CLI equivalent of "No" on the auto-isotropic resample popup
shashank bansal
Dear Dr. Yeh,
I am running batch GQI reconstruction on a pediatric DTI cohort (native voxel size: 1.75 × 1.75 × 2.5 mm; 89 subjects; two timepoints) using the CLI on the Ubuntu 24.04 CPU build of the Hou release (2025.04.16).
I would like to preserve the native voxel size during reconstruction so that downstream atlas-label NIfTIs, which were generated in the original DWI space, remain aligned with the FZ output.
In the GUI workflow, this is straightforward. When the slice thickness exceeds the in-plane resolution, the reconstruction window displays a dialog asking whether to resample to 2 mm isotropic resolution, with Yes / No / Cancel options. Selecting No allows the reconstruction to proceed at the native anisotropic resolution.
However, I have not been able to find an equivalent option in the CLI workflow. Is there a command-line flag that corresponds to selecting No in the GUI, or have I overlooked it? If not, is there a recommended workaround for preserving the native voxel dimensions during batch reconstruction?
Thank you for your time and assistance.
Best regards,
Shashank Bansal
Frank Yeh
doesn't allow turning this off.
I fixed this and updated DSI Studio. The new build (should be ready in
a hour) can turn this off by setting --make_isotropic=0
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