RCBF Analysis using MATLAB and EMMA
Two-compartment regional cerebral blood flow (RCBF) analysis is very
easy to perform using MATLAB and the EMMA toolkit. The
rcbfanalysis function allows the specification of the MINC
file containing the study to analyze, the name of the MINC file to
write the K1 images to, the name of the MINC file to write the V0
image to, and the slices to analyze. Warning: if the K1 file or V0
file already exist, they will be overwritten, destroying any data that
they may contain. Therefore, to analyze the dynamic PET data
stored in the file
produce both a K1 image and a V0 image for all 15 slices, we would
'yates_K1.mnc', 'yates_V0.mnc', 1:15);
The resulting files yates_K1.mnc and yates_V0.mnc
will be written in the current directory.
If only a K1 image is desired, we can specify an empty matrix for
the name of the V0 file:
'yates_K1.mnc', , 1:15);
The same is true if we only want a V0 image file produced:
, 'yates_V0.mnc', 1:15);
Layers of the Onion
The rcbfanalysis function performs its analysis by calling
the EMMA rcbf2 function. This function may also be called by
the user, if it is more convenient to get the K1, k2, or V0 images
without having to produce MINC files for them. The rcbf2
function is very easy to use. Simply specify the name of the MINC
file containing the study to analyze, and the slice numbers to
analyze. The function returns the K1, k2, and V0 images, as well as
the blood delay correction for each slice analyzed:
[K1,k2,V0,delta] = rcbf2(...
This call to rcbf2 will analyze slice eight of the
yates_19445 study, producing K1, k2, and V0 images, as well
as the calculated delta for this slice. The images returned are
stored as EMMA standard vector images, and may be manipulated in the
same way as any EMMA image.
One final point to consider. The study being analyzed must
contain the blood data as well as the PET images. There are several
programs that are capable of doing this, the most important of which
is scxtominc, which creates MINC files from the Scanditronix
format files produced by the PET scanner. This program has a
-bloodfile option which allows the specification of a blood
file whose data should be included in the final MINC file. The blood
file specified must be in BNC (Blood netCDF) format, and is
produced by the blood lab computer and written to $PC_BLOOD. A BNC
file may also be created from a CNT file using the bloodtonc
program. Assuming that we wish to create a MINC file from the raw
images and the BNC file, we might specify a command line to
scxtominc that looks like:
scxtominc -bloodfile $PC_BLOOD/soos_034157.bnc $PC_IMAGE/pcsoos______-dynamic___034157*.ima soos_34157.mnc
This creates a MINC file called soos_34157.mnc from the raw
images and the BNC file.
It is also possible to include blood data in an existing MINC file
using the includeblood program. Simply specify the name of
the MINC file, and the name of the BNC file to include within it.
For more information on RCBF analysis, please see the documentation.
For more information on the EMMA toolkit, please see the documentation.
This page was created by Mark Wolforth