@@ -57,9 +57,18 @@ Please find more information regarding this error from discussions on
57
57
58
58
Additionally, consider using the ``--low-mem `` flag, which will make some memory optimizations at the cost of disk space in the working directory.
59
59
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
+
60
69
ERROR: it appears that ``recon-all `` is already running
61
70
-------------------------------------------------------
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 *.
63
72
FreeSurfer creates files (called ``IsRunning.{rh,lh,lh+rh} ``, under the ``scripts/ `` folder)
64
73
to determine whether it is already executing ``recon-all `` on that particular subject
65
74
in another process, compute node, etc.
@@ -125,7 +134,7 @@ If you would like to run *fMRIPrep* in parallel on multiple subjects please use
125
134
How much CPU time and RAM should I allocate for a typical fMRIPrep run?
126
135
-----------------------------------------------------------------------
127
136
The 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.
129
138
More than 16 CPUs do not translate into faster processing times for a single subject. About 8GB of memory should be
130
139
available for a single subject preprocessing run.
131
140
0 commit comments