16 septembre 2016

MISSION

To offer an

automated pipeline to process diffusion neuroimaging data

Easy to use (to convert, to run the pipeline)
Well documented (English and French version)
- http://unf-montreal.ca/toad/html/en/index.html
Web based QA

10 labs have used TOAD during its first year

Conversion
Analysis
QA
Visualization

Updates

- Works with Skyra scanner (soon with Prisma)

- Get a lot more information from dicom header saved in your config.cfg file

- Single command line -

dcm2toad unf-data.tar.gz

Config.cfg

[prefix]
b0_ap = b0_ap
anat = anat
dwi = dwi
grad = dwi
mag = mag
phase = phase

[correction]
echo_spacing = 0.689982557241
phase_enc_dir = 1
epi_factor = 96.0
echo_time_mag1 = 4.92
echo_time_mag2 = 7.38

[denoising]
number_array_coil = 4

[methodology]
manufacturer = SIEMENS
magneticfieldstrength = 3
mrmodel = TrioTim
t1_tr = 2300.0
t1_te = 2.98
t1_ti = 900.0
t1_flipangle = 9.0
t1_voxelsize = [1.0, 1.0, 1.0]
t1_matrixsize = [256, 256]
t1_numberslices = 176
t1_fov = 256.0
t1_studyuid = 1.3.12.2.1107.5....
dwi_tr = 9300.0
dwi_te = 94.0
dwi_flipangle = 90.0
dwi_voxelsize = [2.0, 2.0, 2.0]
dwi_matrixsize = [96, 96]
dwi_numberslices = 64
dwi_fov = 192.0
dwi_studyuid = 1.3.12.2.1107.5.2....
dwi_bvalue = 1000
dwi_numdirections = 64
dwi_patfactor = 1.0
intrasession = False

[prefix]
b0_ap = b0_ap
anat = anat
dwi = dwi
grad = dwi
mag = mag
phase = phase

[correction]
echo_spacing = 0.689982557241
phase_enc_dir = 1
epi_factor = 96.0
echo_time_mag1 = 4.92
echo_time_mag2 = 7.38

[denoising]
number_array_coil = 4

- Single command line -

toad .

In development

More options

In development

More options

New task

New Tasks

- TractQuerier (Wassermann et al. 2016)

Dictionary

Atlas

Caudate.left |= 11
Caudate.right |= 50
Putamen.right |= 51
Pallidum.right |= 52
Hippocampus.right |= 53
Amygdala.right |= 54
Insula.right |= 55

Dictionary

Caudate.left |= 11
Caudate.right |= 50
Putamen.right |= 51
Pallidum.right |= 52
Hippocampus.right |= 53
Amygdala.right |= 54
Insula.right |= 55

Queries

cc_superiotemporal = 
       superiortemporal.left 
       and superiortemporal.right 
       not in subcortical.left
       not in subcortical.right
       not in cerebellum