software: ashs typos

software/ashs.rst

@@ -24,7 +24,7 @@ set of patches developed at MPIB to work with Torque.
 
 
 Atlases
----
+-------
 
 The atlases available need to match the ashs version to function properly.
 
@@ -44,12 +44,12 @@ download your on. Right now there are:
 
 
 The data in *legacy* is supposed to work with the 0.1.x-branch of ASHS and the
-data in *1.0* have been created with the newer branch.
+atlases in *1.0* have been created with the newer branch.
 
 Parallelization
----
+---------------
 
-The legacy branch of ASHS necessarily relied internally on qsub. Segmentation,
+The legacy branch of ASHS necessarily relied on qsub internally. Segmentation,
 even for a single subject, was almost prohibitively slow to be run on a single
 core. The patched version should distribute nicely over the cluster when using
 the parameter `-Q` (see below for examples).
@@ -62,19 +62,20 @@ original scripts.
 
 The table below shows a comparison for a test segmentation run using the **1.0** branch:
 
-========== ===========
- cores      real time
-========== ===========
+=========  =========
+cores      real time
+=========  =========
 800 (pbs)     20m
 20  (par)     15m
 8             23m
 4             35m
 2             55m
 1            110m
+=========  =========
 
 
 Due to defensive inter-stage delays, the first approach (using cluster-wide
-distribution with `-Q`) was even slower than 20-core parallel version on a
+distribution with `-Q`) was even slower than the 20-core parallel version on a
 single node using `-P`. Even single-threaded performance is at acceptable
 speeds now. With recent workstations a batch segmentation for a small number of
 subjects could be done overnight - without a cluster.
@@ -83,19 +84,18 @@ subjects could be done overnight - without a cluster.
 Segmentation
 -------------
 
-Given your files are already in place a typical invocation for a single subject
+Given your files are already in place, a typical invocation for a single subject
 would then be **either**:
 
-old approach
+Old approach
 ^^^^^^^^^^^^
-(using internal qsub)
 
 .. code-block:: bash
 
-	[krause@master ~] module load ashs
-    [krause@master ~] $ASHS_ROOT/bin/ashs_main.sh \
-                      -a /opt/software/ashs/data/1.0/ashs_atlas_mpib_20180208\
-                      -g T1.nii -f T2.nii -w wdir -T -Q
+   [krause@master ~] module load ashs
+   [krause@master ~] $ASHS_ROOT/bin/ashs_main.sh \
+                     -a /opt/software/ashs/data/1.0/ashs_atlas_mpib_20180208\
+                     -g T1.nii -f T2.nii -w wdir -T -Q
 
 
 
@@ -119,7 +119,9 @@ For a number of image pairs you could use a simple for loop.
 .. code-block:: bash
 
     for id in 01 03 10 32 ; do
-       $ASHS_ROOT/bin/ashs_main.sh -a /opt/ashs/data/atlas_upennpmc/ -g T1_${id}.nii -f T2_${id}.nii -w wdir_${id} -T -Q >ashs_${id}.log 2>&1 &
+       $ASHS_ROOT/bin/ashs_main.sh -a /opt/software/ashs/data/1.0/ashs_atlas_mpib_20180208/ \
+	                               -g T1_${id}.nii -f T2_${id}.nii -w wdir_${id} -T -Q \
+								    >ashs_${id}.log 2>&1 &
     done
 
 Be careful with looping over a large number (>30) of image pairs in this way as
@@ -127,7 +129,7 @@ some intermediate steps will generate a lot of jobs on its own. Also check
 ``qstat`` and the log file you specified to track ASHS' progress.
 
 
-new approach
+New approach
 ^^^^^^^^^^^^
 
 Since ASHS version 1.0 this is the preferred way to submit segmentations for a number of subjects.
@@ -154,12 +156,12 @@ Looping over a number of subject IDs would look something like this.
 
     for id in 01 03 10 32 ; do
         export SUBJECT_ID=$id
-        qsub ashs_job.pbs -l nodes=1,ppn=8,mem=10gb -V
+        qsub ashs_job.pbs -l nodes=1,ppn=8,mem=10gb -v SUBJECT_ID
     done
 
-In this case the option `-V` to qsub instructs qsub to inherit all formerly
-exported variables. This way the variable `SUBJECT_ID` is accessible in the job
-context.
+In this case the option `-v` to qsub instructs qsub to inherit a named,
+formerly exported, variable. This way the variable `SUBJECT_ID` becomes
+accessible in the job context.
 
 Known Issues
 ------------