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This is a new page, and we will be adding to this knowledge base of commonly asked questions about Slicer Dicer. Please write to us at info@slicerdicer.com if you would like to see a specific question addressed here.

Q 1.  To use Slicer Dicer, do I need to convert my data to the HDF or netCDF format?

Q 2.  Should I convert my data to the HDF or netCDF format? What tools are available?

Q 3.  Can I read multiple-slice image files to assemble a volume in Slicer Dicer?

Q 4.  What kinds of data can be used with Slicer Dicer?

Q 5.  My downloaded Demo file won't run; what's wrong?

Q 6.  Why do I get a .DLL file missing error message when trying to install the downloaded Slicer Dicer Demo?

Q 7.  How do I import ASCII or generic binary data?

Q 8.  Why do I get a "Corrupt Installer" error message when installing or running Slicer Dicer?

Q 9.  How do I apply my name and key to unlock the v5 Demo?

 

Q 1.  To use Slicer Dicer, do I need to convert my data to the HDF or netCDF format?

A 1: No. Slicer Dicer will read almost any file containing array data. (See Question 4.) Many users have ad hoc file formats, possibly with headers containing ancillary data. In the Slicer Dicer User's Guide, such files are referred to as generic format files. When one of these files is opened, you will use the Generic File dialog to supply information about the format. This information includes the data type (text, 8-bit, 16-bit, 32-bit integer, float, or double), number of dimensions, sizes of each dimension, and the sizes of any header or footer sections that may be associated with the file or with any dimension. Headers and footers are measured in bytes for a binary (unformatted) file and in lines for a text (formatted) file.

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Q 2.  Should I convert my data to the HDF or netCDF format? What tools are available?

A 2: Although you don't need to have your data in one of these formats to use Slicer Dicer, they do offer convenience advantages. They are designed to be general-purpose formats appropriate for many scientific applications. The key advantages are cross-platform portability (e.g., data written on a supercomputer is readable on a PC) and self-description. The latter means that useful information about the data, often referred to as metadata, is stored with the data. Slicer Dicer will detect and read the metadata and set up coordinates and import transformations automatically. The user can concentrate on data interpretation, not file bookkeeping details.

C and Fortran libraries and utilities for dealing with these formats are available for all commonly used platforms. Support is provided on the Web at the NCSA HDF and Unidata sites.

Of course if you have data in any one of several other standard formats supported by Slicer Dicer (e.g., DICOM, Analyze 7.5, Surfer Grid, TIFF, JPG, BMP, etc.) you will get the same advantages as offered by the general-purpose formats, HDF and netCDF, and there is no need to consider converting your data.

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Q 3.  Can I read multiple-slice image files to assemble a volume in Slicer Dicer?

A 3: Yes. It is easy to read multiple-file data sets. This includes not only image files, but all file types. You could, for example, import a 4D data set consisting of a series of 3D netCDF files.

All you have to do is have the files together in one directory. The file names must be identical except of a numeric field. In the Slicer Dicer Open dialog, select "Open multiple-file data set." Slicer Dicer will automatically detect and open all files satisfying the naming rule.

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Q 4.  What kinds of data can be used with Slicer Dicer?

A 4: Slicer Dicer is designed for data defined on regular, rectangular grids. Such data take the form of n-dimensional Cartesian arrays. The illustration below depicts a regular, rectangular grid.

Regular Grid

The numbers, Nx, Ny, and Nz, defining the size of the grid, are arbitrary, as are the dimensions, dx, dy, and dz, of each grid element. Note that although a grid element can have any shape (dx, dy, and dz can be unequal), grid regularity requires that all elements within the grid be identical in size, i.e., dx is the same for all elements, dy is the same for all elements, etc.

Most commonly, these data sets are three-dimensional, but Slicer Dicer can also be used with 2-d data sets (e.g. image data) and with data defined in four or more dimensions. In the latter case, the user will select a subset of three dimensions to be treated spatially, for visualization purposes, while the other dimensions become parameters with selected values. A parameter dimension can also be used to animate a "sliced and diced" visualization of the volume defined by the spatial dimensions.

Gridded data are very common in science and technology. For example, in environmental studies, a numerical model might be used to predict the distribution of a pollutant in a particular volume. The solution data will be in the form of a 3-d array, representing the pollutant density field. The HDF and netCDF file formats are commonly used to store data of this type. Slicer Dicer recognizes these and many other standard formats (e.g., DICOM, Surfer Grid, TIFF, JPG, BMP, etc.) and uses the metadata stored with the data to determine the grid dimensions. Slicer Dicer will also read non-standard formats but will query the user for the grid dimensions. (See Input Data for a list of the file formats recognized by Slicer Dicer.)

