[DATALAD RUNCMD] Do interactive fixing of some ambigous typos

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

contributing.md

@@ -21,7 +21,7 @@ How do you know that you joined? well, you're here and you likely used PET2BIDS
 
 ## Contributing without writing a line of code
 
-There are many ways you can contribute to the project without having to wite a single line of code!
+There are many ways you can contribute to the project without having to write a single line of code!
 - editing and updating the help/documentation is a fantastic contribution.
 - making any tutorials, examples available is great too
 

docs/usage.rst

@@ -174,7 +174,7 @@ ecatpet2bids for converting ecat data into nii & json
       --nifti file_name, -n file_name
                             Name of nifti output file
       --subheader, -s       Display subheaders
-      --sidecar             Output a bids formatted sidecar for pairing witha nifti.
+      --sidecar             Output a bids formatted sidecar for pairing with a nifti.
       --kwargs [KWARGS ...], -k [KWARGS ...]
                             Include additional values int the nifti sidecar json or override values extracted from the supplied nifti. e.g. including `--kwargs TimeZero='12:12:12'` would override the
                             calculated TimeZero. Any number of additional arguments can be supplied after --kwargs e.g. `--kwargs BidsVariable1=1 BidsVariable2=2` etc etc.

matlab/dcm2niix4pet.m

@@ -43,7 +43,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 %.. note::
 %
 %   See also get_pet_metadata.m to generate the metadata structure
-%            updatejsonpetfile to see how the json file gets updated and checked agains DICOM tags
+%            updatejsonpetfile to see how the json file gets updated and checked against DICOM tags
 %
 % | *Cyril Pernet 2022*
 % | *Copyright Open NeuroPET team*

matlab/get_pet_metadata.m

@@ -233,7 +233,7 @@
             for opt = 1:length(setmetadata)
                 if contains(setmetadata{opt},'=')
                     try
-                        eval(setmetadata{opt}); % shoul evaluate the = sign, creating name/value pairs
+                        eval(setmetadata{opt}); % should evaluate the = sign, creating name/value pairs
                         if isempty(setmetadata{opt})
                             error('''%s'' from %sparameters.txt is empty\n',optional{opt},Scanner)
                         end

pypet2bids/pypet2bids/README.md

@@ -166,7 +166,7 @@ optional arguments:
   --nifti file_name, -n file_name
                         Name of nifti output file
   --subheader, -s       Display subheaders
-  --sidecar             Output a bids formatted sidecar for pairing witha nifti.
+  --sidecar             Output a bids formatted sidecar for pairing with a nifti.
   --kwargs [KWARGS ...], -k [KWARGS ...]
                         Include additional values int the nifti sidecar json or
                         override values extracted from the supplied nifti. e.g.

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -86,7 +86,7 @@
         "DEFAULT_METADATA_JSON", module_folder / "template_json.json"
     )
     # set the default metadata json to the template json included in this library in our environment so
-    # we don't trip up retrival of the default metadata json later
+    # we don't trip up retrieval of the default metadata json later
     environ["DEFAULT_METADATA_JSON"] = str(module_folder / "template_json.json")
     default_metadata_json = module_folder / "template_json.json"
 

spreadsheet_conversion/blood/pmod/convert_pmod_to_blood.m

@@ -95,12 +95,12 @@ function convert_pmod_to_blood(varargin)
         'blood sampling', ...
         'manual', 'autosampler', 'both', 'manual');
     if isempty(type)
-        warning('selection aborded - exiting'); return
+        warning('selection aborted - exiting'); return
     end
 
     outputname = inputdlg('please input the base name for the files to save');
     if isempty(outputname)
-        warning('name aborded - exiting'); return
+        warning('name aborted - exiting'); return
     else
         outputname = fullfile(pathnames,cell2mat(outputname));
     end