Mailman 3 April 2023 - DIPY

How to join virtual workshop?
by Goodale, Sarah Elizabeth April 24, 2023

April 24, 2023

Hello! I just registered this morning and haven't received any information on how to join the sessions that are starting now. Thanks! Sarah Goodale Department of Biomedical Engineering Vanderbilt University | PhD Candidate 541-359-5487 | sarah.e.goodale(a)vanderbilt.edu<mailto:sarah.e.goodale@vanderbilt.edu>

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DIPY Workshop starts in less than an hour!!! - 9AM PDT
by sreekar chigurupati April 24, 2023

April 24, 2023

Hi All, DIPY Workshop 2023 starts at 9AM PDT. You can still register at http://dipy.org/workshops/latest. For those who have already registered, you have been given access to a Discord community. Please ask any questions in the meantime at Discord. 🌟🌟🌟 *Thanks & regards* *Sreekar Chigurupati* *On behalf of the DIPY team*

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DIPY: Free water elimination package
by Sowmya.Sambamoorthy＠utdallas.edu April 23, 2023

April 23, 2023

Hello DIPY experts, https://dipy.org/documentation/1.0.0./examples_built/reconst_fwdti/# I am new to this field and helping out my team with applying the fwdti package on their images to remove possible free water effects. I think I have a fair understanding of the the overall flow of the code reconst_fwdti.py. I am facing some issues with taking the code that uses inbuilt demo data to work with mine. some of the suggestions that you have provided in this thread was helpful: :https://mail.python.org/archives/list/dipy@python.org/message/ILAINLGXNODPLVVZTUBCFNMNFF2VGD3B/ But I have a couple of questions that am facing: 1. I would really appreciate some help with how I can supply my mask data instead of the median_otsu. 2. Also, we captured 50 axial slices. But when I assign axial_slices =50. File "C:\Users\sowsa\Documents\Python\reconst_fwdti.py", line 98, in <module> mask_roi[:, :, axial_slice] = mask[:, :, axial_slice] IndexError: index 50 is out of bounds for axis 2 with size 50 I am guessing this is because the demo data had an array limit to hold axial slices of 40. Any help to get past handling my own mask file is greatly appreciated ! TIA! ================ including the code I have so far below which shows the changes I have made to construct gtab etc. to supply the bvals and bvecs and the image data.======================================= import numpy as np import dipy.reconst.fwdti as fwdti import dipy.reconst.dti as dti import matplotlib.pyplot as plt from dipy.data import fetch_cenir_multib from dipy.data import read_cenir_multib from dipy.segment.mask import median_otsu import nibabel as nib from dipy.core.gradients import gradient_table img = nib.load(r"C:\Users\sowsa\Documents\Python\o01_ecc.nii.gz") import dipy.core.gradients as dpg gtab = dpg.gradient_table(r"C:\Users\sowsa\Documents\Python\fmri65_DTI_o01.bval", r"C:\Users\sowsa\Documents\Python\o01_ecc.nii.gz.eddy_rotated_bvecs") data = img.get_fdata() affine = img.affine """ The free water DTI model can take some minutes to process the full data set. Thus, we remove the background of the image to avoid unnecessary calculations. """ maskdata, mask = median_otsu(data, vol_idx=[0, 1], median_radius=4, numpass=2,autocrop=False, dilate=1) """ Moreover, for illustration purposes we process only an axial slice of the data. """ axial_slice = 40 mask_roi = np.zeros(data.shape[:-1], dtype=bool) mask_roi[:, :, axial_slice] = mask[:, :, axial_slice] """ The free water elimination model fit can then be initialized by instantiating a FreeWaterTensorModel class object: """ fwdtimodel = fwdti.FreeWaterTensorModel(gtab)

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Error installing tutorial data
by Patterson, Dianne K - (dkp) April 22, 2023

April 22, 2023

Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp(a)arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz

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Re: Error installing tutorial data
by Eleftherios Garyfallidis April 22, 2023

