Doc tweaks

bidscoin/bidsapps/deface.py

@@ -21,7 +21,7 @@
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[2]))
 from bidscoin import bcoin, bids, lsdirs, trackusage, DEBUG
-from ..due import due, Doi
+from bidscoin.due import due, Doi
 
 
 @due.dcite(Doi('10.5281/zenodo.3524400'), description='A tool to remove facial structure from MRI images', tags=['reference-implementation'])

bidscoin/bidsapps/medeface.py

@@ -23,7 +23,7 @@
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[2]))
 from bidscoin import bcoin, bids, lsdirs, trackusage, DEBUG
-from ..due import due, Doi
+from bidscoin.due import due, Doi
 
 
 @due.dcite(Doi('10.5281/zenodo.3524400'), description='A tool to remove facial structure from MRI images', tags=['reference-implementation'])

bidscoin/bidsapps/skullstrip.py

@@ -21,7 +21,7 @@
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[2]))
 from bidscoin import bcoin, bids, lsdirs, trackusage, DEBUG
-from ..due import due, Doi
+from bidscoin.due import due, Doi
 
 
 @due.dcite(Doi('10.1016/j.neuroimage.2022.119474'), description='Robust, universal skull-stripping for brain images of any type', tags=['reference-implementation'])

bidscoin/cli/_bcoin.py

@@ -7,11 +7,11 @@
   $ bidsmapper sourcefolder bidsfolder     # This produces a study bidsmap and launches a GUI
   $ bidscoiner sourcefolder bidsfolder     # This converts your data to BIDS according to the study bidsmap
 
-Default settings and template bidsmaps are stored in the ".bidscoin" folder in your home directory
+Default settings and template bidsmaps are stored in the `.bidscoin` folder in your home directory
 (you can modify them to your needs with any plain text editor)
 
-Set the environment variable BIDSCOIN_DEBUG=TRUE to run BIDScoin in a more verbose logging mode and
-BIDSCOIN_CONFIG=/writable/path/to/config.toml if you like to use a different config file.
+Set the environment variable `BIDSCOIN_DEBUG=TRUE` to run BIDScoin in a more verbose logging mode and
+`BIDSCOIN_CONFIG=/writable/path/to/config.toml` if you like to use a different config file.
 Citation reports can be generated with the help of duecredit (https://github.com/duecredit/duecredit)
 
 For more documentation see: https://bidscoin.readthedocs.io

bidscoin/plugins/README

@@ -14,7 +14,7 @@ BIDScoin's library modules named 'bcoin' and, most notably, 'bids'"""
 
 import logging
 from pathlib import Path
-from ..due import due, Doi
+from bidscoin.due import due, Doi
 from bidscoin.bids import Bidsmap, Run, Plugin
 
 LOGGER = logging.getLogger(__name__)

docs/bidsapps.rst

@@ -174,7 +174,7 @@ The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS
 ::
 
     usage: skullstrip [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-m MASKED]
-                      [-o OUTPUT [OUTPUT ...]] [-f] [-a ARGS] [-c {torque,slurm}]
+                      [-o OUTPUT [OUTPUT ...]] [-f] [-a ARGS] [-c] [-n NATIVESPEC]
                       bidsfolder pattern
 
     A wrapper around FreeSurfer's 'synthstrip' skull stripping tool
@@ -211,14 +211,17 @@ The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS
       -f, --force           Process images, regardless whether images have already been skullstripped
                             (i.e. if {'SkullStripped': True} in the json sidecar file) (default: False)
       -a ARGS, --args ARGS  Additional arguments that are passed to synthstrip (NB: Use quotes and
-                            include at least one space character to prevent overearly parsing)
-      -c {torque,slurm}, --cluster {torque,slurm}
-                            Use `torque` or `slurm` to submit the skullstrip jobs to a high-performance
-                            compute (HPC) cluster. Can only be used if `--masked` is left empty
+                            include at least one space character to prevent overearly parsing) (default:)
+      -c, --cluster         Use the DRMAA library to submit the skullstrip jobs to a high-performance
+                            compute (HPC) cluster (default: False)
+      -n NATIVESPEC, --nativespec NATIVESPEC
+                            Opaque DRMAA argument with native specifications for submitting skullstrip
+                            jobs to the HPC cluster (NB: Use quotes and include at least one space
+                            character to prevent overearly parsing) (default: -l walltime=0:05:00,mem=8gb)
 
     examples:
       skullstrip myproject/bids anat/*_T1w*
-      skullstrip myproject/bids anat/*_T1w* -p 001 003 -a ' --no-csf'
+      skullstrip myproject/bids anat/*_T1w* -p 001 003 -a " --no-csf"
       skullstrip myproject/bids fmap/*_magnitude1* -m fmap/*_phasediff* -o extra_data fmap
       skullstrip myproject/bids fmap/*_acq-mylabel*_magnitude1* -m fmap/*_acq-mylabel_* -o fmap
 
