Measure of the random Brownian motion of water molecules within a voxel of tissue
Diffusion weighted Imaging
Publications
Multiple softwares
Mission
DTI and HARDI reconstruction
and metrics extraction
Streamlines reconstruction
Diffusion weighted Imaging
Multiple softwares
Mission
Publications
Soares et al (2013) Frontiers in neuroscience
DTIStudio
CAMINO
DTIQuery
TrackVis
Tracula
MRDiffusion
JIST
SATURN
TORTOISE
Offer an
automated pipeline to process diffusion neuroimaging data
Diffusion weighted Imaging
Multiple softwares
Mission
Publications
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
Freesurfer
Conversion
Analyses
Quality Assessment
Visualization
- Single command line -
dcm2toad unf-data.tar.gz
Conversion
Analyses
Quality Assessment
Visualization
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
[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
- Single command line -
toad .
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Analyses
Quality Assessment
Visualization
00 Backup
01 Preparation
Create "missing" files
Check orientations
Conversion
Analyses
Quality Assessment
Visualization
Preparation
Preprocessing
Reconstruction
Outputs
02 Parcellation
02 Parcellation
04 Correction
03 Denoising
05 Upsampling
06 Registration
04 Correction
03 Denoising
05 Upsampling
Conversion
Analyses
Quality Assessment
Visualization
Preparation
Preprocessing
Reconstruction
Outputs
07 Masking
06 Registration
Future enhancement
Automatic creation of ROIs for tractographies
08-10 Tensor reconstruction
11-12 fODF reconstruction
08-10 Tensor reconstruction
11-12 fODF reconstruction
13-14 Tractographies
FA
AD
RD...
CSD PEAKS
NUFO
Conversion
Analyses
Quality Assessment
Visualization
Preparation
Preprocessing
Reconstruction
Outputs
Conversion
Analyses
Quality Assessment
Visualization
16 Outputs
dwi.nii.gz
suj01_lpca.b
suj01.bvals
suj01.bvecs
anat.nii.gz
atlas.nii.gz
dipy_ad.nii.gz
dipy_csd.nii.gz
dipy_fa.nii.gz
dipy_gfa.nii.gz
dipy_md.nii.gz
dipy_nufo.nii.gz
dipy_rd.nii.gz
mask.nii.gz
fsl_ad.nii.gz
fsl_fa.nii.gz
fsl_md.nii.gz
fsl_rd.nii.gz
mrtrix_ad.nii.gz
mrtrix_csd.nii.gz
mrtrix_fa.nii.gz
mrtrix_md.nii.gz
mrtrix_nufo.nii.gz
mrtrix_rd.nii.gz
Preparation
Preprocessing
Reconstruction
Outputs
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Quality Assessment
Visualization
Analyses
DWI
FA
SSE
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Quality Assessment
Visualization
Analyses
Conversion
Quality Assessment
Visualization
Analyses
http://www.tractometer.org/
http://unf-montreal.ca/toad/
toadunf.criugm@gmail.com