Post-mortem macaque tractography

Post-mortem macaque tractography#

QuNex support processing of post-mortem macaque tractography. Below are the steps included in this processing pipeline.

Study creation#

Just like any other processing we have to start by creating a study:

qunex create_study \
    --studyFolder=/data/macaque_study

Importing the data into QuNex#

For onboarding post-mortem macaque data QuNex uses a specialized function called import_nhp. The import_nhp is capable of importing folders and archives (.zip and .tar) with data. The visualization below depicts how the input data should be structured.

sessions
|
├─ session1
|  └─ dMRI
|     ├─ bvals
|     ├─ bvecs
|     ├─ data.nii.gz
|     └─ nodif_brain_mask.nii.gz
|
└─ session2
   └─ dMRI
      ├─ bvals
      ├─ bvecs
      ├─ data.nii.gz
      └─ nodif_brain_mask.nii.gz

If the data onboarding process was successful dMRI images for each session will be stored in:

<sessionsfolder>/<session>/dMRI

Below is an example of data import:

qunex import_nhp \
    --sessionsfolder=/data/macaque_study/sessions \
    --inbox=/data/macaque_raw \
    --overwrite=yes

DTIFIT#

The next processing step in this pipeline is FSL's DTIFIT:

qunex dwi_dtifit \
    --sessionsfolder=/data/macaque_study/sessions \
    --sessions="hilary,jane" \
    --species="macaque"

BEDPOSTX#

After DTIFIT comes FSL's BEDPOSTX:

qunex dwi_bedpostx_gpu \
    --sessionsfolder=/data/macaque_study/sessions \
    --sessions="hilary,jane" \
    --species="macaque" \
    --bash="module load CUDA/9.1.85" \
    --scheduler="SLURM,time=12:00:00,cpus-per-task=1,mem-per-cpu=16000,gpus=1,jobname=qx_bedpostx"

Since QuNex uses FSL's GPU BEDPOSTX implementation the example above schedules the command for execution on a GPU node. It also loads the appropriate CUDA module through the bash parameter.

F99 registration#

Next, we use the dwi_f99 QuNex command to register our diffusion to the F99 atlas:

qunex dwi_f99 \
    --sessionsfolder=/data/macaque_study/sessions \
    --sessions="jane,hilary"

XTRACT tractography#

Finally, we can use dwi_xtract to get the tracts:

qunex dwi_xtract \
    --sessionsfolder=/gpfs/project/fas/n3/Studies/MBLab/HCPDev/jd_tests/macaque_study/sessions \
    --sessions="jane,hilary" \
    --species="macaque"

QuNex documentation