Skip to content

Commit ea4e7b4

Browse files
oestebaneffigies
andauthored
Apply suggestions from code review
Co-Authored-By: Chris Markiewicz <[email protected]>
1 parent 29b05be commit ea4e7b4

File tree

1 file changed

+13
-12
lines changed

1 file changed

+13
-12
lines changed

docs/usage.rst

Lines changed: 13 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -106,28 +106,29 @@ Reusing precomputed derivatives
106106
Reusing a previous, partial execution of *fMRIPrep*
107107
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108108
*fMRIPrep* will pick up where it left off a previous execution, so long the work directory
109-
points to the same location, and such directory has not been changed/manipulated.
109+
points to the same location, and this directory has not been changed/manipulated.
110110

111111
Using a previous run of *FreeSurfer*
112112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
113-
*fMRIPrep* will automatically reuse a previous run of *FreeSurfer* if the ``$SUBJECTS_DIR``
114-
points to a subfolder called ``freesurfer/`` under the folder selected as output directory
115-
(``<output_dir>/freesurfer``).
116-
Please note that derivatives for all participants, as generated by FreeSurfer_ must be found
117-
under that directory.
118-
Alternatively, you can use the ``--fs-subjects-dir`` flag to specify a different location
119-
for the existing FreeSurfer outputs.
113+
*fMRIPrep* will automatically reuse previous runs of *FreeSurfer* if a subject directory
114+
named ``freesurfer/`` is found in the output directory (``<output_dir>/freesurfer``).
115+
Reconstructions for each participant will be checked for completeness, and any missing
116+
components will be recomputed.
117+
You can use the ``--fs-subjects-dir`` flag to specify a different location to save
118+
FreeSurfer outputs.
119+
If precomputed results are found, they will be reused.
120120

121121
The *anatomical fast-track*
122122
~~~~~~~~~~~~~~~~~~~~~~~~~~~
123123
Starting with version 20.1.0, *fMRIPrep* has a command-line argument (``--anat-derivatives <PATH>``)
124-
to prescribe a path from which the preprocessed information derived from the T1w, T2w (if present) and
124+
to indicate a path from which the preprocessed information derived from the T1w, T2w (if present) and
125125
FLAIR (if present) images.
126126
This feature was envisioned to help process very large multi-session datasets where the anatomical
127127
images can be averaged (i.e., anatomy is not expected to vary substantially across sessions).
128-
An example of this kind of processing is `My Connectome <https://openneuro.org/datasets/ds000031/>`__.
129-
The dataset contains 107 sessions for a single-subject.
130-
Most of them containing anatomical information which, given the design of the dataset, can be averaged
128+
An example where this kind of processing would be useful is
129+
`My Connectome <https://openneuro.org/datasets/ds000031/>`__, a dataset that contains
130+
107 sessions for a single-subject.
131+
Most of these sessions contain anatomical information which, given the design of the dataset, can be averaged
131132
across sessions as no substantial changes should happen.
132133
In other words, the anatomical information of the dataset can be considered as *cross-sectional*.
133134
Before version 20.1.0, preprocessing this dataset would be hard for two limitations:

0 commit comments

Comments
 (0)