![]() Siemens has helpfully included this information in the DICOM file with the parameter "Bandwidth Per Pixel Phase Encode", stored in DICOM tag (0019, 1028). We use the "effective" echo spacing, rather than the actual echo spacing, in order to include the effects of parallel imaging, phase oversampling, etc. There are two parameters you will frequently need when calculating and applying field maps: the effective echo spacing and the total readout time for an EPI sequence. Each will contain a single magnitude volume, and one will have the opposite phase encoding direction from the other.Įffective echo spacing and total readout time If you used the se-epi with opposite phase encode method (method 2), you will also get two series. The second series will contain a single phase difference image, a subtraction of the two phase images from each echo. The first will contain two magnitude images, one for each echo. If you don't know what kind of data you acquired, it should be clear once you look at the results: if you used the stock double-echo gradient echo field map sequence (method 1), you'll have two series. If you are an LCNI user, we use both methods. Method 2 uses two separate acquisitions with opposite phase encoding directions to calculate a field map based on the difference in distortion between the two acquisitions. Method 1 calculates a field map based on the difference in phase between two different echos in a double echo sequence. This article covers how to do that for two different methods. You have data that you will use to calculate a field map. If you are asking this question, the answer is that you don't have a field map yet. I already took the data, what kind of field map do I have? Your acquisition parameters could very well be different from theirs. If after applying distortion correction your images look worse, or about the same, you should look for a mistake somewhere in your processing.Īnother really important thing: please don't take scripts written by someone else in your lab for their project and just assume everything will work. Make sure you read this partĪpplying distortion correction should make your images look LESS distorted, not more. This document focuses on the practicalities of how to generate and use the field maps. This document discusses two methods used at the center to acquire images that can be used to create field maps, and how to use tools in FSL and SPM to create and apply field maps. While signal lost to these inhomogeneities cannot be recovered, signal that has been merely displaced can be returned to its proper location in the image if a map of the B0 field has been acquired. I accessed sunset/sunrise times for everyday of my dataset using sunriset() from the Maptools package.EPI images can be quite distorted due to B0 inhomogeneities, which in the brain are especially pronounced near the sinuses. I do not have any mathematical background. ![]() I should mentioned that I am a marine biologist, working on cetaceans. The values 0 and 2Pi represent dawn, while Pi represents dusk." Zein et al., 2019 "To standardise daylight, radian values were calculated. A scientific paper uses this method, I contacted one of the authors but no answer so far. I've been looking everywhere and couldn't find any solution. Instead, I would need to set 0/2Pi to be sunrise and Pi to be sunset times. I need my data to be standardised, considering that sunrise/sunset time varies through the year. I do not want 0/2Pi to correspond to 0h/24h and Pi to noon. The problem that I am facing is the following: I need now to do the same with the time of the day. I have a big dataset (continuous across months), and I need to perform circular statistics to assess a potential effect of diel cycles.įor this, I converted all cyclic data into radians.
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