BundleParc-flow

BundleParc-flow is a workflow for parcellating white matter bundles from diffusion MRI using BundleParc and nextflow.

Paper submitted to Medical Image Analysis. In the meantime, please contact us for acknowledgments.

Requirements

• Nextflow
• Docker or Singularity

Installation

1. Clone the repository:

   git clone [email protected]:scil-vital/BundleParc-flow.git
   cd BundleParc-flow

That's it !

Usage

1. From FOD

  nextflow run main.nf --fodf <input> -profile docker --nb_pts <nb>

2. From DWI

nextflow run main.nf --dwi <input> -profile docker --nb_pts <nb>

See USAGE for more instructions on how to run the workflow. Have a question ? Found a problem ? Please open an issue or contact me at antoine (dot) theberge (at) usherbrooke (dot) ca.

Bundles

Bundle defintions follow TractSeg's, without the whole corpus callosum. However it is still represented in 7 subparts which should be coherent between their parcellations.

For completeness the bundle definitions are listed below

AF_left        (Arcuate fascicle)
AF_right
ATR_left       (Anterior Thalamic Radiation)
ATR_right
CA             (Commissure Anterior)
CC_1           (Rostrum)
CC_2           (Genu)
CC_3           (Rostral body (Premotor))
CC_4           (Anterior midbody (Primary Motor))
CC_5           (Posterior midbody (Primary Somatosensory))
CC_6           (Isthmus)
CC_7           (Splenium)
CG_left        (Cingulum left)
CG_right   
CST_left       (Corticospinal tract)
CST_right 
MLF_left       (Middle longitudinal fascicle)
MLF_right
FPT_left       (Fronto-pontine tract)
FPT_right 
FX_left        (Fornix)
FX_right
ICP_left       (Inferior cerebellar peduncle)
ICP_right 
IFO_left       (Inferior occipito-frontal fascicle) 
IFO_right
ILF_left       (Inferior longitudinal fascicle) 
ILF_right 
MCP            (Middle cerebellar peduncle)
OR_left        (Optic radiation) 
OR_right
POPT_left      (Parieto‐occipital pontine)
POPT_right 
SCP_left       (Superior cerebellar peduncle)
SCP_right 
SLF_I_left     (Superior longitudinal fascicle I)
SLF_I_right 
SLF_II_left    (Superior longitudinal fascicle II)
SLF_II_right
SLF_III_left   (Superior longitudinal fascicle III)
SLF_III_right 
STR_left       (Superior Thalamic Radiation)
STR_right 
UF_left        (Uncinate fascicle) 
UF_right 
T_PREF_left    (Thalamo-prefrontal)
T_PREF_right 
T_PREM_left    (Thalamo-premotor)
T_PREM_right 
T_PREC_left    (Thalamo-precentral)
T_PREC_right 
T_POSTC_left   (Thalamo-postcentral)
T_POSTC_right 
T_PAR_left     (Thalamo-parietal)
T_PAR_right 
T_OCC_left     (Thalamo-occipital)
T_OCC_right 
ST_FO_left     (Striato-fronto-orbital)
ST_FO_right 
ST_PREF_left   (Striato-prefrontal)
ST_PREF_right 
ST_PREM_left   (Striato-premotor)
ST_PREM_right 
ST_PREC_left   (Striato-precentral)
ST_PREC_right 
ST_POSTC_left  (Striato-postcentral)
ST_POSTC_right
ST_PAR_left    (Striato-parietal)
ST_PAR_right 
ST_OCC_left    (Striato-occipital)
ST_OCC_right

To cite

Journal paper submitted. Please contact us for acknowledgement.