MIDS | Medical Imaging Data Structure

 by   BIMCV-CSUSP Python Version: 0.1.0-alpha License: GPL-3.0

kandi X-RAY | MIDS Summary

kandi X-RAY | MIDS Summary

MIDS is a Python library. MIDS has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However MIDS build file is not available. You can download it from GitHub.

In order to add to the scientific knowledge, methods that yield reliable and reproducible results must be used. High test-retest reliability of the methods applied is the foundation of research irrespective of the scientific discipline and it is in the prime interest of every scientist that results are reproducible. While such reproducibility was considered of utmost importance in the positron emitting tomography (PET) field [Adams et al., 2010], the quantitative assessment of reproducibility has largely been neglected in the fMRI community, or as Bennett and Miller described it: “Reliability is not a typical topic of conversation” between fMRI investigators [Bennett and Miller, 2010]. This situation changed significantly in 2016, following the establishment of the Committee on Best Practices in Data Analysis and Sharing ([COBIDAS] www.humanbrainmapping.org/cobidas/)) by the most important neuroimaging society - the Organisation for Human Brain Mapping (OHBM). The objective of BIMCV (Medical Imaging Bank Valencia Region) is that all this scientific knowledge be colected in a correct and efficient way. More concretely, all that knowledge is refered to data imaging. Find a way to organize this information is necesary. Currently, distinc forms to store images and medical information exist, but there is not a standard that indicates how this information should be organized and shared. The CEIB idea is to use a simple organisation that any researcher can understand the distribution of data. This desing is called MIDS (Medical Imaging Data Structure). MIDS is a new standard that contains every type of medical information and images in simple hierarchy folders. This is born as an extension of the standard BIDS (Brain Imaging Data Structure). BIDS [Gorgolewski et al.] is a structure that collect medical brain images, but MIDS pretend to extend it far away and not limit it the use to medical brain images. the idea is to create the same structure with both brain, column images or torso,... whether Resonance magnetic, Computed tomography, ecography,... This structure will definitely follow the same process regardless of the type and shape of the image.
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            kandi-support Support

              MIDS has a low active ecosystem.
              It has 6 star(s) with 2 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              MIDS has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of MIDS is 0.1.0-alpha

            kandi-Quality Quality

              MIDS has no bugs reported.

            kandi-Security Security

              MIDS has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              MIDS is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              MIDS releases are available to install and integrate.
              MIDS has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed MIDS and discovered the below as its top functions. This is intended to give you an instant insight into MIDS implemented functionality, and help decide if they suit your requirements.
            • Create directory mids
            • Reset the index
            • Gets the XMLs for a scan
            • Remove metabolites from MIDS
            • Loads a dictionary of data files
            • Save data to a pickle file
            • Load a pickle file
            • Convert a CSV file to a dictionary
            • Downloads all the files in the specified directory
            • Format a message
            • Download a dicom to a directory
            • Try to get a request
            • Creates directorio_mids dictionaries
            • Perform the perfusion procedure
            • The anatomic procedure
            • Creates the directorio MIDS
            • Performs an anatomic procedure on a given subject
            • Add tag to json file
            • Downloads all ROI files
            • Download all experiments
            • Download all scans
            • Downloads all sources resources
            • Download all subjects to the given path
            • Download projects
            • Download nifti files
            • List project names in project directory
            Get all kandi verified functions for this library.

            MIDS Key Features

            No Key Features are available at this moment for MIDS.

            MIDS Examples and Code Snippets

            Aplications,XNAT2MIDS,Options
            Pythondot img1Lines of Code : 19dot img1License : Strong Copyleft (GPL-3.0)
            copy iconCopy
                download one project from xnat aplicatión:
            
                arguments:
            
                    + Prefix  -w --web PAGE_WEB        1) The ULR page where XNAT is.
                    + Prefix  -p --project [PROJECTS]  2) The project name to download
                    + Prefix  -i --input PATH	     
            Aplications,XNAT2MIDS
            Pythondot img2Lines of Code : 1dot img2License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            python3.5 main.py -w Project_id -i dirXNAT -o dirOutput
              

            Community Discussions

            QUESTION

            add new array into an array from its array's subarray
            Asked 2022-Apr-12 at 01:45

            I have an array,

            ...

            ANSWER

            Answered 2022-Apr-11 at 12:21

            You can use the forEach (documentation) and the map (documentation) methods

            Source https://stackoverflow.com/questions/71827638

            QUESTION

            Recode a variable within the mids object of the mice library in R
            Asked 2022-Mar-15 at 17:50

            The following dataset is available

            ...

