Minor doc tweaks

docs/bidsapps.rst

@@ -3,9 +3,7 @@ BIDS-apps
 
 Metadata editing
 ----------------
-If you have a previously converted BIDS data repository and you would like to retrospectively change or replace one or more metadata fields in the json sidecar files you can use ``fixmeta``. Fixmeta is more powerful than conventional find-and-replace tools in that fixmeta can leverage BIDScoin's `special bidsmap features <./bidsmap.html#special-bidsmap-features>`__
-
-::
+If you have a previously converted BIDS data repository and you would like to retrospectively change or replace one or more metadata fields in the json sidecar files you can use ``fixmeta``. Fixmeta is more powerful than conventional find-and-replace tools in that fixmeta can leverage BIDScoin's `special bidsmap features <./bidsmap.html#special-bidsmap-features>`__::
 
     usage: fixmeta [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-b BIDSMAP]
                    bidsfolder pattern metadata
@@ -44,9 +42,7 @@ If you have a previously converted BIDS data repository and you would like to re
 Multi-echo combination
 ----------------------
 
-Before sharing or pre-processing their images, you may want to combine the separate the individual echos of multi-echo MRI acquisitions. The ``echcombine``-tool is a wrapper around ``mecombine`` that writes BIDS valid echo-combined output data.
-
-::
+Before sharing or pre-processing their images, you may want to combine the separate the individual echos of multi-echo MRI acquisitions. The ``echcombine``-tool is a wrapper around ``mecombine`` that writes BIDS valid echo-combined output data.::
 
     usage: echocombine [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT]
                        [-a {PAID,TE,average}] [-w [WEIGHTS ...]] [-f]
@@ -94,9 +90,7 @@ Before sharing or pre-processing their images, you may want to combine the separ
 Defacing
 --------
 
-Before sharing or pre-processing your data, you may want to deface your anatomical MRI scans to protect the privacy of your participants. The ``deface``-tool is a wrapper around `pydeface <https://github.com/poldracklab/pydeface>`__ that writes BIDS valid defaced output images. NB: pydeface requires `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation>`__ to be installed on the system.
-
-::
+Before sharing or pre-processing your data, you may want to deface your anatomical MRI scans to protect the privacy of your participants. The ``deface``-tool is a wrapper around `pydeface <https://github.com/poldracklab/pydeface>`__ that writes BIDS valid defaced output images. NB: pydeface requires `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation>`__ to be installed on the system.::
 
     usage: deface [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT] [-c] [-n NATIVESPEC]
                   [-a ARGS] [-f]
@@ -149,9 +143,7 @@ Before sharing or pre-processing your data, you may want to deface your anatomic
 Multi-echo defacing
 -------------------
 
-This utility is very similar to the `deface <#defacing>`__ utility above, except that it can handle multi-echo data.
-
-::
+This utility is very similar to the `deface <#defacing>`__ utility above, except that it can handle multi-echo data.::
 
     usage: medeface [-h] [-m MASKPATTERN] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT] [-c]
                     [-n NATIVESPEC] [-a ARGS] [-f]
@@ -210,9 +202,7 @@ This utility is very similar to the `deface <#defacing>`__ utility above, except
 Skull-stripping
 ---------------
 
-The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS valid brain extracted output data
-
-::
+The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS valid brain extracted output data::
 
     usage: skullstrip [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-m MASKED]
                       [-o OUTPUT [OUTPUT ...]] [-f] [-a ARGS] [-c] [-n NATIVESPEC]
@@ -269,9 +259,7 @@ The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS
 Quality control
 ---------------
 
-``Slicereport`` is a very flexible QC report generator for doing visual inspections on your BIDS data.
-
-::
+``Slicereport`` is a very flexible QC report generator for doing visual inspections on your BIDS data.::
 
     usage: slicereport [-h] [-o OUTLINEPATTERN] [-i OUTLINEIMAGE]
                        [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-r REPORTFOLDER]

docs/utilities.rst

@@ -4,9 +4,7 @@ Utilities
 bidscoin
 --------
 
-The bidscoin command-line utility serves as a central starting point to test and manage your BIDScoin installation
-
-::
+The bidscoin command-line utility serves as a central starting point to test and manage your BIDScoin installation::
 
     usage: bidscoin [-h] [-l] [-p] [-i INSTALL [INSTALL ...]] [-u UNINSTALL [UNINSTALL ...]]
                     [-d DOWNLOAD] [-t [TEST]] [-b BIDSMAPTEST] [-c CREDITS [CREDITS ...]]
@@ -65,9 +63,7 @@ The bidscoin command-line utility serves as a central starting point to test and
 dicomsort
 ---------
 
