From 699c2320e90a5263436953c83c9bc118e9f6b357 Mon Sep 17 00:00:00 2001 From: Pierre <65797646+pierre-nedelec@users.noreply.github.com> Date: Fri, 29 Sep 2023 10:43:58 -0700 Subject: [PATCH] [DOC] add `--recon-only` flag in `reconstruction.rst` (#628) * Mention --recon-only * formatting as note * Update .zenodo.json thanks @matt * Update .zenodo.json --------- Co-authored-by: Matt Cieslak --- docs/reconstruction.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/reconstruction.rst b/docs/reconstruction.rst index e35d0d71..6fba7886 100644 --- a/docs/reconstruction.rst +++ b/docs/reconstruction.rst @@ -11,6 +11,10 @@ by specifying a JSON file with the ``--recon-spec`` option. Here we use "reconstruction" to mean reconstructing ODFs/FODs/EAPs and connectivity matrices from the preprocessed diffusion data. +.. note:: + In the current implementation, if you want to only run reconstruction, you will + need to pass the ``--recon-only`` argument as well. + The easiest way to get started is to use one of the :ref:`preconfigured_workflows`. Instead of specifying a path to a file you can choose from the following: @@ -556,4 +560,4 @@ The nifti images should be registered to the `MNI152NLin2009cAsym `_ included in ``qsiprep``. It is essential that your images are in the LPS+ orientation and have the sform zeroed-out -in the header. **Be sure to check for alignment and orientation** in your outputs. \ No newline at end of file +in the header. **Be sure to check for alignment and orientation** in your outputs.