Which version is "stable"?

Software Support
6

Hi @stbmtx,

Yes, it may soon be updated to allow for different spaces, but even when it does, it is not a path input, but rather a templateflow template name.

Download templateflow set with datalad (GitHub - templateflow/templateflow: The TemplateFlow Archive - A DataLad super-dataset · GitHub), datalad get the tpl-MNI152NLin2009cAsym folder (there may be other folders too, but at least that one to start), set export SINGULARITYENV_TEMPLATEFLOW_HOME='/your/downloaded/templateflow. Make sure it is mounted tin the container too.

Or if you want to use python instead of datalad get, here is basically what qsiprep is doing internally (as you can see here: qsiprep/qsiprep/interfaces/anatomical.py at c4dd8765ce47c3e00aa2eb3b976d451bf1fc5ade · PennLINC/qsiprep · GitHub):

from templateflow.api import get as get_template

anatomical_contrast = "T1w"
template_name = “MNI152NLin2009cAsym”
cohort = None
if "+" in template_name:
    template_name, cohort = template_name.split("+")

template_path = get_template(
    template_name,
    cohort=cohort,
    resolution="1",
    desc=None,
    suffix=anatomical_contrast,
    extension=".nii.gz",
)
mask_path = get_template(
    template_name,
    cohort=cohort,
    resolution="1",
    desc="brain",
    suffix="mask",
    extension=".nii.gz",
)

QSIRecon will now consider any < 1.0.0rc1 outputs legacy which are supported for now, but can’t guarantee for how long it will be supported for. Many of the changes in 1.0.0+ (prep and recon) deal with session wise longitudinal data. I don’t know your dataset, planned recon, or analysis goals, so I can’t say if it will be a big deal for you.

This shouldn’t impact longitudinal workflows, if it does, let us know!

Best,
Steven