Multi-band reverse phase encoding

[Loxlan]

Great tool! A quick question, how would you use the tool for a multi-band reverse-phase encoding DWI dataset similar to the HCP dataset.

eg, sub-xx_acq-multiband_run-01_dwi.bval sub-xx_acq-multiband_run-01_dwi.bvec sub-xx_acq-multiband_run-01_dwi.json sub-xx_acq-multiband_run-01_dwi.nii.gz

and reverse encoding as,
sub-xx_acq-multiband_run-02_dwi.bval sub-xx_acq-multiband_run-02_dwi.bvec sub-xx_acq-multiband_run-02_dwi.json sub-xx_acq-multiband_run-02_dwi.nii.gz

Any example of how to process this data with singularity will be helpful.

Thanks

[TheJaeger]

Hi @Loxlan. You would parse all of those series into PyDesigner with the syntax

pydesigner -s -o [PATH TO OUTPUT]  sub-xx_acq-multiband_run-01_dwi.nii.gz,sub-xx_acq-multiband_run-01_dwi.nii.gz

NOTE: No spaces between commas separating paths to input files.

This will allow PyDesigner to make its own internal decisions on achieving the highest possible SNR. Protocol information stored in JSON files is used to determine whether or not to run Gibbs unringing and figure out phase encoding information.

While we have not personally tested this with the HCP dataset, it should work if all relevant information is available in the JSON file. Running this in containers like Docker and Singularity will follow the same syntax with changes to file paths relative to mount point and/or other container control flags. An example on running PyDesigner within NeuroDock is available here.

[Loxlan]

OS-ubuntu 16.04, singularity 3.8 , neurodoc_v1.0-RC10 and the command,

singularity exec -B /home/john/test_data/sub-001:/mnt -e /scratch/jhon/neurodock_v1.0-RC10.sif pydesigner --standard --output /mnt/processed /mnt/dwi/sub-001_acq-multiband_run-01_dwi.nii.gz,/mnt/dwi/sub-001_acq-multiband_run-02_dwi.nii.gz

I should add, this error is given only when running on the cluster.

[TheJaeger]

It seems that the Singularity image is not equipped with a library required to run one or more Python packages. Depending on the configuration of Singularity image (I believe it may be Ubuntu), you can add the following line to neurodock_v1.0-RC10.sif:

apt-get install gcc-7 g++-7 gfortran-7

Rebuild the image and see if it solves the issue.

[Loxlan]

Thanks, will give it a shot.

[Loxlan]

Got the container working. Just one think, I have a partial fourier data and wanted to use the -eddy_options "--slm=linear", don't see how to specify this amoung the PyDesigner available options. Thanks

[TheJaeger]

PyDesigner does not allow users to specify any control flags for susceptibility induced distortion and eddy corrections. Control flags are internally handled to produce the most optimized image correction.

In your case, PyDesigner determines whether or not your input data set is fully shelled using the function preprocessing.mrinfoutil.isfullsphere to toggle between --slm=linear or --data_is_shelled in preprocessing.mrpreproc.undistort.

Note: Partial Fourier acquisitions affect Gibbs ringing correction rather than distortion correction, where the former is also automatically controlled by PyD.