Common questions and answers
About program execution
Q: How do I run the software on PC/Windows? When I click the program icon,
I see only a flashing window and nothing else happens.
A: Most software are designed to run on all platforms (PC and SUN, MS Windows,
Solaris, and Linux). Therefore the user-interface is very simple, and they must be
operated from command line.
S: Open the "Command prompt" window. On Windows XP it is found in
Start > Programs > Accessories > Command Prompt. If used frequently,
make a shortcut (Send to Desktop). Then you can write the program name threre
and press Enter.
Q: I am working on my PC/Windows and try to run the software in command
prompt window. It prints an error message "'XXX' is not recognized as an
internal or external command, operable program or batch file."
A: You have not installed that program on your PC. In PET Centre and hospital network
the software are automatically installed, but if they are not, then contact the IT group.
S: Outside PET Centre you have to
download and
install
the software by yourself.
Q: I am working on my PC/Windows and try to run a program in command
prompt window. The program does not work as the instructions say that it should do.
A: Check that you have the correct software version. Run the
program with command-line option -v, and check that the version matches
with the number that you can see in the documentation and in your analysis
instructions. Check also again that you have given correct command line parameters.
S: Download and install the latest version from
http://www.turkupetcentre.net/programs/
or
http://www.turkupetcentre.net/software/
or, in TPC, enter the command with appropriate program version, e.g.
imgflow_0_8_3.
Q: Can I run the analysis programs in Linux?
A: Yes, although most software is not yet compiled for Linux. In future,
all software will be compiled and available for download for PC/Linux instead
of Sun/Solaris.
S: Compiling the C codes is easier in Linux than in Windows.
No modification of source codes or makefiles is necessary. Please see the
instructions for SW development in TPC. Inside Turku PET Centre, the PC/Linux
executables are located in /pet-storage/petsoftware/bin/linux/
Q: Why do I get an "Exec format error"?
A: You are trying to run a command on a SUN workstation with a SunOS or Solaris
operating system version that is different to the one on which the program was
compiled.
S: Either run the program on another workstation with newer Solaris version, or
compile the program again on your workstation.
Q: Can I use the software on Windows NT?
A: Probably yes, but there may be problem with user-interfaces, because on Windows NT
the maximium command line length is 128 characters. Another problem with DOS is the
filename length. It can only be 8 characters long plus 3 characters for the suffix.
PET data filenames also frequently contain more than one dot, which may not be
handled correctly in Windows NT.
S: Move the datafiles to directories that are closer to the root (eg. C:\temp), or
use Windows 2000 or XP, since they should not have the same problem with command
line lengths.
Q: Can I use the software in Windows Vista?
A: So far we have found no problems in using our software in Windows Vista.
S: If you run into problems, then contact the PET center IT group, or write
a software bug report in intranet.
Q: I get a nasty Windows error message when I try to run a .NET 2.0 program
before it even starts.
A: Your computer may be set up to prevent running programs from network.
S: Give this command as administrator (modifying the path if necessary) to
increase the permissions:
C:\"WINDOWS\Microsoft.NET\Framework\v2.0.50727"\CasPol.exe -quiet -m -cg 1.2. FullTrust.
About Excel
Q1: When importing data files into Excel, the decimal values are not read
correctly. Why?
Q2: When saving numerical data from Excel, the decimal separator is comma.
Is that a problem?
A: Windows software is, by default, using local
decimal separator,
which is comma in Finland, Germany, France and Italy, and point in UK, USA and
Japan. In-house software is mainly assuming decimal points.
S1: Change the
decimal
separator from comma to dot in Windows or in Excel.
S2: Use the latest versions of
dft2html or
dft2html
to convert data files into XHTML table format and import those in Excel.
Q: When importing result files / ROI TAC files into Excel, the data is not aligned
in columns, and cannot be used in formulas.
A: When you import a .res or .dft file directly into Excel, it reads the contents
as text into one spreadsheet column.
S: Convert the data files to XHTML table format using
dft2html or
dft2html
and import those in Excel.
About analysis software
Q1: I try to make a sum image, but I get an error "in integration".
Q2: I try to calculate a parametric image, but I get an error "cannot interpolate input
data".
A: You have a problem with your dynamic PET image. Most common reasons are that some frames are missing
check that image file size is the same as in other studies, or that there is a problem with frame
times.
S: If image is of wrong size, then get a new copy of it.
You can correct the frame time problem by yourself.
Q: Usually program just does what it is intended and quits, but sometimes
program prints on screen a lot of stuff?
A: You have unintentionally ran the program in its test mode. Lots of printing
on screen may even slow down the program.
S: Do not use the string 'test' in output filenames or other arguments for the
program.
Q: The MRI images look strange, the lowest part of patient head are located
above the head. Is there a problem in DICOM files or format conversion?
A: There is no problem in programs or image files. This is a common artefact
in MRI, called aliasing or wrap-around.
S: This artefact can not be corrected after the MRI scan. Show the images
to MRI physicist, because the artefact can be reduced in the future MR scans.
Q: Results from HR+ or PET-CT are orders of magnitude higher than they should be.
A: Check that the units of radioactivity (kBq/ml, Bq/ml) are the same in your
input data (plasma and blood) and in image/regional TAC data.
S: Follow the instructions in
http://www.turkupetcentre.net/analysis/doc/calibration.html.
Q: I try to run program on Windows 2000/XP, but get an error message "The
system cannot execute the specified program".
A: Programs are compiled with MinGW or DJGPP, and Windows 2000/XP does not
always treat these programs correctly.
S: Try to avoid very long filenames and deeply nested directories.
Alternatively, you can write the command into an ASCII text file and execute it
using program execlong.
About Imadeus
Q: "Floating point division by zero" error when reading Analyze 7.5 image
A: Analyze image may be in 32-bit format.
S: Convert image to 16-bit data using Matlab program ana32to16.
Scripts / batch files
Q: How to make a script?
A:
http://www.turkupetcentre.net/analysis/batch_info.html#how
Q: How to call blood input scripts from my own scripts?
A: You have to use cscript engine to execute WSH scripts and you have to
enter full path to the VBScript file.
S: For example, cscript P:\bin\windows\PK11195_input.vbs ...
