[RESOLVED] Dwi_legacy_gpu support for muitlple dwi files in each subject

Issues
1

Dear Jure,

How to run dwi_legacy_gpu command for a dataset with multiple dwi nii files in each subject as shown below?

qunex_pipeline_run1…
sessions
xyz
Diffusion
sub-xyz_ses-01_run-01_dwi.bval
sub-xyz_ses-01_run-01_dwi.bvec
sub-xyz_ses-01_run-01_dwi.json
sub-xyz_ses-01_run-01_dwi.nii.gz
sub-xyz_ses-01_run-02_dwi.bval
sub-xyz_ses-01_run-02_dwi.bvec
sub-xyz_ses-01_run-02_dwi.json
sub-xyz_ses-01_run-02_dwi.nii.gz

I am unable to use the below dwi_legacy_gpu command at subject level as the diffdatasuffix param is a string and is not allowing wildcard like “run.*_dwi” .

Please let me know if I am missing anything or you have any other alternative solution.

qunex dwi_legacy_gpu \
    --sessionsfolder='qunex_pipeline_run1/sessions' \
    --sessions='xyx' \
    --pedir='1' \
    --echospacing='0.69' \
    --te='2.46' \
    --unwarpdir='x-' \
    --diffdatasuffix='run-01_dwi' \
    --usefieldmap='yes' \
    --overwrite='yes'

Thanks
Suhas Reddy

2

Hi Suhas,

In this case, we usually merge the data manually into a single image and then process it, see [RESOLVED] Hcp_diffusion on a diffusion dataset with a single phase encoding direction - #9 by ehui for details.

I will think about whether we could somehow easily integrate this into the command itself.

Jure

3

In the next version, we will add the option of specifying multiple input images. If multiple images are provided then QuNex will automatically merge the data and continue with processing.

Jure

4

We are close to the QuNex 0.98.1 release, in this release you can provide a comma separated list for the diffdatasuffix parameter. QuNex will then use the provided suffixes to merge the images behind them into a single one and run dwi_legacy_gpu over the merged image.