) is 0 then it is set to 1.0 mm, in order to allow overlaying.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pasl_readdat.pro)
NAME:
pASL_WriteAnalyze
PURPOSE:
Write a volume or a series of volumes (a scan) to a file.
CATEGORY:
ASL
CALLING SEQUENCE:
pASL_WriteAnalyze, MyFilename, MDIO
INPUTS:
Filename: Name of the file (including the suffix, e.g. .img)
MDIO : Scan to written do file
KEYWORD PARAMETERS:
VE: Store images in ANALYZE VE format. In this case the whole scan in written to
one file.
Force: Overwrite files without query.
Access: Set the write access flags:
"u": Only the owner can modify the data set
"g": The group and the owner can modify the data set
"o": Every one can modify the data set
These flags can only be set to "no access" manually.
Status: Returns the status of the function on exit (-1=failed,
1=ok)
MODIFICATION HISTORY:
2001/02/19 Writing long (type 8) volumes implemented.
2001/02/27 Error handler implemented.
2001/03/02 Affine transformation parameters are always written to disk.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/pasl_writeanalyze.pro)
NAME:
fPWI_BloodVolumeChange
PURPOSE:
Calculate the percent blood volume change of a CTC from a pre contrast scan,
a post contrast scan and the CTC time series. This function is usefull to
analyze functional imaging data, where USPIO or SPIO were infused before
the experiment to visualize functional activation.
CATEGORY:
Perfusion analysis
CALLING SEQUENCE:
Y = fPWI_BloodVolumeChange(PreScan, PostScan, CTC)
INPUTS:
PreScan: MDIO of size (xs,ys,zs,1)
PostScan: MDIO of size (xs,ys,zs,1)
CTC: MDIO of size (xs,ys,zs,n)
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
Range: Voxel values of the PostScan to be included into analysis.
Atten: On exit, this keyword contains the attenuation map,
which was calculated from the pre- and post-contrast scans.
Status: Status of the calculation (-1: error; 1: success)
OUTPUTS:
MDIO, containing the result of the calculation. If the calculation has failed,
-1 is returned.
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
MODIFICATION HISTORY:
2000/02/14 Function created.
2000/02/15 Status keyword and input checks added.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fpwi_bloodvolumechange.pro)
NAME:
fPWI_CTC
PURPOSE:
Calculate the concentration time curve from dynamic imaging
data. The raw data can be a T1- or T2 weighted scan and must
be defined by the keyword Contrast. If this keyword is not
provided, T2/T2*-weighting is used as default.
CATEGORY:
PWI
CALLING SEQUENCE:
Y = fPWI_CTC(MDIO, Threshold, n1, n2, last)
INPUTS:
MDIO : Scan containing the raw data.
Threshold: Minimum voxel value, for which the CTC will be
calculated. The threshold will be applied to the
mean of the baseline-volumes. In addition, only
those voxels will be considered, were there is at
least one volume with signal exceeds 10% of the
threshold.
N1: First Baseline volume. Volumes before N1 will be
disregarded (e.g. signal not in steady state).
N2: Last baseline volume.
Last: Last volume to be included into analysis.
KEYWORD PARAMETERS:
SpatialFilter : Spatial filter of the form created by
fFTB_CreateFilter()
TemporalFilter: Spatial filter of the form created by
fFTB_CreateFilter()
Contrast: 0: For T2- or T2*-weighted scans using the relation
-ln(S/Baseline)
1: For T1-weighted scans using the 1st order
approximation S / Baseline -1.
OUTPUTS:
Array of the form (xs,ys,zs,n) containing the result of the analysis.
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fpwi_ctc.pro)
NAME:
fPWI_gpdf_atd
PURPOSE:
Return a Gamma-Probability-Density function, defined by three parameters
CATEGORY:
Functions for PWI and fMRI
CALLING SEQUENCE:
Y = fPWI_GpDF_atd(t, AM, PT, SH)
INPUTS:
t: Time for which the function should be calculated. Can be a scalar or an array
AM: Amplitude
PT: Peak time
SH: Sharpness
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
None.
OUTPUTS:
The value calculated by the function
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
The parameter a discribes somehow the dispersion of the curve. Small values indicate large
width and vice versa. Beside that the dispersion depends on the center of the peak m. For larger
m the dispersion increases slightly.
MODIFICATION HISTORY:
REQUIREMENTS & BUGS
SRK
(See /usr/people/ivm/rauscma1/programs/biomap/source/fpwi_gpdf_atd.pro)
NAME:
fPWI_Map
PURPOSE:
Calculate basic parametric maps from dynamic imaging data
using contrast agent.
CATEGORY:
PWI
CALLING SEQUENCE:
Y = fPWI_Map(MDIO, N1, N2, TE, Threshold)
INPUTS:
MDIO: Scan to be processed.
N1: First Baseline volume. Volumes before N1 will be
disregarded (e.g. signal not in steady state).
N2: Last baseline volume.
