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    Niklas Pallast
    @npallast
    Here, we provide a suitable discussion platform for the development and implementation of a common analysis platform using the Atlas-based Imaging Data Analysis processing pipeline (AIDA) tools.
    Niklas Pallast
    @npallast
    All related tools are freely available on GitHub: https://github.com/maswendt
    salma1601
    @salma1601

    Dear Aida experts,
    I have the same question about FSL. It required version is 5.0.1 but I have FSL 5.0.9 and I do not want to downgrade it. Is it possible to make AIDA work in this case ?

    Thanks
    Salma

    Niklas Pallast
    @npallast
    Hi Salma, We never tried it, but I'm sure AIDAmri will work with FSL 5.0.9.. AIDAmri calls FSL by a nipype.interfaces and there are no restrictions on the versions in the related documentation. Best regards Niklas
    stephanwu89
    @stephanwu89

    Hi,
    I am trying to process step preProcessing_T2.py, but I always end up after 50% with the following error

    "File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 97, in _raise_linalgerror_singular
    raise LinAlgError("Singular matrix")"

    preprocess.log:
    Frac: 0.15
    Radius: 45
    Gradient: 0.0

    Do you have any idea?
    Thanks,
    Steph

    Markus Aswendt
    @maswendt
    Hi Steph, which Numpy version? Try to change the default Frac, Radius and Gradient, especially the Radius to fit to your data.
    stephanwu89
    @stephanwu89

    The latest np version. I used a lot of different numbers but it keeps being the same
    The whole error is:
    Traceback (most recent call last):######################################################## |
    File "preProcessing_T2.py", line 108, in <module>
    outputMICO = applyMICO.run_MICO(inputFile,os.path.dirname(inputFile))
    File "/Users/Wu/Desktop/Research/MouseGlioma/AIDAmri-master/bin/2.1_T2PreProcessing/applyMICO.py", line 98, in run_MICO
    M, b, C = MICO.runMICO(Img, q, ROI, M, C, b, Bas, GGT, ImgG, 1, 1)
    File "/Users/Wu/Desktop/Research/MouseGlioma/AIDAmri-master/bin/2.1_T2PreProcessing/MICO.py", line 41, in runMICO
    b_out = updateB(Img, q, C, M, Bas, GGT, ImgG)
    File "/Users/Wu/Desktop/Research/MouseGlioma/AIDAmri-master/bin/2.1_T2PreProcessing/MICO.py", line 70, in updateB
    w = np.dot(np.linalg.inv(A) , V)
    File "<__array_function__ internals>", line 6, in inv
    File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 551, in inv
    ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
    File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 97, in _raise_linalgerror_singular
    raise LinAlgError("Singular matrix")

    And the problem was in appyMICO.py "ROIt = Img > 20". All the values in my image are below 1.0 and consequently everything was set to 0 in the matrix and then it is a singular matrix.

    Are there any specific changes to the image in the first step? (converttoNIFTI)
    Since I did not do the first step, because I convert 20 .dcm files to one singular nifti file with MRIcron which is my mouse brain image(T2 coronar).
    The vol of my file is of dimension (256,256,16)

    When I change "ROIt = Img > 20" to 0.2, I get stuck at pre_Processing_T2 line 41 when executing Nifti1Image
    error : SVD did not converge

    Markus Aswendt
    @maswendt
    (1) downgrade to nipype=1.1.2. (2) Yes orientation is important. conerttoNIFTI overwrites the header to RAS. Compare your data orientation to the test data set, it should be the same (as explained in the Manual, page (3). If the error persists, send me a link to your data, I will take a look.