Skip to content

Commit

Permalink
Update FLAGS.md
Browse files Browse the repository at this point in the history
  • Loading branch information
m-reuter authored Mar 20, 2024
1 parent ddbb8c4 commit f69e54d
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions doc/overview/FLAGS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# FastSurfer_Flags
# FastSurfer Flags
Next, you will need to select the `*fastsurfer-flags*` and replace `*fastsurfer-flags*` with your options. Please see the Examples below for some example flags.

The `*fastsurfer-flags*` will usually include the subject directory (`--sd`; Note, this will be the mounted path - `/output` - for containers), the subject name/id (`--sid`) and the path to the input image (`--t1`). For example:
Expand Down Expand Up @@ -54,4 +54,4 @@ In the following, we give an overview of the most important options, but you can
* `--py`: Command for python, used in both pipelines. Default: python3.10
* `--conformed_name`: Name of the file in which the conformed input image will be saved. Default location: \$SUBJECTS_DIR/\$sid/mri/orig.mgz
* `--ignore_fs_version`: Switch on to avoid check for FreeSurfer version. Program will terminate if the supported version (see recon-surf.sh) is not sourced. Can be used for testing dev versions.
* `-h`, `--help`: Prints help text
* `-h`, `--help`: Prints help text

0 comments on commit f69e54d

Please sign in to comment.