@@ -57,9 +57,18 @@ Please find more information regarding this error from discussions on
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5858Additionally, consider using the ``--low-mem `` flag, which will make some memory optimizations at the cost of disk space in the working directory.
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60+
61+ I have already run ``recon-all `` on my subjects, can I reuse my outputs?
62+ ------------------------------------------------------------------------
63+ Yes, as long as the FreeSurfer _ version previously used was ``6.0.0 `` or newer.
64+ If running with FreeSurfer, *fMRIPrep * checks if the output directory contains a ``freesurfer ``
65+ directory and reuses the outputs found.
66+ Alternatively, you can use the ``--fs-subjects-dir `` flag to specify a different location for the existing FreeSurfer outputs.
67+
68+
6069ERROR: it appears that ``recon-all `` is already running
6170-------------------------------------------------------
62- When running FreeSurfer _ 's ``recon-all ``, an error may say *it appears it is already running *.
71+ When running FreeSurfer 's ``recon-all ``, an error may say *it appears it is already running *.
6372FreeSurfer creates files (called ``IsRunning.{rh,lh,lh+rh} ``, under the ``scripts/ `` folder)
6473to determine whether it is already executing ``recon-all `` on that particular subject
6574in another process, compute node, etc.
@@ -125,7 +134,7 @@ If you would like to run *fMRIPrep* in parallel on multiple subjects please use
125134How much CPU time and RAM should I allocate for a typical fMRIPrep run?
126135-----------------------------------------------------------------------
127136The recommended way to run fMRIPrep is to process one subject per container instance. A typical preprocessing run
128- without surface processing with freesurfer can be completed in about 2 hours with 4 CPUs or in about 1 hour with 16 CPUs.
137+ without surface processing with FreeSurfer can be completed in about 2 hours with 4 CPUs or in about 1 hour with 16 CPUs.
129138More than 16 CPUs do not translate into faster processing times for a single subject. About 8GB of memory should be
130139available for a single subject preprocessing run.
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