Mailman 3 July 2019 - DIPY

[Neuroimaging] [DIPY] track simple (not DWI) vector field np.ndarray data
by Francesco Giardini July 18, 2019

July 18, 2019

Hi, I'm a complete novice at the field of Dipy so, first thank you very much to all of you. I would like to exploit Dipy tractography tools to draw my own data (not DWI), but I have some problem about the fiber directions representation. I work with 3D images of heart muscle tissue, and I developed a simple code that extract the fibers orientation by means of a Structure Tensor Analysis. So, I have a 3d matrix 'R' (numpy.ndarray); every R(z, y, x) element contains: - three eigenvalues (3x1 matrx) - three R3 eigenvectors (3x3 matrix) - others informations (for example, the Fractional Anisotropy, useful (i think) for the stop criterium) In the attached, there is an example (only one XY plane displayed) of the orientations maps, plotted with mayavi. I'm trying to understand how to format my data to generate the streamlines. I have reproduced some examples. Here ( http://nipy.org/dipy/examples_built/tracking_quick_start.html#example-track…) i find that csd_peaks contains the vectors informations (the source of the tractography process?) while here ( http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti) seems that tenfit contains the same vector field. I'm reading also the documentation about dipy.tracking.local.LocalTracking and dipy.tracking.local.DirectionGetter. The question is: How I can create the streamlines from my data (numpy.ndarray)? I'am looking forward to your reply. Thank you very much. Francesco -- Dr. Francesco Giardini (giardini(a)lens.unifi.it) LENS - European Laboratory for Non-linear Spectroscopy Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy University of Florence - Biomedical Engineering Tel. 055 457 2477 (off.) http://www.lens.unifi.it

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[Neuroimaging] [DIPY] track simple (not DWI) vector field data
by Francesco Giardini July 15, 2019

July 15, 2019

Hi, I'm a complete novice at the field of Dipy so, first, thank you very much to all of you. I would like to exploit Dipy tractography tools to draw my own data (Not DWI), but I have some problem about the fiber directions representation. I work with 3D images of heart muscle tissue, and I developed a simple code that extract the fibers orientation by means of a Structure Tensor Analysis. So, I have a 3d matrix 'R' (numpy.ndarray); every R(z, y, x) element contains: - three eigenvalues (3x1 matrx) - three R3 eigenvectors (3x3 matrix) - others informations (for example, the Fractional Anisotropy, useful for the stop criterium) In the attached, there is a one-frame example (only one XY plane analyzed) of the orientations maps, plotted with matplotlib and mayavi. I'm trying to understand how to format my data to generate the streamlines. I have reproduced some examples. Here ( http://nipy.org/dipy/examples_built/tracking_quick_start.html#example-track…) i find that csd_peaks contains the vectors informations (the source of the tractography process?) while here ( http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti) seems that tenfit contains the same vector field. I'm reading also the documentation about dipy.tracking.local.LocalTracking and dipy.tracking.local.DirectionGetter. How I can merge my data with the Dipy structures, to generate and display my streamlines? I'am looking forward to your reply. Thank you very much. Francesco Giardini -- Dr. Francesco Giardini (giardini(a)lens.unifi.it) LENS - European Laboratory for Non-linear Spectroscopy Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy University of Florence - Biomedical Engineering Tel. 055 457 2477 (off.) http://www.lens.unifi.it

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[Neuroimaging][DIPY] track simple (not DWI) vector field data
by francesco giardini July 15, 2019

July 15, 2019

Hi, I'm a complete novice at the field of Dipy so, first, thank you very much to all of you. I would like to exploit Dipy tractography tools to draw my own data (Not DWI), but I have some problem about the fiber directions representation. I work with 3D images of heart muscle tissue, and I developed a simple code that extract the fibers orientation by means of a Structure Tensor Analysis. So, I have a 3d matrix 'R' (numpy.ndarray); every R(z, y, x) element contains: - three eigenvalues (3x1 matrx) - three R3 eigenvectors (3x3 matrix) - others informations (for example, the Fractional Anisotropy, useful for the stop criterium) In the attached, there is a one-frame example (only one XY plane analyzed) of the orientations maps, plotted with matplotlib and mayavi. I'm trying to understand how to format my data to generate the streamlines. I have reproduced some examples. Here ( http://nipy.org/dipy/examples_built/tracking_quick_start.html#example-track…) i find that csd_peaks contains the vectors informations (the source of the tractography process?) while here ( http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti) seems that tenfit contains the same vector field. I'm reading also the documentation about dipy.tracking.local.LocalTracking and dipy.tracking.local.DirectionGetter. How I can merge my data with the Dipy structures, to generate and display my streamlines? I'am looking forward to your reply. Thank you very much. Francesco Giardini -- Dr. Francesco Giardini (giardini(a)lens.unifi.it) LENS - European Laboratory for Non-linear Spectroscopy Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy University of Florence - Biomedical Engineering Tel. 055 457 2477 (off.) http://www.lens.unifi.it

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