TE: Array of echo times. Echo time must be specified
for each individual slice. Its length must be equal
to the number of slices.
Threshold: Minimum voxel value, for which the CTC will be
calculated. The threshold will be applied to the
mean of the baseline-volumes. In addition, only
those voxels will be considered, were there is at
least one volume with signal exceeds 10% of the
threshold.
KEYWORD PARAMETERS:
The following keywords spcify the type of map, which will be calculated.
CTC: concentration-time-curve. It can be either
calculated from T2- or T2*-weighted scan or from a
T1-weighted scan.
Note: If the scan is T2/T2*-weighted a scaling factor of 100/TE will be applied.
CBV: CBV (integral between N2 and Last.
TTP: Time to peak.
CPeak: Peak concentration.
MSD: Maximum signal drop.
MTT: Mean transit time (calculated from the first moment
of the CTC; N2 is taken as t=0)
Other keywords:
Last: Last volume to be considered for analysis.
Contrast: T2 or T2* weighting = 0 (default)
T1 weighting = 1
VAT: Volume acquisition time. This parameter is used when
calculating time related parameter maps
(e.g. TTP). If VAT is not defined, 1 sec is used as default.
OUTPUTS:
MDIO, containing the calculated map
MODIFICATION HISTORY:
2001/02/20 Function bm_pwi renamed to fPWI_Map;
Keyword "CMT1" defined.
2002/12/06 Keyword VAT implemented.
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fpwi_map.pro)
NAME:
fSTAT_SampleSize
PURPOSE:
Calculate the number of samples required to achieve the
desired sensitivity. The relation calculates the group size
with respect to a two-sided test.
CATEGORY:
STAT
CALLING SEQUENCE:
N = fSTAT_SampleSize(ExpDiffMeans, ExpStdev, Power, Alpha)
INPUTS:
ExpDiffMeans: Expected difference in means. This is the
difference, which should be detected.
ExpStdev: Expected standard deviation
Power: The power, which is a value between 0 and
1. The power reflects the sensitivity of the
test, which is not to miss a true difference in
the means of the group.
Alpha: Probability to reject H_0, although it is true.
OUTPUTS:
Group size
MODIFICATION HISTORY:
Last Modification:
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fstat_samplesize.pro)
NAME:
fSTAT_SolveGlm
PURPOSE:
Calculate parameter estimates for factors described by a
design matrix according to the "General Linear Model". If no
input was provided test data will be used to validate the
calculations.
Note: Results of the example should be according to the
software STATGRAPHICS:
Number of factors : 3
Number of samples : 8
Degrees of freedom : 5
Parameter estimates:
[6335.51, -23.7486, 150.306]
Standard error for b's:
[2942.95, 12.8955, 112.070]
t-value for b's:
[2.15277, -1.84161, 1.34117]
CATEGORY:
STAT
CALLING SEQUENCE:
Result = fSTAT_SolveGLM(X, Y)
INPUTS:
X: 2-dimensional design matrix of the form
(Number of samples, Number of factors)
Y: 1-dimensional matrix containing the measurements
KEYWORD PARAMETERS:
P: Projection matrix. These allow to make inferences about the
differences between several factors. The number of
elements along the first index must be equal to the
number of factors. The second index corresponds to
the number of projections to be calculated.
KeepData: Calculations performed on X are stored in a common
block. If this keyword is set this calculations will
not be performed again but data is taken from the
common block. This helps to save computation time if
large design matrices have to be processed.
Verbose: Print the result of the calculation
OUTPUTS:
Structure containing the results:
NFactors: Number of factors
NSamples: Number of samples
Estimate: Parameter estimates
SError : Standard error for every estimate
t : T-value for every estimate
tp : T-value for linear combinations of factors
(projections)
MODIFICATION HISTORY:
Last Modification: 23.10.2002
REQUIREMENTS & BUGS
(See /usr/people/ivm/rauscma1/programs/biomap/source/fstat_solveglm.pro)
NAME:
fWID_GetValues
PURPOSE:
Create a widget, which provides basic input fields. Additionally, an info
field can be created and a window or device for output can be selected.
The input fields can contain either strings or numbers. But types can't
be mixed. If no type is specified, input fields will contain integers.
CATEGORY:
Widget
CALLING SEQUENCE:
Y = fWID_GetValues(VarNames, InitialValues, string = string, Int = Int, Status = Status, $
Title = Title, Info = Info, Device = Device, Reference = Reference
INPUTS:
VarNames : String array containing the names of the input fields
OPTIONAL INPUT PARAMETERS:
InitialValues : Array of same length as VarNames, which contains the initial values
KEYWORD PARAMETERS:
Int : Values are interpreted as integers
Float : Values are interpreted as floats
String : Values are interpreted as strings
Title : String containing the title to be displayd
Info : String to be displayed at the bottom of the widget
Device : The variable (must be non-zero) contains the selected device on exit.
-1 : File;
0,...,NWindows: Window device
OUTPUTS:
Array containing the new values of the input fields.
