Title Text

MISSION

 

  • Parallel analyses
  • Easy for novices and experts
  • Not a black box
  • Creation of a convergent and unified platform
    • Tutorials
    • Support
    • Allow knowledge transfer
    • Promoting good practice

Offer an

 automated pipeline to process diffusion neuroimaging data

TOAD

http://unf-montreal.ca/toad/

Development

Contribution

S.Brambati
J.Doyon
J-S.Provost
C.Vien
G.Chedid
A.Hanganu
J.Jarret
J.Chen
C.Bedetti
G.Vallet
A.Boré
B.Pinsard
M.Desrosiers
C.Hurst
A.Cyr

Thanks to

M.Descoteaux
J-C.Houde
E.Garyfallidis
G.Girard
M-A.Côté

B.De Leener

T.Duval

J.Cohen-Adad

JD.Tournier

S.St-Jean

Technical  support

R.Paquin

A framework

based on

Freesurfer

4 steps

  • Conversion
  • Analyses
  • Quality Assessment
  • (Visualization)

Conversion

Analyses

Quality Assessment

Visualization

Conversion

- Single command line -

dcm2toad unf-data.tar.gz

Conversion

Analyses

Quality Assessment

Visualization

Conversion

dcm2toad unf-data.tar.gz
---------------------------------------
Please choose a subject to convert
 0.    None or exit
 1.    suj01
 2.    suj02
Enter your choice [0-2]: Default None [0]  :

---------------------------------------
Please select the Diffusion weighted image (DWI - DTI) image
 0.    None or exit
 1.    01-anat
 2.    02-dwi
 3.    03-b0_pa
Enter your choice [0-2]: Default None [0]  :2

Warning: thoses subjects seem's to share exactly the same layout?

    suj01,
    suj02 

Convert them all at the same time (y or n)? Default y :

Conversion

Analysis

Quality Assessment

Visualization

Parse archive

Conversion of each modality

Multiple subjects conversion

  • Parse archive
  • Conversion of each modality
  • Multiple subjects conversion
  • Extraction of parameters

config.cfg

[prefix]
anat = anat
dwi = dwi
grad = dwi
b0_pa = b0_pa

[denoising]
number_array_coil = 32

[correction]
#the phase encoding is from anterior to posterior
phase_enc_dir = 1
epi_factor = 120
echo_spacing = 0.689988270199
echo_time_dwi = 94

Conversion

Analysis

Quality Assessment

Visualization

Conversion

Analyses

Quality Assessment

Visualization

Analyses

- Single command line -

toad .

Conversion

Quality Assessment

Visualization

Analyses

Analyses

4 steps

  • Preparation
  • Preprocessing
  • Reconstruction
  • Outputs

Conversion

Analyses

Quality Assessment

Visualization

Conversion

Quality Assessment

Visualization

Analyses

Quality Assessment

  • One task - one QA
  • General summary
  • Global information
  • Visual output
  • Easy interface web-based

Conversion

Quality Assessment

Visualization

Analyses

Quality Assessment

Conversion

Quality Assessment

Visualization

Analyses

Conversion

Quality Assessment

Visualization

Analyses

Future developments

  • Dipy tractography
  • Add personal atlases
  • Artefact detection
  • Tractography post-processing
  • Metrics on tractography
  • ...

How to contribute:

             developers

  • Suggest new tasks
  • Get involved in the development 
  • Help us improving TOAD 
  • Suggest new tasks 
  • Help us improving TOAD 

             non-developers

http://unf-montreal.ca/toad/
toadunf.criugm@gmail.com

Thank you

TOAD presentation - SCIL

By Arnaud Boré

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TOAD presentation - SCIL

29 Octobre 2015

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