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tools:freesurfer [2024/03/15 12:13] – created vsydnortools:freesurfer [2025/04/01 17:07] (current) – will
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 Freesurfer commands (recon-all and many, many more) can be run via the command line if you install the software and be sure to set up your terminal correctly with: Freesurfer commands (recon-all and many, many more) can be run via the command line if you install the software and be sure to set up your terminal correctly with:
 +
 +<code>
 export FREESURFER_HOME=/path/to/fs/software export FREESURFER_HOME=/path/to/fs/software
 source $FREESURFER_HOME/SetUpFreesurfer.sh source $FREESURFER_HOME/SetUpFreesurfer.sh
 export SUBJECTS_DIR=/path/to/fs/output export SUBJECTS_DIR=/path/to/fs/output
 +</code>
  
-However for ease + reproducibility, you can also use the freesurfer BIDS app: https://github.com/bids-apps/freesurfer +However for ease + reproducibility, you can also use the freesurfer BIDS app: https://github.com/bids-apps/freesurfer. Here is an [[https://github.com/LabNeuroCogDevel/corticalmyelin_maturation/blob/main/longitudinal_freesurfer/longitudinal_freesurfer_call.sh|example]]
  
  
 +For [[:grants:7t]] freesurfer has been run many times with different versions and different inputs. See [[:grants:7t:mr:freesurfer]].