Quick Guide to InVivoScope/VivoQuant CT/NM Atlas Tools

Transcription

1 Pre- Clinical Imaging Software and Services I. Load Data Quick Guide to InVivoScope/VivoQuant CT/NM Atlas Tools Each run of the CT/NM atlas tool operates on a single CT image and at least one NM dataset. The tool will automatically process all provided NM data sets. If data are loaded prior to running the tool, these preloaded datasets will automatically be used. If no data are loaded when the tool is called, a dialog will appear allowing the user to make a selection dynamically; this option is ideal for very large datasets. Supported data types include DICOM, mhd/raw and Inveon hdr/img. Loading data from the DICOM browser.

2 Loading mhd/raw data. III. Start the Tool A. Go to Tools Segmentation Tools Atlas NM/CT Analysis (screenshot above). If data were loaded prior to starting to the tool, move on to Step B. Otherwise, make selections for the desired CT and NM/PT data using the window that appears.

3 B. Select options: once you have selected the Atlas NM/CT Analysis segmentation tool, a window will appear. 1. Output folder : Path to the directory where the results of the atlas analysis will be stored. Use the '...' button to the right of this field to browse the file system for the output folder. 2. Pre- registration : choose Already done if the CT and NM images are already registered, choose Quick Translation to perform a fast registration using only translation, or choose Full 3D to perform a registration using both translation and rotation. In most cases, a Quick Translation will be sufficient for aligning unregistered images.

4 3. Cropping : It is important for the images to be cropped for fast and accurate atlas fits. Choose Already done if the input data have been cropped tightly around the skull. Choose Automatic to enable automated cropping. In most cases, it will not hurt to choose Automatic cropping, even if the images are already cropped. In cases where automatic cropping is failing (or to be particularly safe) the cursor/crosshair must be placed in the center of the skull prior to opening the Atlas NM/CT Analysis window. In the Cropping drop- down menu, choose Manual. The skull will be cropped based on the center point provided. 4. Method : To fit the brain atlas to the input data without altering the data, choose Fit atlas to data. The alternative method, Fit data to atlas manipulates the data to best fit the provided atlas. See the Appendix for a fuller explanation of these options. 5. Atlas : the base atlas, typically species- specific (e.g., rat or mouse). 6. Key : The key specifies a mapping of the brain atlas regions to a subset of those regions. Select All to use every region in the selected atlas. See the Creating New Atlas Keys companion guide for instructions on setting up custom mappings for use with the Atlas NM/CT Analysis tool.

5 Patlak Analysis (Optional) Enabling the Advanced options will expand additional selections available for performing Patlak analyses on time- series data. 1. Input Curve File : Click the button to make a selection of input curve file. Input curves must be provided as a.csv file in a specific format. There must be a minimum of two columns, where the first column lists times in units of minutes, and the remaining columns list concentrations in units of uci/mm^3 (one column per input curve). The first row must contain headers. Part of an example input curve file is shown below. It is important to ensure that the units are correct in this file.

6 2. Patlak (min) : Use the arrows to specify the time points to be considered in the Patlak analysis by selecting the time (in minutes) of the first time point to be used. To include all time points, set this value to 0. The time points before the time specified here will be excluded from the Patlak analysis. Other Advanced Options 1. Dual Animal : Use the dropdown menu to select the animal to be processed: None if there is only one animal in the image, Left/anterior to process the animal on the left or anterior side of a dual animal image, or Right/posterior to process the animal on the right or posterior side of a dual animal image. Use the checkboxes to specify the orientation of the second animal with respect to the first: L/R for a left/right flip, A/P for an anterior/posterior flip, or U/D for a head/feet (up/down) flip. Once all selections are made (including advanced Patlak options, if applicable), click OK. The window will show status messages in the Progress section while the program is running (example shown below). If a pre- registration method has been selected, a separate small window will appear for the duration of the registration. Once the program is complete, a dialog will appear indicating completion.

7 II. Review Your Results A. The VivoQuant display: once the program has completed, the output images will be loaded into the data manager. If the Fit atlas to data method was selected, the loaded output includes the fitted atlas loaded as Input 1 with a special color palette that assigns distinct colors for each atlas region; the NM datasets are loaded in the remaining inputs, and the CT is still loaded as reference. If the Fit data to atlas method was selected, the loaded output includes the processed CT loaded as reference, the atlas loaded as Input 1, and the processed NM data loaded in the remaining inputs.

