The BatchTool Generator automates the process of assembling HiSPECT batch-mode files for SPECT data sets in which identical reconstruction parameters are desired.
SPECT reconstruction data sets are sent to the BatchTool Generator from the Data Browser. After highlighting a group of SPECT data sets in the browser, right-click and select "Send to BatchTool" to open the BatchTool Generator.
The tool automates the process of assembling HiSPECT batch-mode files for SPECT data sets in which identical reconstruction parameters are desired. This function is especially valuable for studies in which multiple SPECT data sets are rapidly acquired, such as dynamic imaging and cardiac-gated imaging.
After loading the data sets, the reconstruction options may be set using the fields arrayed across the top of the tool.
The fields in the BatchTool Generator include:
|Noise Suppression (inter-iteration smoothing)||
Sets the amount of smoothing applied during the reconstruction
(after each sub-iteration), where "High" indicates more
smoothing and thus higher noise suppresion.
It is advised to use lower smoothing when reconstructing proections with good statistics. Otherwise, the underlying MLEM algorithm will overexpress noise in the image data. The Gaussian smoothing kernel is applied as a FWHM of the given ratio to the voxel size.
|Low, Medium, High|
|Resolution (voxel size)||Sets the aperture-dependent reconstructed voxel size, where
"Fine" indicates smaller voxels, requires higher statistics in the projections (counts)
and leads to longer reconstruction times.
Values are given relative to the default voxel size of the aperture, e.g. 0.4 mm for aperture 1 (standard mouse) and 0.6 mm for aperture 2 (standard rat).
|Fast, Standard, Fine|
|Reconstruction parameter (number of iterations)||Sets the sequence of iterations and subset sizes used by the reconstruction
algorithm, where "Fine" indicates more iterations and requires
longer processing time. Longer reconstructions do not necessarily lead to better
image quality, since the underlying MLEM algorithm will in later iterations only increase
the noise in the image data.
The sequence consists of comma separated groups, each stating the number of iterations and the subset size (e.g. 6x4,7x8 means 6 iterations with subset size of 4 followed by 7 iterations with 8 projections per subset). The special subset size '*' (asterisk) can be used to choose subset sizes of 5, 6 or 7, which ever best fits to the number of projections.
|Fast, Standard, Fine|
|Advanced Options||Provides access to the application of various smoothing and post-processing procedures. It is highly recommended that these settings be left at their default value.||Quantification Factor (has to be disabled for quantification calibrations), Projection Smoothing (using Noise suppression parameter above), Volumetric Smoothing (using Noise suppresion parameter above), Resolution Recovery (model detector blur into point-spread function)|
|Description Placeholders||The reconstruction descriptions (placed in the "Series" field) may be manually entered or may be in parts automatically set using these shortcuts. Lower-case letters will produce an abbreviated version of the information represented by the placeholder.||For a complete description, please see below.|
|Default Description||The reconstruction descriptions (placed in the "Series" field) may be filled simultaneously from this field which can contain simple text or the description placeholders described above. The Set All button will fill the "Series" field in the reconstruction according to the text/placeholders in the description.||Set All: Update all description fields, overwriting existing values.|
The same reconstruction parameters are used for each data set. The individual reconstruction names (represented by the highlighted "Series" field) may be entered manually for each reconstruction or all set simultaneously using the "Set All" button in the Default Description field described above. The Default Description may be simply text, or may contain information pertinent to each reconstruction through use of the Description Placeholders. These shortcuts allow the automatic naming of each reconstruction to include a variety of useful information. Use of a lower-case letter results in an abbreviated form of the information (i.e., "Standard" becomes "Std").Description Placeholders include:
|%N||Noise Suppression Setting: Low, Medium, High, N40%|
|%n||Noise Suppression Setting: Lo, Med, Hi, 40|
|%R||Resolution Setting: Fast, Standard, Standard, R110.0%|
|%r||Resolution Setting: Fast, Std, Std, 110.0|
|%I||Reconstruction Parameter Setting (Iterations): Fast, Standard, Standard, I6x*|
|%i||Reconstruction Parameter Setting (Iterations): Fast, Std, Std, I6x*|
|%Q||Quantification Factor: Quant, NoQuant|
|%q||Quantification Factor: Qnt, NQnt|
|%D||Date & Time: YYYYMMDD HHMMSS|
|%V||Voxel size: 0.40 mm|
|%v||Voxel size: 0.40|
|%L||Row number: 001|
|%l||Row number: 1|
|%F||Number of frames: 48frames|
|%f||Number of frames: 48|
A couple of examples of automatic series descriptions are shown below.
After setting the reconstruction parameters and default descriptions (reconstruction names), the "Save Batch" button is used to save a .bmf file used for SPECT batch jobs. If the "Start BatchTool" checkbox is clicked, the reconstructions will begin processing immediately. If not, the .bmf file will be saved and the reconstructions may be started at a more convenient time, by calling the HiSPECT Batch Mode Tool.