April 22, 2023

Hi Dianne and all, Thank you for reporting. This is a known issue. There is a bug fix coming up concerning the HBN dataset. So this is expected. No further action needed on your side for now. You have already downloaded many datasets! An email to upgrade to a new version that has this issue resolved should appear before the workshop starts. See you soon!, Elef On Sat, Apr 22, 2023 at 1:51 PM Patterson, Dianne K - (dkp) <dkp(a)arizona.edu> wrote: > Dear DiPy, > > > I am following the instructions for DiPy 2023 and installing the tutorial > data. The process seems to get quite far (3.6 GB) but then gets an error. > Rerunning the command gets the same error, though nicely reports what is > going on (see below) > > *Environment* > > Mac OS Monterey 12.6.3 > > *Miniconda* > conda --version > conda 22.11.1 > > > conda list dipy > # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: > # > # Name Version Build Channel > dipy 1.6.0 pypi_0 pypi > > python --version > Python 3.10.2 > > *Conda Install Details* > > `conda create -n dipy` > `conda activate dipy` > `conda install -c conda-forge dipy` > `conda install -c conda-forge fury` > `conda clean --all` > > > *Command* > > dipy_fetch all > > *Error (Scroll down)* > > (dipy) [saci:dipy: 4121] $ dipy_fetch all > > INFO:------------------------------------------ > INFO:Fetching at DiB_217_lte_pte_ste > INFO:------------------------------------------ > INFO:Data size is approximately 166.3 MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste > INFO:------------------------------------------ > INFO:Fetching at DiB_70_lte_pte_ste > INFO:------------------------------------------ > INFO:Data size is approximately 51.1 MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste > INFO:------------------------------------------ > INFO:Fetching at bundle_atlas_hcp842 > INFO:------------------------------------------ > INFO:Data size is approximately 300MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 > INFO:------------------------------------------ > INFO:Fetching at bundle_fa_hcp > INFO:------------------------------------------ > INFO:Data size is approximately 230kb > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/bundle_fa_hcp > INFO:------------------------------------------ > INFO:Fetching at bundles_2_subjects > INFO:------------------------------------------ > INFO:Data size is approximately 234MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps > INFO:------------------------------------------ > INFO:Fetching at cenir_multib > INFO:------------------------------------------ > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/cenir_multib > INFO:------------------------------------------ > INFO:Fetching at cfin_multib > INFO:------------------------------------------ > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/cfin_multib > INFO:This data was provided by Brian Hansen and Sune Jespersen More > details about the data are available in their paper: > https://www.nature.com/articles/sdata201672 > INFO:------------------------------------------ > INFO:Fetching at file_formats > INFO:------------------------------------------ > INFO:Data size is approximately 25MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/bundle_file_formats_example > INFO:------------------------------------------ > INFO:Fetching at fury_surface > INFO:------------------------------------------ > INFO:Data size is approximately 11MB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/fury_surface > INFO:------------------------------------------ > INFO:Fetching at gold_standard_io > INFO:------------------------------------------ > INFO:Data size is approximately 47.KB > INFO:Dataset is already in place. If you want to fetch it again please > first remove the folder /Users/dpat/.dipy/gold_standard_io > INFO:------------------------------------------ > INFO:Fetching at hbn > INFO:------------------------------------------ > Traceback (most recent call last): > File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in > <module> > run_flow(FetchFlow()) > File > "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", > line 89, in run_flow > return flow.run(**args) > File > "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", > line 185, in run > fetcher_function() > TypeError: fetch_hbn() mi > > *Solutions Attempted* > > I initially tried installing in the Mac's native zshell with my active > conda environment. > After that failed, I switched to a bash shell, just in case. > > I get the same error message for both shells. > In every case, I am in my dipy environment. > > I tried creating a separate environment using pip instead of conda for > install. That did not get far. > > I have repeated the command, with equivalent results. > > Thoughts? > > > Thank you, > > Dianne > > > Dianne Patterson, Ph.D <https://profiles.arizona.edu/person/dkp> > dkp(a)arizona.edu > Office: BSRL, Room 235 > RII Neuroimaging Staff Scientist > Program Coordinator Neuroimaging Methods Certificate > <https://cogsci.arizona.edu/programs/certificate> > Cognitive Science GIDP affiliate member > Faculty Lead OpenClass.ai <https://openclass.ai> > Mastodon: @dpat@scicomm.xyz >

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Question about DIPY Workshop
by Raquel González Alday April 21, 2023