8 a) Fit atlas to data original CT and fitted atlas. b) Fit data to atlas manipulated CT and atlas. Additionally, a file data.csv will open once the program has completed. (To change the program that data.csv opens in, change the default program for *.csv files in the Windows settings.) This file contains statistics regarding the fitted atlas. This file must be closed prior to running the tool again. See section III.B.1. (below) for further details concerning data.csv. invicro, LLC 2 Oliver St., Suite 609 Boston, MA (617) info@invicro.com

9 B. The output directory: once the program has completed, the following files will appear in the output directory: 1. data.csv : a comma- separated table with the volume, uptake, and concentration in each atlas region for each NM dataset. The atlas regions span the rows of the table while the NM datasets span the columns. For each NM dataset, 3 columns exist: Volume (mm^3), Dose (kbq), and Concentration (kbq/mm^3). These columns contain volume, uptake, and concentration statistics. A sample file is shown below. 2. atlasfinal.mhd/raw : the final fitted atlas in mhd/raw format. This atlas may be opened in VivoQuant at any time by using File Open and selecting atlasfinal.mhd. 3. atlasfinal.dcm : the final fitted atlas in DICOM format. 4. filelist.txt and settings.txt : these files are used internally by the atlas tool. There is no use for these files once the program is completed, but they may be useful to the invicro support staff in the case that support is needed for the atlas tool.

10 5. mhd/raw data: Also found in the output directory will be mhd/raw copies of the original CT and NM data (tmp- 000.mhd/raw, tmp- 001.mhd/raw, etc.). IV. Adjust the Atlas (optional) In the event that the atlas fit is not perfect, it is possible to scale and reorient the atlas and then reanalyze the data according to the adjusted atlas. For details on how to perform this step, see the Atlas Reorientation Quick Guide. V. Troubleshooting If the skull in the final CT appears to have been excessively cropped: Turn off auto- cropping and crop the data with the IVS cropping tool prior to running the Atlas tool. If the final CT and NM data are poorly registered: Register the datasets by hand using the Reorientation or Registration tool in IVS. With the atlas and newly registered data loaded, rerun the atlas tool. A dialog will ask if the loaded atlas should be used; choose Yes and the analysis will be performed on the registered data with the loaded atlas. If the atlas fit is too poor for minor manual adjustments: First, simply try rerunning the tool on the original data without changing any settings. The precise results of the various registration steps within the tool can differ on each run, and most poor fits disappear when the tool is rerun. If rerunning the tool is ineffective, try cropping the skull manually prior to running the tool. Center and crop very close to the skull to leave out other features of the skeleton that might disrupt the fits. Rerun the tool without checking Auto crop. In some images, the skull might be rotated too extremely for the tool to make a good fit with the available atlas. Check the orientation of the desired atlas (the orientation will be preserved in data- to- atlas fits), and use the reorientation tool in IVS to rotate the data (CT + all NM) prior to running the atlas tool. If errors pertaining to memory allocation occur: The images loaded are too large for your machine to process effectively. Crop and downsample the data as needed before processing to avoid further memory issues. For further assistance with the brain tool, please contact support@invicro.com.

11 Appendix. Choosing the Method: Atlas- to- Data vs. Data- to- Atlas Fits invicro currently offers two methods of quantifying activity in various brain regions: atlas- to- data and data- to- atlas. Atlas- to- data fits do not alter the input data, and transform the atlas to fit the data. This method should be used if it is imperative or desired that the data not be modified in any way. Additionally, atlas- to- data fitting is generally faster than data- to- atlas fitting (sometimes as much as twice as fast). The disadvantage to this approach is that narrow atlas regions are prone to being distorted during the interpolations necessary to rotate the atlas. Data- to- atlas fits morph the data to match the provided atlas with rotations and translations; the atlas is then scaled to fit the reoriented data (no scaling is applied to the data). The advantage of the data- to- atlas fitting method is that delicate brain regions with fine structure do not get washed out as the atlas is transformed to fit the skull, as is the case in the atlas- to- data method. The data- to- atlas method provides more consistently sized regions across datasets than the atlas- to- data method. In most cases though, there will not be statistically significant differences in results from one method to the other.