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How to cite LIFEx?
Please see the How to cite LIFEx? page.
What is the ideal solution between the absolute or relative resampling in PET ?
In PET images, we do not recommend to use the relative resampling. As explained in https://www.ncbi.nlm.nih.gov/pubmed/26669541, relative resampling induces a high correlation between texture indices and metabolic volume, and we proposed to use the absolute resampling instead. In PET, we resample with 64 number of grey levels (size bin equals to 0.3) between 0 and 20 SUV units (because this is the standard range of SUVs in oncology with FDG). We think the same effect is observed in CT images, but if using the absolute resampling (which we recommend), you have to set yourself the range of HU and the number of bins (or bin size) for your data, as a function of the data content. Basically, the bin size has to be set as a function of the meaning of HU difference. If a HU difference of 10 does not mean much, then the bin size could be set to 10 for instance, using a smaller value is useless, and a range of HU between -1000HU and 3000HU for example (including all HU possible variations).
What is the ideal solution between the absolute or relative resampling in MR ?
In MR, the impact of different resampling schemes has been studied in http://iopscience.iop.org/article/10.1088/1361-6560/aabd21. Based on that paper, we recommend using a fixed bin width, which corresponds to absolute resampling.
In PET, the DICOM fields that have to be properly filled for correct SUV correction are:
DICOM fields to SUV conversion :
(0008,0032) TM #6  Acquisition Time
(0010,1020) DS #6  Patient’s Size
(0018,1074) DS #10  Radionuclide Total Dose
(0018,1075) DS #12  Half Life
(0018,1072) TM #6  Radiopharmaceutical Start Time
(0054,1001) CS #4  Units
(0028,1052) DS #2  Rescale Intercept
(0028,1053) DS #8  Rescale Slope
About the Spatial resampling XYZ spacing.
Which values should be used?
The main point of the spatial resampling XYZ spacing is to make sure that all calculations are performed with the same voxel size whatever the voxel size of the input image. This is important because textural feature values depend on voxel size. If all input images have the same voxel size, the user does not have to worry about this spacing, as it will be set by default to the voxel size so will always be the same. If the voxel size is not always the same for the different images processed in a study, then a fixed voxel size should be chosen (eg 2 x 2 x 2 mm in PET), and then used that for all images. This will remove the variability in texture values due to different voxel size.
Parameters for "Intensity of Discretization" in MR images. How to determine these values? And how will the values impact our results?
Intensity discretization setting does depend on the MR sequence that is used, but usually, we would recommend using 128 bins and so-called absolute resampling.
Min and max setting completely depends on the MR sequence and the type of lesion of interest. A way to identify the min and max value setting is to go over all patients, look at the min and max in each patient ROI and then take the min of min and max of max over all patients. And use these values for each patient. What is important is that you use the same min and max values for all patients. Yet, in MR, you first have to check that the MR intensity values in a reference healthy tissue are about the same for all patients. Otherwise, you have to correct for the inter-scan variability first, before performing radiomic analysis. What we could recommend is that you first focus on a healthy reference region and check that in that region, you observe consistent radiomic feature values across patients (ie that they follow a distribution close to a Gaussian distribution). Only after this first step is validated, you can go on and analyze lesions.