April 21, 2023

Hello I am writing to inquire about my registration for the upcoming DIPY online workshop and to request information on how to connect to the session. I completed the registration process for the workshop and I also made the payment for the registration fee via wire transfer this wednesday, and sent the receipt to iuconfs(a)iu.edu. However, I have yet to receive any confirmation or response from the university that my registration and payment have been received and processed correctly. As the workshop is starting on monday, and I made an international wire transfer, I am concerned and would like to confirm if everything is in order. Could you please confirm if I am correctly registered for the workshop and if the payment has been received? Also, could you please provide me with the details on how to connect to the session, such as the platform or link to access it, and any login credentials or codes required? I appreciate your prompt attention to this matter, and I am looking forward to attending the workshop. Please let me know if you require any additional information or documents from my side. Thank you very much for your kind assistance and sorry for any inconvenience. Best regards, Raquel González-Alday Registration number: #449170

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DIPY Workshop 2023 - What to do if you live in a different timezone than PDT
by Eleftherios Garyfallidis April 21, 2023

April 21, 2023

Dear all, We hope you are as excited as we are about the upcoming online DIPY workshop starting this Monday April 24 at 9 am PDT (LA time) ! As you make your plans to attend this educational event, we wanted to provide you with important information about the registration options available to ensure you get the most out of the workshop. To optimize your experience and accommodate different time zones, we highly recommend selecting the Platinum registration option. This will grant you full access to the workshop's recordings, allowing you to view them at your convenience. For example, if you are attending the DIPY workshop from Europe or Asia. While you will still be able to watch the early morning talks (PDT) live on the same day (late evening for you), choosing the Platinum option will enable you to watch the later afternoon (PDT) talks in the mornings of the subsequent days. For example, watch the late Monday talks on Tuesday morning. This is an excellent opportunity to catch up on any missed sessions and stay informed on the latest developments in the field. Additionally, Platinum registration comes with access to additional support and 1-to-1 meetings long after the workshop is completed. This will facilitate meaningful discussions and help you get the most out of the workshop. To register for the DIPY workshop and select the Platinum registration option, please visit here <https://dipy.org/workshops/dipy-workshop-2023#Registration>. We look forward to your participation and can't wait to see you there! If you are in financial hardship, be brave and ask for a discount. Please contact our conference manager Kelsey Daniel (cc'ed) for more information. Excited to see you all very soon! Best regards, Eleftherios Garyfallidis, PhD DIPY Workshop 2023 (Chair) Associate Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.luddy.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/>

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dipy mri workshop question
by Erez Simony April 18, 2023

April 18, 2023

Dear dipy, I would like to attend your workshop from israel. Due to time differences (i think 10 houres ahead in israel) , will the sessions will be recorded, and i could watch it later on ? thank you, erez simony Erez Simony, PhD, Faculty of Engineering, HIT - Holon Institute of Technology Weizmann Institute of science (Visiting Scientist) E-mail: erezs(a)hit.ac.il Web:https://erezsim.wixsite.com/website

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DIPY Workshop 2023 - Financial Support Options
by Eleftherios Garyfallidis April 18, 2023

April 18, 2023

Dear all, We hope this message finds you in good health and eagerly anticipating our upcoming online workshop, scheduled for April 24-28. We have recently received numerous requests for registration fee discounts from participants in countries facing economic challenges. At DIPY, we have always been committed to extending educational opportunities as far and wide as the internet can reach. Our organization takes pride in supporting talented students worldwide to pursue their aspirations, find rewarding careers, and contribute to cutting-edge research. In light of our mission, we are pleased to offer assistance to those facing financial difficulties. If you are in need of support, please contact Kelsey Daniel, our conference manager, and provide evidence of your current address (e.g. bill or driving license). Upon verification, Kelsey will supply you with a discount code for use during registration. We look forward to your active participation in the online workshop and are excited about the diverse perspectives that our global community brings to the table. Should you have any questions or require further information, please do not hesitate to reach out to Kelsey (CC'ed). Warm regards, Eleftherios

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DIPY WORKSHOP
by Reut Moran April 16, 2023

April 16, 2023

Hey My name is Reut and I'm a student and would like to register for the workshop. However, since of the time zone difference, I won't be able to take part in the guided practical sessions and study groups. Would you recommend me to join the workshop? I want to join the platinum registration, in order to access the materials after the workshop. Since I'll be missing part of the workshop, is there a possibility to get a discount? thank you Reut

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