@@ -231,8 +234,8 @@ Quality control
 
     usage: slicereport [-h] [-o OUTLINEPATTERN] [-i OUTLINEIMAGE]
                        [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-r REPORTFOLDER]
-                       [-x XLINKFOLDER [XLINKFOLDER ...]] [-q QCSCORES [QCSCORES ...]] [-c {torque,slurm}]
-                       [--operations OPERATIONS] [--suboperations SUBOPERATIONS]
+                       [-x XLINKFOLDER [XLINKFOLDER ...]] [-q QCSCORES [QCSCORES ...]]
+                       [-c {torque,slurm}] [--operations OPERATIONS] [--suboperations SUBOPERATIONS]
                        [--options OPTIONS [OPTIONS ...]] [--outputs OUTPUTS [OUTPUTS ...]]
                        [--suboptions SUBOPTIONS [SUBOPTIONS ...]]
                        [--suboutputs SUBOUTPUTS [SUBOUTPUTS ...]]
@@ -247,6 +250,8 @@ Quality control
 
     Requires an existing installation of FSL
 
+    Set the environment variable BIDSCOIN_DEBUG=TRUE to save intermediate data
+
     positional arguments:
       bidsfolder            The bids-directory with the subject data
       pattern               Globlike search pattern to select the images in bidsfolder to be reported,
@@ -255,9 +260,9 @@ Quality control
     options:
       -h, --help            show this help message and exit
       -o OUTLINEPATTERN, --outlinepattern OUTLINEPATTERN
-                            Globlike search pattern to select red outline images that are projected on top
-                            of the reported images (i.e. 'outlinepattern' must yield the same number of
-                            images as 'pattern'. Prepend `outlinedir:` if your outline images are in
+                            Globlike search pattern to select red outline images that are projected on
+                            top of the reported images (i.e. 'outlinepattern' must yield the same number
+                            of images as 'pattern'. Prepend `outlinedir:` if your outline images are in
                             `outlinedir` instead of `bidsdir` (see examples below)`
       -i OUTLINEIMAGE, --outlineimage OUTLINEIMAGE
                             A common red-outline image that is projected on top of all images
@@ -284,13 +289,13 @@ Quality control
                             space character to prevent overearly parsing, e.g. " -Tmean" or "-Tstd -s 3"
                             (default: -Tmean)
       --suboperations SUBOPERATIONS
-                            The same as OPERATIONS but then for the sub-report instead of the main report:
-                            `fslmaths inputimage SUBOPERATIONS subreportimage` (default: -Tmean)
+                            The same as OPERATIONS but then for the sub-report instead of the main
+                            report: `fslmaths inputimage SUBOPERATIONS subreportimage` (default: -Tmean)
       --options OPTIONS [OPTIONS ...]
                             Main options of slicer (see below). (default: "s 1")
       --outputs OUTPUTS [OUTPUTS ...]
-                            Output options of slicer (see below). (default: "x 0.4 x 0.5 x 0.6 y 0.4 y 0.5
-                            y 0.6 z 0.4 z 0.5 z 0.6")
+                            Output options of slicer (see below). (default: "x 0.4 x 0.5 x 0.6 y 0.4 y
+                            0.5 y 0.6 z 0.4 z 0.5 z 0.6")
       --suboptions SUBOPTIONS [SUBOPTIONS ...]
                             Main options of slicer for creating the sub-reports (same as OPTIONS, see
                             below). (default: OPTIONS)

docs/utilities.rst

@@ -19,10 +19,11 @@ The bidscoin command-line utility serves as a central starting point to test and
       $ bidsmapper sourcefolder bidsfolder     # This produces a study bidsmap and launches a GUI
       $ bidscoiner sourcefolder bidsfolder     # This converts your data to BIDS according to the study bidsmap
 
-    Default settings and template bidsmaps are stored in the ".bidscoin" folder in your home directory
+    Default settings and template bidsmaps are stored in the `.bidscoin` folder in your home directory
     (you can modify them to your needs with any plain text editor)
 
-    Set the environment variable BIDSCOIN_DEBUG=TRUE to run BIDScoin in a more verbose logging mode.
+    Set the environment variable `BIDSCOIN_DEBUG=TRUE` to run BIDScoin in a more verbose logging mode and
+    `BIDSCOIN_CONFIG=/writable/path/to/config.toml` if you like to use a different config file.
     Citation reports can be generated with the help of duecredit (https://github.com/duecredit/duecredit)
 