-The ``dicomsort`` command-line tool is a utility to move your flat- or DICOMDIR-organized files (see `above <#required-source-data-structure>`__) into a 'seriesfolder' organization. This can be useful to organize your source data in a more convenient and human readable way (DICOMDIR or flat DICOM directories can often be hard to comprehend). The BIDScoin tools will run dicomsort in a temporary folder if your data is not already organized in series-folders, so in principle you don't really need to run it yourself (unless when you have a single multi-subject DICOMDIR file for your entire repository). Running dicomsort beforehand does, however, give you more flexibility in handling special cases that are not handled properly and it can also give you a speed benefit. If dicomsort do not satisfy your needs, then have a look at this `DICOM reorganize <https://github.com/robertoostenveld/bids-tools/blob/master/doc/reorganize_dicom_files.md>`__ tool.
-
-::
+The ``dicomsort`` command-line tool is a utility to move your flat- or DICOMDIR-organized files (see `above <#required-source-data-structure>`__) into a 'seriesfolder' organization. This can be useful to organize your source data in a more convenient and human readable way (DICOMDIR or flat DICOM directories can often be hard to comprehend). The BIDScoin tools will run dicomsort in a temporary folder if your data is not already organized in series-folders, so in principle you don't really need to run it yourself (unless when you have a single multi-subject DICOMDIR file for your entire repository). Running dicomsort beforehand does, however, give you more flexibility in handling special cases that are not handled properly and it can also give you a speed benefit. If dicomsort do not satisfy your needs, then have a look at this `DICOM reorganize <https://github.com/robertoostenveld/bids-tools/blob/master/doc/reorganize_dicom_files.md>`__ tool.::
 
     usage: dicomsort [-h] [-i SUBPREFIX] [-j SESPREFIX] [-f FOLDERSCHEME] [-n NAMESCHEME] [-p PATTERN]
                      [--force] [-d]
@@ -121,9 +117,7 @@ The ``dicomsort`` command-line tool is a utility to move your flat- or DICOMDIR-
 rawmapper
 ---------
 
-Another command-line utility that can be helpful in organizing your source data is ``rawmapper``. This utility can show you an overview (map) of all the values of DICOM-attributes of interest in your data-set and, optionally, used to rename your source data sub-folders. The latter option can be handy e.g. if you manually entered subject-identifiers as [Additional info] at the scanner console and you want to use these to rename your subject folders.
-
-::
+Another command-line utility that can be helpful in organizing your source data is ``rawmapper``. This utility can show you an overview (map) of all the values of DICOM-attributes of interest in your data-set and, optionally, used to rename your source data sub-folders. The latter option can be handy e.g. if you manually entered subject-identifiers as [Additional info] at the scanner console and you want to use these to rename your subject folders.::
 
     usage: rawmapper [-h] [-s SESSIONS [SESSIONS ...]] [-f FIELD [FIELD ...]] [-w WILDCARD]
                      [-o OUTFOLDER] [-r] [-c] [-n SUBPREFIX] [-m [SESPREFIX]] [-d]
@@ -178,9 +172,7 @@ Another command-line utility that can be helpful in organizing your source data
 bidsparticipants
 ----------------
 
-The bidsparticipants tool is useful for (re-)generating a participants.tsv file from your source data (without having to run bidscoiner)
-
-::
+The bidsparticipants tool is useful for (re-)generating a participants.tsv file from your source data (without having to run bidscoiner)::
 
     usage: bidsparticipants [-h] [-k KEYS [KEYS ...]] [-d] [-b BIDSMAP] sourcefolder bidsfolder
 

docs/workflow.rst

@@ -21,7 +21,6 @@ If you add new subjects all you need to do is re-run the bidscoiner -- unless th
 
 Step 1a: Running the bidsmapper
 -------------------------------
-
 ::
 
     usage: bidsmapper [-h] [-b BIDSMAP] [-t TEMPLATE] [-p PLUGINS [PLUGINS ...]] [-n SUBPREFIX]
@@ -94,7 +93,6 @@ After the source data has been scanned, the bidsmapper will automatically launch
 
 Step 1b: Running the bidseditor
 -------------------------------
-
 ::
 
     usage: bidseditor [-h] [-b BIDSMAP] [-t TEMPLATE] bidsfolder
@@ -176,7 +174,6 @@ Field maps are typically acquired to be applied to specific other scans from the
 
 Step 2: Running the bidscoiner
 ------------------------------
-
 ::
 
     usage: bidscoiner [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-b BIDSMAP] [-f] [-c]