            ANSWER

            Answered 2022-Mar-15 at 17:50

            To do a calculation on the imputed datasets, we can use complete to get a dataframe of the imputed data. Then, we can use mutate as normal to make the calculation. Then, you can use as.mids to turn it back into a mids object.

            Source https://stackoverflow.com/questions/71474122

            QUESTION

            Async function returning empty array, and then the desired data - causing app to crash
            Asked 2022-Feb-20 at 05:39

            In my react project, I have a function getDetails that takes in the data retrieved from a database call (filteredVenue), and then console logs that data. This function exists inside a component called MidSection.js. When this component is rendered and getDetails is invoked, the following is logged to the brower:

            MidSection.js:9 [ ]
            MidSection.js:9 [{…}]

            The problem is this - initially, an empty array is being returned which means that is I try to access the data inside filteredReviews, I get an undefined error.

            As an example the following code

            ...

            ANSWER

            Answered 2022-Feb-20 at 05:39

            just add a check wherever you feel , it is undefined or null.

            Source https://stackoverflow.com/questions/71191619

            QUESTION

            Result from audio FFT function makes it near impossible to inspect low/mid frequencies
            Asked 2022-Feb-17 at 17:32

            I am trying to build a graphical audio spectrum analyzer on Linux. I run an FFT function on each buffer of PCM samples/frames fed to the audio hardware so I can see which frequencies are the most prevalent in the audio output. Everything works, except the results from the FFT function only allocate a few array elements (bins) to the lower and mid frequencies. I understand that audio is logarithmic, and the FFT works with linear data. But with so little allocation to low/mid frequencies, I'm not sure how I can separate things cleanly to show the frequency distribution graphically. I have tried with window sizes of 256 up to 1024 bytes, and while the larger windows give more resolution in the low/mid range, it's still not that much. I am also applying a Hann function to each chunk of data to smooth out the window boundaries.

            For example, I test using a mono audio file that plays tones at 120, 440, 1000, 5000, 15000 and 20000 Hz. These should be somewhat evenly distributed throughout the spectrum when interpreting them logarithmically. However, since FFTW works linearly, with a 256 element or 1024 element array only about 10% of the return array actually holds values up to about 5 kHz. The remainder of the array from FFTW contains frequencies above 10-15 kHz.

            Here's roughly the result I'm after:

            But this is what I'm actually getting:

            Again, I understand this is probably working as designed, but I still need a way to get more resolution in the bottom and mids so I can separate the frequencies better.

            What can I do to make this work?

            ...

            ANSWER

            Answered 2022-Feb-17 at 11:22

            What you are seeing is indeed the expected outcome of an FFT (Fourier Transform). The logarithmic f-axis that you're expecting is achieved by the Constant-Q transform.

            Now, the implementation of the Constant-Q transform is non-trivial. The Fourier Transform has become popular precisely because there is a fast implementation (the FFT). In practice, the constant-Q transform is often implemented by using an FFT, and combining multiple high-frequency bins. This discards resolution in the higher bins; it doesn't give you more resolution in the lower bins.

            To get more frequency resolution in the lower bins of the FFT, just use a longer window. But if you also want to keep the time resolution, you'll have to use a hop size that's smaller than the window size. In other words, your FFT windows will overlap.

            Source https://stackoverflow.com/questions/71155035

            QUESTION

            tab_corr, tab_df, and psych::describe on a mice mids object
            Asked 2022-Feb-12 at 00:27

            I have imputed data saved as a mids object and am trying to adapt my usual workflow around imputed data. However, I cannot figure out how to use sjPlot's tab_corr() and tab_df() and psych's describe on a mids object.

            My goal is to generate a table of descriptive statistics and a correlation matrix without averaging the imputed datasets together. I was able to generate correlations using miceadds::micombine.cor, but the output isn't formatted like a typical correlation matrix. I also can individually compute means, SDs, etc. of variables from the mids object, but I'm looking for something that will generate a table.

            ...

            ANSWER

            Answered 2022-Feb-12 at 00:27

            The previous code was incorrect. I have created two functions, mice_df and mice_cor (link to Github repo here) that will generate a correlation matrix and a table of descriptive statistics from a mids object using Rubin's Rules.

            gtsummary will neatly format models based on mids objects.