COMMON BLOCKS:
None.
SIDE EFFECTS:
__________________________________
RESTRICTIONS:
__________________________________
PROCEDURE:
__________________________________
MODIFICATION HISTORY:
2002/12/11 Parameters xoffset and yoffset removed.
Floating-keyword applied if group_leader is defined.
REQUIREMENTS & BUGS
SRK ______________________________
(See /usr/people/ivm/rauscma1/programs/biomap/source/fwid_getvalues.pro)
NAME: FWID_INPUT PURPOSE: This widget cluster function manages a data entry field widget. The field consists of a label and a text widget. FLIB_XINPUT's can be string fields, integer fields or floating-point fields. The default is an editable string field. CATEGORY: Widget Clusters. CALLING SEQUENCE: Result = FLIB_INPUT(Parent) INPUTS: Parent: The widget ID of the widget to be the field's parent. KEYWORD PARAMETERS: TITLE: A string containing the text to be used as the label for the field. The default is "Input Field:". VALUE: The initial value in the text widget. This value is automatically converted to the type set by the STRING, INTEGER, and FLOATING keywords described below. UVALUE: A user value to assign to the field cluster. This value can be of any type. FRAME: The width, in pixels, of a frame to be drawn around the entire field cluster. The default is no frame. RETURN_EVENTS: Set this keyword to make cluster return an event when ais pressed in a text field. The default is not to return events. Note that the value of the text field is always returned when the WIDGET_CONTROL, field, GET_VALUE=X command is used. ALL_EVENTS: Like RETURN_EVENTS but return an event whenever the contents of a text field have changed. COLUMN: Set this keyword to center the label above the text field. The default is to position the label to the left of the text field. ROW: Set this keyword to position the label to the left of the text field. This is the default. XSIZE: An explicit horizontal size (in characters) for the text input area. The default is to let the window manager size the widget. Using the XSIZE keyword is not recommended. YSIZE: An explicit vertical size (in lines) for the text input area. The default is 1. STRING: Set this keyword to have the field accept only string values. Numbers entered in the field are converted to their string equivalents. This is the default. FLOATING: Set this keyword to have the field accept only floating-point values. Any number or string entered is converted to its floating-point equivalent. INTEGER: Set this keyword to have the field accept only integer values. Any number or string entered is converted to its integer equivalent (using FIX). For example, if 12.5 is entered in this type of field, it is converted to 12. LONG: Set this keyword to have the field accept only long integer values. Any number or string entered is converted to its long integer equivalent (using LONG). FONT: A string containing the name of the X Windows font to use for the TITLE of the field. FIELDFONT: A string containing the name of the X Windows font to use for the TEXT part of the field. NOEDIT: Normally, the value in the text field can be edited. Set this keyword to make the field non-editable. OUTPUTS: This function returns the widget ID of the newly-created cluster. COMMON BLOCKS: None. PROCEDURE: Create the widgets, set up the appropriate event handlers, and return the widget ID of the newly-created cluster. EXAMPLE: The code below creates a main base with a field cluster attached to it. The cluster accepts string input, has the title "Name:", and has a frame around it: base = WIDGET_BASE() field = FLIB_XINPUT(base, TITLE="Name:", /FRAME) WIDGET_CONTROL, base, /REALIZE MODIFICATION HISTORY: Written by: Keith R. Crosley June 1992 KRC, January 1993 -- Added support for LONG integers. AB, 7 April 1993, Removed state caching. JWG, August 1993, Completely rewritten to make use of improved TEXT widget functionality ACY, 25 March, 1994, fix usage of FRAME keyword KDB, May 1994, Initial value =0 would result in a null text field. Fixed keyword check.
(See /usr/people/ivm/rauscma1/programs/biomap/source/fwid_input.pro)
NAME:
fWID_Editvalues
PURPOSE:
Create a widget, which provides basic input fields. Additionally, an info
field can be created and a window or device for output can be selected.
The input fields can contain either strings or numbers. But types can't
be mixed. If no type is specified, input fields will contain integers.
CATEGORY:
Widget
CALLING SEQUENCE:
Y = fWID_Editvalues(VarNames, InitialValues, string = string, Int = Int, Status = Status, $
Title = Title, Info = Info, Device = Device, Reference = Reference
INPUTS:
VarNames : String array containing the names of the input fields
OPTIONAL INPUT PARAMETERS:
InitialValues : Array of same length as VarNames, which contains the initial values
KEYWORD PARAMETERS:
Int : Values are interpreted as integers
Float : Values are interpreted as floats
String : Values are interpreted as strings
Title : String containing the title to be displayd
Info : String to be displayed at the bottom of the widget
Device : The variable (must be non-zero) contains the selected device on exit.
-1 : File;
0,...,NWindows: Window device
OUTPUTS:
Array containing the new values of the input fields.
COMMON BLOCKS:
None.
(See /usr/people/ivm/rauscma1/programs/biomap/source/pwid_editvalues.pro)