- How can I load a study? In which format?
- What happens if my study does not have start and end frame times?
- Can I change or save the frame times of the loaded study? How can I do this?
- What is the format of the times file?
- Can I check the times consistency? How can I do this?
- How can I load a mask? What are the accepted formats?
- What is the format of the mask names file?
- Can I directly load the time-activity curves?
- Can I generate a mask for a loaded PET study? How can I do this?
- How can I see the TACs?
- Can I see and save the numerical values of the TACs? Can I save the plotted TACs?
- Can I change the reference and interest region?
How can I load a study? In which format?
To load a dynamic PET study, press the Load Study button. A new auxiliary window will open, to allow searching and loading the study from your folder structure. The supported formats are Analyze (hdr/img) or NIfTI(nii). Single-file (multiframe) or multiple-file (one file for each frame of the PET study) studies can be loaded. Once the file/s are chosen, press the Done button and the PET study will be loaded.
What happens if my study does not have start and end frame times?
Nothing. A warning window will appear, and default start and end times will be used, unless you specify values for your scan. See next question on how to specify these values.
Can I change or save the frame times of the loaded study? How can I do this?
Yes. You can do this by clicking on the Change Times button. A new auxiliary window will open. Then, you can change or save current times, load new times from a file or check the consistency of the time values.
What is the format of the times file?
You can load new frame times from a file. This file must have the following format:
- One row for each frame of the study.
- One column for the starting times and one for the ending times
- Units must be seconds
In the first line, the starting and ending times of the first frame of the study, in the second line, the starting and ending times of the second frame of the study, and so on.
Can I check the times consistency? How can I do this?
Yes, there are two ways:
- By the Change Times button on the main window.
- By the toolbar of QModeling: Click QModeling->Configuration and check the Consistency check option. With this, the times consistency will be automatically checked. A warning will appear if they are not consistent.
How can I load a mask? What are the accepted formats?
To load a mask with regions of interest (ROIs) press the Load Mask/TACs button. It must include only one ROI for the reference region, and an indefinite number of ROIs representing specific-uptake areas for the preprocessing step. Only one of these shall be used for the preprocessing. When the button is pressed, a new auxiliary window opens, which allows searching and loading the mask from the folder structure. The allowed formats are Analyze (hdr/img) or NIfTI (nii). All the ROIs must be included in one single file. A numeric index (an integer) specifies each ROI. Clicking the Done button, the mask will be loaded. The name of the ROI associated with each numeric index can be specified in a plain text file. If such a file exists at the same path and with the same name as the mask, it will be automatically loaded*. If not, a new auxiliary window will appear asking for that text file*. If no text file is chosen or detected, the TACs associated to each mask will receive generic names (TAC1, TAC2, ...) with numeric indexes following a correlative order with the indexes in the mask.
*Specific format is required. Please, go to the "What is the format of the mask names file?" question.
What is the format of the mask names file?
It must be a plain text file including the different regions on different rows. The name of each region must be at the first column and the corresponding integer at a second column. In order to be automatically loaded by the application, this text file and the mask file must be at the same path and have the same name. If they are in separate folders, the program will automatically open a window asking for the mask names file.
Can I directly load the time-activity curves?
Yes. Instead of using a mask file, you can directly load the time-activity curves of the region(s) of interest and the reference region. The accepted formats are .txt, .xls, .xlsx and .mat. If a .mat file is used, it must contain a variable called TACs_names with the names of the regions and another one called TACs with the values of each region as columns. If the file is in .txt, .xls, or .xlsx format, there must be a first row with the names of the regions. The following rows will contain the values of the TACs for each frame. Each column will represent the TAC of a specific region. In the .txt case, you have to split the columns by the tabulator key. At /QModeling/help/template_TACs you have a template of TACs file for each format option.
Can I generate a mask for a loaded PET study? How can I do this?
Yes. The WFU_PickAtlas toolbox for SPM must be downloaded (http://www.nitrc.org/projects/wfu_pickatlas/ or http://fmri.wfubmc.edu/software/PickAtlas) and installed to enable Create mask with pickatlas button in the main window.
How can I see the TACs?
Once you have succesfully loaded the PET study and the mask file, you can obtain the TACs by clicking on the Prepare TACs button. If the time-activity curves have been directly loaded, the same button has to be pressed. If everything is correct, the TACs will be displayed in the Plots panel of the main window; otherwise, an error message will be shown.
Can I see and save the numerical values of the TACs? Can I save the plotted TACs?
Yes. Right-button click on the Plots panel.
Can I change the reference and interest region?
Yes, you can choose whatever you want on the appropriate drop-down list.