[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 <[email protected]>
PennLINC · Sep 29, 2023 · 699c232 · 699c232
1 parent 52f0b0d
commit 699c232
Showing 1 changed file with 5 additions and 1 deletion.
diff --git 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 <https://github.com/PennBBL/qsiprep/blob/master/qsiprep/data/mni_1mm_t1w_lps.nii.gz>`_
 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.
+in the header. **Be sure to check for alignment and orientation** in your outputs.