Doc tweaks

bidscoin/cli/_medeface.py

@@ -36,7 +36,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
     parser.add_argument('-m','--maskpattern',       help="Globlike search pattern (relative to the subject/session folder) to select the images from which the defacemask is computed, e.g. 'anat/*_part-mag_*_T2starw*'. If not given then 'pattern' is used")
     parser.add_argument('-p','--participant_label', help='Space separated list of sub-# identifiers to be processed (the sub-prefix can be left out). If not specified then all sub-folders in the bidsfolder will be processed', nargs='+')
     parser.add_argument('-o','--output',            help=f"A string that determines where the defaced images are saved. It can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives'. If output is left empty then the original images are replaced by the defaced images")
-    parser.add_argument('-c','--cluster',           help='Submit the deface jobs to a high-performance compute (HPC) cluster', action='store_true')
+    parser.add_argument('-c','--cluster',           help='Use the DRMAA library to submit the deface jobs to a high-performance compute (HPC) cluster', action='store_true')
     parser.add_argument('-n','--nativespec',        help='DRMAA native specifications for submitting deface jobs to the HPC cluster', default='-l walltime=00:30:00,mem=2gb')
     parser.add_argument('-a','--args',              help='Additional arguments (in dict/json-style) that are passed to pydeface. See examples for usage', type=json.loads, default={})
     parser.add_argument('-f','--force',             help='Process all images, regardless if images have already been defaced (i.e. if {"Defaced": True} in the json sidecar file)', action='store_true')

bidscoin/cli/_slicereport.py

@@ -30,11 +30,11 @@ def get_parser():
   c                  : Add a red dot marker to top right of image
 
 OUTPUTS:
-  x/y/z [SLICE] [..] : Output sagittal, coronal or axial slice (if [SLICE] > 0 it is a
-                       fraction of image dimension, if < 0, it is an absolute slice number)
+  x/y/z [SLICE] [..] : Output sagittal, coronal or axial slice (if SLICE > 0 it is a fraction of
+                       image dimension, if < 0, it is an absolute slice number)
   a                  : Output mid-sagittal, -coronal and -axial slices into one image
-  A [WIDTH]          : Output _all_ axial slices into one image of _max_ width [WIDTH]
-  S [SAMPLE] [WIDTH] : As `A` but only include every [SAMPLE]'th slice
+  A [WIDTH]          : Output _all_ axial slices into one image of _max_ width WIDTH
+  S [SAMPLE] [WIDTH] : As `A` but only include every SAMPLE'th slice
   LF                 : Start a new line (i.e. works like a row break)
 
 examples:

docs/bidsapps.rst

@@ -147,8 +147,8 @@ This utility is very similar to the `deface <#defacing>`__ utility above, except
                             name of a BIDS datatype folder, such as 'anat', or of the derivatives folder,
                             i.e. 'derivatives'. If output is left empty then the original images are
                             replaced by the defaced images (default: None)
-      -c, --cluster         Submit the deface jobs to a high-performance compute (HPC) cluster (default:
-                            False)
+      -c, --cluster         Use the DRMAA library to submit the deface jobs to a high-performance compute
+                            (HPC) cluster (default: False)
       -n NATIVESPEC, --nativespec NATIVESPEC
                             DRMAA native specifications for submitting deface jobs to the HPC cluster
                             (default: -l walltime=00:30:00,mem=2gb)
@@ -230,9 +230,9 @@ Quality control
 
     usage: slicereport [-h] [-o OUTLINEPATTERN] [-i OUTLINEIMAGE]
                        [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-r REPORTFOLDER]
-                       [-x XLINKFOLDER [XLINKFOLDER ...]] [-q QCSCORES [QCSCORES ...]] [-c]
-                       [--options OPTIONS [OPTIONS ...]] [--outputs OUTPUTS [OUTPUTS ...]]
-                       [--suboptions SUBOPTIONS [SUBOPTIONS ...]]
+                       [-x XLINKFOLDER [XLINKFOLDER ...]] [-q QCSCORES [QCSCORES ...]]
+                       [-c {torque,slurm}] [--options OPTIONS [OPTIONS ...]]
+                       [--outputs OUTPUTS [OUTPUTS ...]] [--suboptions SUBOPTIONS [SUBOPTIONS ...]]
                        [--suboutputs SUBOUTPUTS [SUBOUTPUTS ...]]
                        bidsfolder pattern
 
@@ -275,7 +275,6 @@ Quality control
       -c {torque,slurm}, --cluster {torque,slurm}
                             Use `torque` or `slurm` to submit the slicereport jobs to a high-performance
                             compute (HPC) cluster
-      -c, --cluster         Use `qsub` to submit the slicer jobs to a high-performance compute (HPC) cluster
       --options OPTIONS [OPTIONS ...]
                             Main options of slicer (see below). (default: "s 1")
       --outputs OUTPUTS [OUTPUTS ...]
@@ -301,11 +300,11 @@ Quality control
       c                  : Add a red dot marker to top right of image
 
     OUTPUTS:
-      x/y/z [SLICE] [..] : Output sagittal, coronal or axial slice (if [SLICE] > 0 it is a
-                           fraction of image dimension, if < 0, it is an absolute slice number)
+      x/y/z [SLICE] [..] : Output sagittal, coronal or axial slice (if SLICE > 0 it is a fraction of
+                           image dimension, if < 0, it is an absolute slice number)
       a                  : Output mid-sagittal, -coronal and -axial slices into one image
-      A [WIDTH]          : Output _all_ axial slices into one image of _max_ width [WIDTH]
-      S [SAMPLE] [WIDTH] : As `A` but only include every [SAMPLE]'th slice
+      A [WIDTH]          : Output _all_ axial slices into one image of _max_ width WIDTH
+      S [SAMPLE] [WIDTH] : As `A` but only include every SAMPLE'th slice
       LF                 : Start a new line (i.e. works like a row break)
 
     examples: