Mailman 3 February 2020 - DIPY

[DIPY] FWDTI and DTI recon questions including if default output is upper or lower triangle
by dr.ajay.kurani＠gmail.com May 24, 2020

May 24, 2020

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 sys import os import bz2file 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 fdwi="dwi_tpl_max2000.nii.gz" fbval="dwi_tpl_max2000.bvals" fbvec="dwi_tpl_max2000.bvecs" mask_wb="mask.tpl.final.nii.gz" 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. warnings.warn(errors[info][0], RuntimeWarning) ...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) nib.save(img, 'FWms_quadratic_form.nii.gz') 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. Thanks, Ajay

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Affine issue with atlas of 80 Bundles in MNI space
by Giulia Berto' March 19, 2020

March 19, 2020

Hi, I am trying to use the atlas of 80 bundles you distribute here https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737… <https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737…>, but I am encountering some issues. It is written that the files are in MNI space ICBM 2009a, which has affine equal to 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. [image: ifof_r_dipy_trackvis.png] 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 bundles? Thank you a lot for your help, best regards, Giulia -- -- Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.

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DIPY IVIM does not work correctly
by Maurizio Bergamino March 17, 2020

March 17, 2020

Hello, I am using DIPY for the first time because I would like to analyze IVIM data. 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 values. [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? Thanks, Maurizio.

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DIPY 2020 workshop
by Daniel Callow Feb. 29, 2020

Feb. 29, 2020

Hello, 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? Thank you, *Daniel Callow* *Graduate Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Code for segmentation of the brain using direction-averaged signal of DWI images
by Fan Zhang Feb. 28, 2020

Feb. 28, 2020

Hi! 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!! Regards, Fan

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Important request, participation in software development study
by arco_uml＠yahoo.es Feb. 28, 2020

Feb. 28, 2020

Dear Engineers, 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. If you have a Google account: Google Forms - create and analyze surveys, for free. Reply without logging in: 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.

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Re: DIPY workshop
by Eleftherios Garyfallidis Feb. 25, 2020

Feb. 25, 2020

Hi Ann, 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. Best, Eleftherios On Tue, Feb 25, 2020 at 3:06 PM Ann M Alvar <aalvar(a)purdue.edu> wrote: > Hi, > 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. > > Thanks, > > Ann Alvar > > *Ann Alvar* > > Ph.D. Candidate, *Purdue University* > > Department of Speech, Language, & Hearing Sciences > <http://www.purdue.edu/hhs/slhs/> > > Purdue Association for Magnetic Resonance President > > aalvar(a)purdue.edu >

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DIPY workshop
by Ann M Alvar Feb. 25, 2020

Feb. 25, 2020

Hi, 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. Thanks, Ann Alvar Ann Alvar Ph.D. Candidate, Purdue University Department of Speech, Language, & Hearing Sciences <http://www.purdue.edu/hhs/slhs/> Purdue Association for Magnetic Resonance President aalvar(a)purdue.edu

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DIPY WORKSHOP 2020
by Ellison Cardoso Feb. 21, 2020

Feb. 21, 2020

Dear all, 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. https://workshop.dipy.org/ The exchange of brazilian currency to american dollar made trips to the united states really expensive: https://www.bnnbloomberg.ca/brazil-central-bank-steps-in-to-help-world-s-wo… Is it possible to pay a discounted rate in order to make feasible to attend the workshop ? Best regards, Ellison F Cardoso

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Mailing list
by Daniel Scott Feb. 21, 2020

Feb. 21, 2020

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