fix paths in doc [skip CI]

Author: fliem

README.md

@@ -60,15 +60,15 @@ The Freesurfer reconstruction should be performed with the
     Performs the three steps (prep, bedp, path) of Tracula's `trac-all`,
     reconstructing major fiber tracts form Freesurfer outputs and
     DWI raw data.
-    All data is written into *<output_dir>*.
+    All data is written into `{output_dir}`.
 
 - **group1**: Motion statistics
 
     Collects motion statistics for multiple subjects into one file.
     Additionally, total motion index (TMI, according to
     [Yendiki et al., 2013](http://doi.org/10.1016/j.neuroimage.2013.11.027)).
     Output is written to
-    *<output_dir>/00_group1_motion_stats/group_motion.tsv*.
+    `*{output_dir}/00_group1_motion_stats/group_motion.tsv`.
 
     *Note*: In deviation to the original equation
     (which includes rotation, translation, bad slices, dropout score),
@@ -84,59 +84,58 @@ The Freesurfer reconstruction should be performed with the
     Collects characteristics of a tract (average FA...)
     for multiple subjects.
     Output is written to
-    *<output_dir>/00_group2_tract_stats/<tract_name>_stats.tsv*.
+    `{output_dir}/00_group2_tract_stats/{tract_name}_stats.tsv`.
 
 
 ### Usage
 This App has the following command line arguments:
 
-        usage: phys.py [-h] --license_key LICENSE_KEY
-                       [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
-                       [--freesurfer_dir FREESURFER_DIR]
-                       [--stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]] [-v]
-                       bids_dir output_dir {participant,group1,group2}
-
-        BIDS App for Tracula processing stream.
-        https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
-
-        positional arguments:
-          bids_dir              The directory with the input dataset formatted
-                                according to the BIDS standard.
-          output_dir            The directory where the output files should be stored.
-                                If you are running group level analysis this folder
-                                should be prepopulated with the results of
-                                theparticipant level analysis.
-          {participant,group1,group2}
-                                Level of the analysis that will be performed.
-                                "participant": reconstructs paths (trac-all -prep,
-                                -bedp and -path), "group1": collects motion stats in
-                                one file, "group2": collects single subject overall
-                                path stats in one file.
-
-        optional arguments:
-          -h, --help            show this help message and exit
-          --license_key LICENSE_KEY
-                                FreeSurfer license key - letters and numbers after "*"
-                                in the email you received after registration. To
-                                register (for free) visit
-                                https://surfer.nmr.mgh.harvard.edu/registration.html
-                                (default: None)
-          --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
-                                The label of the participant that should be analyzed.
-                                The label corresponds to sub-<participant_label> from
-                                the BIDS spec (so it does not include "sub-"). If this
-                                parameter is not provided all subjects should be
-                                analyzed. Multiple participants can be specified with
-                                a space separated list. (default: None)
-          --freesurfer_dir FREESURFER_DIR
-                                The directory with the freesurfer data. If not
-                                specified, output_dir is assumed to be populated with
-                                freesurfer data. (default: None)
-          --stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]
-                                Participant-level trac-all stages to run. Passing "all" will
-                                run "prep", "bedp" and "path". (default: ['all'])
-          -v, --version         show program's version number and exit
-
+    usage: run.py [-h] --license_key LICENSE_KEY
+                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
+                  [--freesurfer_dir FREESURFER_DIR]
+                  [--stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]] [-v]
+                  bids_dir output_dir {participant,group1,group2}
+
+    BIDS App for Tracula processing stream.
+    https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
+
+    positional arguments:
+      bids_dir              The directory with the input dataset formatted
+                            according to the BIDS standard.
+      output_dir            The directory where the output files should be stored.
+                            If you are running group level analysis this folder
+                            should be prepopulated with the results of
+                            theparticipant level analysis.
+      {participant,group1,group2}
+                            Level of the analysis that will be performed.
+                            "participant": reconstructs paths (trac-all -prep,
+                            -bedp and -path), "group1": collects motion stats in
+                            one file, "group2": collects single subject overall
+                            path stats in one file.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --license_key LICENSE_KEY
+                            FreeSurfer license key - letters and numbers after "*"
+                            in the email you received after registration. To
+                            register (for free) visit
+                            https://surfer.nmr.mgh.harvard.edu/registration.html
+                            (default: None)
+      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
+                            The label of the participant that should be analyzed.
+                            The label corresponds to sub-<participant_label> from
+                            the BIDS spec (so it does not include "sub-"). If this
+                            parameter is not provided all subjects should be
+                            analyzed. Multiple participants can be specified with
+                            a space separated list. (default: None)
+      --freesurfer_dir FREESURFER_DIR
+                            The directory with the freesurfer data. If not
+                            specified, output_dir is assumed to be populated with
+                            freesurfer data. (default: None)
+      --stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]
+                            Participant-level trac-all stages to run. Passing"all"
+                            will run "prep", "bedp" and "path". (default: ['all'])
+      -v, --version         show program's version number and exit
 
 
 ##
@@ -154,9 +153,9 @@ To run it in participant level mode (for one participant):
          --freesurfer_dir /freesurfer
 
 **Note that** the path specified in --freesurfer_dir needs to be the
-mount point inside the docker container (e.g., */freesurfer*, specified
+mount point inside the docker container (e.g., `/freesurfer`, specified
 in the 4th line of the previous command, after the ":"), not the
-path on your hard drive (e.g., */data/ds114/derivates/freesurfer*)
+path on your hard drive (e.g., `/data/ds114/derivates/freesurfer`)
 
 #### Group level