In cryogenics, a specimen can be frozen and then sliced along a series of equally spaced, parallel planes. Each slice can be imaged digitally and saved as a TIFF image (or BMP, DICOM, Analyze 7.5, or other image format). This is an example of a multi-file data set. Although each image is two-dimensional, taken together the entire sequence constitutes a 3-d array. Slicer Dicer has a convenient facility for importing data in this form.

Not all volume data fit into this scheme. Data defined on unstructured grids, which often take the form of tables with X-Y-Z-Value columns, cannot be directly visualized with Slicer Dicer.  Measured geologic, ocean, or atmospheric data often are of this form.  In order to use Slicer Dicer with these data it is necessary to resample them onto a regular grid. (Of course, the fact that a data set is in X-Y-Z-Value form doesn't necessarily imply that the grid is unstructured. If the underlying grid satisfies our regularity requirements, these data can be directly read and visualized with Slicer Dicer.)

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Q 5.  My downloaded Demo file won't install;  what's wrong?

A 5: Check the size of the downloaded file. Slicer_Dicer_52_104.exe should be 8,827,619 bytes.  If  not, either download it again or e-mail your mailing address to us (info@slicerdicer.com) so we can mail you a Demo CD.

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Q 6.  Why do I get a .DLL file missing error message when trying to install the downloaded Slicer Dicer Demo?

A 6: If you get a .DLL file missing error message when trying to install or run the demo, you may have a corrupted file.  Check the downloaded Slicer_Dicer_v52_104.exe file size.  It should be 8,827,619 bytes. If it is not, either download it again or e-mail your mailing address to us (info@slicerdicer.com) so we can mail you a Demo CD.

If the downloaded file size is correct, your windows installation probably is missing a required DLL.  Please e-mail our tech support (support@slicerdicer.com) the details, including the name(s) of the missing files.

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Q 7.  How do I import generic ASCII or binary data?

A 7: Importing generic ASCII or binary data into Slicer Dicer can be confusing the first time around. The main thing to remember is that Slicer Dicer imports data only, NOT coordinate values. It requires that data be evenly gridded; for example, if you had 
spatial data in a 3-dimensional xyz volume, the delta-x intervals have to be the same throughout the volume, as do the delta-y and delta-z intervals (though they can be different from each other). There must be a data value for each (x,y,z) location.  (See Question 4 for a detailed description of gridded data.)

Slicer Dicer needs to know the number of dimensions, and the size of each one. This information is input by the user during the process of loading a generic file. If the data are in an ASCII file, they are then read in order, from left to right, one line after another from top to bottom, and assigned an (x,y,z) location based on the assumption the first dimension (x, in this case) varies slowest, and the last dimension (z) varies fastest. If the data are in a binary file, the number of bytes read per data value is determined by a user-selectable data-type.

For example, say we have a data set that is x=2 by y=3 by z=4 in size. This means we would have 2*3*4 = 24 total data values to be loaded. If we wanted the (x,y,z) data locations to be assigned properly, the data would need to be ordered such that the first 4 values corresponded to the locations (x=1, y=1, z=1,2,3,4). The next 4 values would need to correspond to the locations (x=1 ,y=2, z=1,2,3,4). The next 4 values would need to corresponded to the locations (x=1, y=3, z=1,2,3,4). The ordering would continue in a similar fashion to fill the rest of the 3D grid. Note that the number of rows and columns of an ASCII data file itself are not constrained by these dimensions. There could be 6 rows of 4 values each, 2 rows of 12 values each, and so on, as long as there were a total of 24 values in the proper order.

If the generic data to be imported are on an irregular grid, they will need to be interpolated to a regular grid prior to loading into Slicer Dicer. We hope to add the capability of importing irregularly gridded data to Slicer Dicer in the future.

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Q 8.  Why do I get a "Corrupt Installer" error message when installing or running Slicer Dicer?

A 8: When installing Slicer Dicer or the Demo version, on a Windows NT, 2000, XP, Vista or Win 7 or Win 8 computer, one must be the administrator or a user with administrative privileges.  If the software is installed without administrative privileges, this "Corrupt Installer" error message will result.  The remedy is to log in as administrator before installing the software, or to have your network administrator install the software.

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Q 9.  How do I apply my name and key to unlock the v5 Demo?

To unlock the Demo (to the remove the timelock) you must have a Name and Key combination, such as:

John Smith
0000KU-XYXZP0-XHW2X6-2DHD4X-J98C59-EA7Y25-FGW2H2

The Name and Key must be entered (cut and paste, or typed) exactly as provided to you on your order confirmation page or in the email sent to you.

When you run the demo version of Slicer Dicer v5, it opens with a Reminder Window.  Press "Enter Key" and paste in (or type) the Name and the Key in the appropriate boxes.  You may also enter the Name and Key while Slicer Dicer is running by selecting Help/Register from the top menu.

 


 

 

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