     For more documentation see: https://bidscoin.readthedocs.io
@@ -202,8 +203,9 @@ The bidsparticipants tool is useful for (re-)generating a participants.tsv file
       -d, --dryrun          Do not save anything, only print the participants info on screen
       -b BIDSMAP, --bidsmap BIDSMAP
                             The study bidsmap file with the mapping heuristics. If the bidsmap filename
-                            is just the basename (i.e. no "/" in the name) then it is assumed to be located in
-                            bidsfolder/code/bidscoin. Default: bidsmap.yaml
+                            is just the basename (i.e. no "/" in the name) then it is assumed to be
+                            located in the current directory or in bidsfolder/code/bidscoin. Default:
+                            bidsmap.yaml
 
     examples:
       bidsparticipants myproject/raw myproject/bids

docs/workflow.rst

@@ -46,13 +46,14 @@ Step 1a: Running the bidsmapper
       -h, --help            show this help message and exit
       -b BIDSMAP, --bidsmap BIDSMAP
                             The study bidsmap file with the mapping heuristics. If the bidsmap filename
-                            is just the basename (i.e. no '/' in the name) then it is assumed to be located in
-                            bidsfolder/code/bidscoin. Default: bidsmap.yaml
+                            is just the basename (i.e. no '/' in the name) then it is assumed to be
+                            located in the current directory or in bidsfolder/code/bidscoin. Default:
+                            bidsmap.yaml
       -t TEMPLATE, --template TEMPLATE
                             The bidsmap template file with the default heuristics (this could be provided
-                            by your institute). If the bidsmap filename is just the basename (i.e. no '/' in
-                            the name) then it is assumed to be located in the bidscoin config folder. Default:
-                            bidsmap_dccn
+                            by your institute). If the bidsmap filename is just the basename (i.e. no '/'
+                            in the name) then it is assumed to be located in the bidscoin config folder.
+                            Default: bidsmap_dccn
       -p PLUGINS [PLUGINS ...], --plugins PLUGINS [PLUGINS ...]
                             List of plugins to be used. Default: the plugin list of the study/template
                             bidsmap)
@@ -112,13 +113,14 @@ Step 1b: Running the bidseditor
       -h, --help            show this help message and exit
       -b BIDSMAP, --bidsmap BIDSMAP
                             The study bidsmap file with the mapping heuristics. If the bidsmap filename
-                            is just the basename (i.e. no "/" in the name) then it is assumed to be located in
-                            bidsfolder/code/bidscoin. Default: bidsmap.yaml
+                            is just the basename (i.e. no "/" in the name) then it is assumed to be
+                            located in the current directory or in bidsfolder/code/bidscoin. Default:
+                            bidsmap.yaml
       -t TEMPLATE, --template TEMPLATE
                             The template bidsmap file with the default heuristics (this could be provided
-                            by your institute). If the bidsmap filename is just the basename (i.e. no "/" in
-                            the name) then it is assumed to be located in the bidscoin config folder. Default:
-                            bidsmap_dccn
+                            by your institute). If the bidsmap filename is just the basename (i.e. no "/"
+                            in the name) then it is assumed to be located in the bidscoin config folder.
+                            Default: bidsmap_dccn
 
     examples:
       bidseditor myproject/bids
@@ -182,7 +184,7 @@ Step 2: Running the bidscoiner
     information from the bidsmap.yaml file. Edit this bidsmap to your needs using the bidseditor
     tool before running this function or (re-)run the bidsmapper whenever you encounter unexpected
     data. You can run bidscoiner after all data has been collected, or run / re-run it whenever
-    new data has been added to your source folder (presuming the scan protocol hasn't changed).
+    new data has been added to your source folder (presuming the scan protocol has not changed).
     Also, if you delete a subject/session folder from the bidsfolder, it will simply be re-created
     from the sourcefolder the next time you run the bidscoiner.
 
@@ -203,8 +205,9 @@ Step 2: Running the bidscoiner
                             be selected
       -b BIDSMAP, --bidsmap BIDSMAP
                             The study bidsmap file with the mapping heuristics. If the bidsmap filename
-                            is just the basename (i.e. no "/" in the name) then it is assumed to be located in
-                            bidsfolder/code/bidscoin. Default: bidsmap.yaml
+                            is just the basename (i.e. no "/" in the name) then it is assumed to be
+                            located in the current directory or in bidsfolder/code/bidscoin. Default:
+                            bidsmap.yaml
       -f, --force           Process all subjects, regardless of existing subject folders in the
                             bidsfolder. Otherwise these subject folders will be skipped
       -c, --cluster         Use the DRMAA library to submit the bidscoiner jobs to a high-performance