by

Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Ariel Rokem
    @arokem
    Hello!
    I <3 gitter
    :-)
    Franco Pestilli
    @francopestilli
    Yeah! This rocks!!
    Ariel Rokem
    @arokem
    I'm actually just writing you an email
    Franco Pestilli
    @francopestilli
    OK cool waiting for it.
    sepehrband
    @sepehrband
    Hi Franco,
    great work.
    I'm using Mrtrix for tractography and would like to compare the results using diffusion prediction error. How can I input Mrtrix tractography nifti files to your Matlab routine?
    Franco Pestilli
    @francopestilli
    Take a look at this: francopestilli.github.io/life A script called life_demo.m is introduced there and explains how to get started. Let me know if this helps.
    Ariel Rokem
    @arokem
    Also, mrtrix_tck2pdb.m will convert from the mrtrix format to the pdb format, which can then be read into memory using mtrImportFibers. When you save the resulting output of that function into a mat-file, you can feed it directly into the LiFE routines, as demonstrated here: https://github.com/francopestilli/life/blob/master/scripts/life_demo.m#L73
    sepehrband
    @sepehrband
    Thanks guys, I also found the DiPy version of your method pretty awesome. Thanks !
    Ariel Rokem
    @arokem
    Great to hear. Note that there's a somewhat faster version of the dipy implementation, coming here: nipy/dipy#575
    Franco Pestilli
    @francopestilli
    Good. Dipy is less tested and so far speed is comparable between matlab and python. Choose the one you prefer.
    I wrote a script that shows how to preprocess raw data in matlab all the way dow to running life. take a look: https://github.com/francopestilli/life_scripts/blob/master/tutorial/LiFEData_preprocess.m
    Franco Pestilli
    @francopestilli
    @sepehrband
    sepehrband
    @sepehrband
    Great. Thanks Franco.
    sepehrband
    @sepehrband
    One more question guys. In the Supp. figure 6b of your paper, there is a decreasing trend in the median RMSE moving from low b-value to high b-values. Does this mean that higher b-value outperform lower b-values, or it's because of increased attenuation with high b-value?
    sepehrband
    @sepehrband
    Correction: "Supplementary figure 5b"
    Franco Pestilli
    @francopestilli
    @sepehrband I am not sure I can answer the question as it is formulated. The RMSE goes down, this means that the model fits the data better. But I have not yet looked at how the SNR in the data interacts with the RMSE calculations.
    sepehrband
    @sepehrband
    Thanks for your helps!
    johncplass
    @johncplass
    Hello all. Thanks for the awesome software. Quick question from a dMRI beginner: can I use LiFE with DSI data? I wanted to get started using LiFE with some freely available data -- looks like WUMinn-HCP data has gradient non-linearities that MRTrix can't handle yet, so I was looking into trying out the MGH-USC (DSI) data using TrackVis (or something else).
    johncplass
    @johncplass
    Thanks for any help you can give! @francopestilli @arokem
    Franco Pestilli
    @francopestilli
    Hi John Thanks for the interest. We have software to read TrackVis fiber groups into formats that LIE can handle: https://github.com/vistalab/vistasoft/blob/5e40ca8bd08993212b43bfe027a3c85fd513d379/fileFilters/mrtrix/read_trk_to_fg.m I never tried using those but I would give it a try, let me know if it fails or not.
    johncplass
    @johncplass
    Awesome, thank you! I will take a look and let you know how it works out.
    Franco Pestilli
    @francopestilli
    God please keep me posted! I previously analyzed the HCP data set (StLouis) using a single b-value at the time. Never tried the MGH_USC data set I am curious to learn how it goes for you please!