            Source https://stackoverflow.com/questions/70321021

            QUESTION

            Service timed out: Spreadsheets
            Asked 2022-Feb-10 at 05:22

            I always get the exception: "Exception: Service timed out: Spreadsheets" Why does this happen and would it help to try the method updateSpec(spec)? It always happens when I got to this specific line:

            ...

            ANSWER

            Answered 2022-Feb-10 at 05:22

            The cause of the error is that you are calling sheet too many times, and each call is a request which takes time to process and ultimately leads to the timeout. The easy sounding solution is reduce the calls of sheet.getRange() and sheet.setValue() and sheet.getName() etc… so that you ideally do them once per each sheet you are working on. A simple example would be as follows, where everything is done once (except the api call, which ideally should also be done using a bulk api).

            Source https://stackoverflow.com/questions/71047139

            QUESTION

            How to retrieve the original data from nls model in R?
            Asked 2022-Feb-09 at 17:28

            non-linear least square (nls() function in core R) generates a list object with a bunch of useful info inside, is there also the original data that were the input of the model? I suspect yes, as functions as predict() or fitted() are actually defined on this object and generate predictions in ranges of the original fitted data. So, how can one access this data through the model object?

            Imagine this setting

            ...

            ANSWER

            Answered 2022-Feb-08 at 18:28

            The data indeed is there but it's a bit buried within the environment of the model that is also saved within the object, I figured it out looking at the source code. You can access the input values of through getEnv() function which is available through the m object and that is part of the list returned by nls.

            So on the dummy example:

            Source https://stackoverflow.com/questions/71039024

            QUESTION

            How to plot histograms in base R in the margin of a plot
            Asked 2022-Feb-09 at 16:48

            I'd like to add histograms in base R to the margins of a plot, I've tried many ways, and used points and segments to plot the values calculated from a histogram. The challenge is that after plotting the data, the width of the bars have to be set manually in order to show a histogram like margin plot.

            ...

            ANSWER

            Answered 2022-Feb-09 at 16:48
            1. Using layout, you can set a space to 0 so that it does not require a plot, it is empty space.

            2. hist does not support horizontal mode, and recommendations (example) to use barplot are constrained in that one cannot fix where on the x-axis the bars are positioned. Yet another workaround is needed: since barplot is a wrapper around rect, we can write our own.

            This function mimics some of barplot but allows us to set where the bars are located. This is to ensure that the shared axis can be the same dimensions.

            Source https://stackoverflow.com/questions/71052975

            QUESTION

            Issue with user-defined function for descriptive statistics from imputed data
            Asked 2022-Jan-30 at 04:44

            I am trying to write a function that will calculate the mean and SD for a variable from a multiply imputed dataframe (mids). The code works fine outside of the function (as shown in two examples below), but will produce unreliable results when placed inside of a function. The function seems to keep giving results for bmi despite calling upon chl.

            Any insight into this issue is appreciated. Eventually I would like this function to be able to calculate means and SDs for multiple variables at once (i.e., bmi and chl) but that is likely a separate question.

            ...

            ANSWER

            Answered 2022-Jan-30 at 04:44

            Two and a half problems here:

            1. b = bmi looks like an object bmi, which does not exist in our global environment. We can use deparse(susbtitute(x)) for this, to tell the function to wait with the evaluation.
            2. Accessor function $, see ?Extract: Both [[ and $ select a single element of the list. The main difference is that $ does not allow computed indices

            Source https://stackoverflow.com/questions/70911659

            QUESTION

            runMI function error: 'no slot of name "internalList" for this object of class "lavaanList"'
            Asked 2022-Jan-24 at 18:05

            I have run a multiple imputation (m=45, 10 iterations) using MICE and am attempting to fit a series of confirmatory factor analysis and structural equation models on the imputed datasets using the runMI function from semTools. Nearly all of my variables are Likert scales, coded as ordered/ordinal. Here is my code for the first CFA, where mi.res.train is the mice-generated mids object:

            ...

            ANSWER

            Answered 2022-Jan-24 at 18:05

            Hi all: thanks for this feedback--unfortunately am using a restricted-use dataset so could not share much data without some extra steps. Fortunately, I updated a few packages and the code now appears to be working. I'd tried that previously but apparently missed the lavaan package itself.

            Source https://stackoverflow.com/questions/70814596

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install MIDS

            You can download it from GitHub.
            You can use MIDS like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            https://github.com/BIMCV-CSUSP/MIDS.git

          • CLI

            gh repo clone BIMCV-CSUSP/MIDS

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            git@github.com:BIMCV-CSUSP/MIDS.git

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