Hi DIPY Experts,
I am interested in saving the diffusion tensor as a NIFTI file created as part of the free water implementation. I ran the following commands:
import numpy as np
import nibabel as nib
import dipy.reconst.fwdti as fwdti
import dipy.reconst.dti as dti
import matplotlib.pyplot as plt
img = nib.load(fdwi)
data = img.get_data()
affine = img.affine
mask = nib.load(mask_wb)
maskdata = mask.get_data()
fwdtimodel = fwdti.FreeWaterTensorModel(gtab,fit_method='NLS')
fwdtifit = fwdtimodel.fit(data, mask=maskdata)
1) The following errors were displayed even though the code ran after running the fwidtifit command above:
.../python_local/scipy/optimize/minpack.py:447: RuntimeWarning: Number of calls to function has reached maxfev = 1800.
...python_local/dipy/reconst/fwdti.py:454: RuntimeWarning: overflow encountered in exp
y = (1-f) * np.exp(np.dot(design_matrix, tensor[:7])) + \
I wanted to verify if this is just due to imperfect masking near the edge or if this means the code did not fully run and that there are errors to fix.
2) I ran the following code to save the tensor, as from my understanding fwdtifit uses the DTI tensorfit module:
img = nib.Nifti1Image(fwdtifit.quadratic_form, affine)
Is this the upper or lower triangle? The NIFTI standard is lower triangle, but given that in the DTI module has a lower_triangular function I am guessing DIPY default is the upper triangle.
I am having trouble using the lower_triangular function so if you can send me the correct way to interface with this command that would be much appreciated.
I am trying to use the atlas of 80 bundles you distribute here
but I am encountering some issues.
It is written that the files are in MNI space ICBM 2009a, which has affine
array([[ 1., 0., 0., -98.],
[ 0., 1., 0., -134.],
[ 0., 0., 1., -72.],
[ 0., 0., 0., 1.]])
However, all the trk files have affine equal to the identity matrix. Is
there a reason why you stored in the header of the trk files the identity
matrix? This for example prevents their correct visualization in TrackVis.
Another question: the file whole_brain_MNI.trk, besides having the same
issue with the affine, has 144678 streamlines. Is it the same whole brain
tractogram Yeh is referring to in their paper? In that paper they obtained
a tractogram of 550000 streamlines. Or is it maybe the union of the 80
Thank you a lot for your help,
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I am using DIPY for the first time because I would like to analyze IVIM
I created my python script and I ran the fit for my data.
However, the results are not, in my opinion, correct.
I analyzed only one slice, because the script needs time, and I wanted to
be sure that it worked correctly.
However, for the f index, I have 3/4 of the brain with 0.19999999999999
[image: Screen Shot 2019-12-18 at 2.58.36 AM.png]
I also tried your 'example' but, also, I have similar results.
Am I making some errors?
I am attending the DIPY 2020 workshop March 16th and wanted to ask a few
clarifying questions before making my final travel arrangements.
First, is there any plan to cancel the workshop due to Coronavirus issues?
- I have booked my flight and preregistered for the workshop, however, I
wanted to reach out before getting a hotel room/booking a shuttle.
Secondly, what material should we bring with us if any, to the workshop?
*Graduate Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
I was just reading a recent paper, entitled “Segmentation of the brain using direction-averaged signal of DWI images”, published at Magnetic Resonance Imaging.
In the Data and code availability statement, it says:
"The code was written in Matlab (MathWorks, Natick, MA, USA) and can be shared upon request. A python version of the method has been implemented in DIPY (https://dipy.org/) and will be available once the paper is published.”
I wonder how I can get access to the code in DIPY? Thank you!!
I am a PhD student at UMA and I study the use of models in the software industry. I understand that this group discusses many issues related to agile development software, programming languages, standards such as CMMI, IEEE, quality and Jobs, and I think you can help me by sharing your experiences.
There is some research that states that agile development is no longer agile when models are used, others report that models are important. There is other research that shows that developers use their own annotations, their own models, these "ad-hoc" models must be identified and formalized, and the programming languages have evolved to be a modeling language themselves. You represent the truth of today's software development and therefore we need your help. Our purpose is to formalize the non-formal or ad-hoc annotations that are used for agile development and propose improvements for agile modeling with UML.
I beg you to answer this survey, and please send this survey to your friends and colleagues.
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Methodologies, Modeling languages and use in the software industry
This form requests some personal data as an optional form, I request it because it is possible that you provide some important experience and I need to contact you later. I promise that your participation in the possible publications will be recognized and if anyone wants to work with me and publish an article it will be an honor.
Thank you so much.
Here is what I am suggesting.
If you are new to DIPY I would suggest to take the 3 days as Monday,
Tuesday and Wednesday.
If you are already advanced you can do Wednesday, Thursday and Friday.
But nothing better than going for all 5 days. In that way you will have
more time to work on your own
data during the hands-on sessions.
On Tue, Feb 25, 2020 at 3:06 PM Ann M Alvar <aalvar(a)purdue.edu> wrote:
> I am a PhD student at Purdue University and I am interested in attending
> the DIPY workshop. I saw that there was a three day and a five day option
> and I was wondering which of the scheduled days were part of the three day
> workshop vs the five day workshop.
> Ann Alvar
> *Ann Alvar*
> Ph.D. Candidate, *Purdue University*
> Department of Speech, Language, & Hearing Sciences
> Purdue Association for Magnetic Resonance President
I am a PhD student at Purdue University and I am interested in attending the DIPY workshop. I saw that there was a three day and a five day option and I was wondering which of the scheduled days were part of the three day workshop vs the five day workshop.
Ph.D. Candidate, Purdue University
Department of Speech, Language, & Hearing Sciences <http://www.purdue.edu/hhs/slhs/>
Purdue Association for Magnetic Resonance President
I am a brazilian radiologist who works in São Paulo University with a
background in applied mathematics who is working on diffusion research. I
am familiar to Python and believe this workshop can add a lot to my
knowledge and I would like to go.
The exchange of brazilian currency to american dollar made trips to the
united states really expensive:
Is it possible to pay a discounted rate in order to make feasible to attend
the workshop ?
Ellison F Cardoso