Merge pull request #228 from arnaudbore/revert_doc_2.1.9

Revert doc to 2.1.9
UNFmontreal · Jul 6, 2023 · 26840f3 · 26840f3
2 parents d305b0a + 0e8c576
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diff --git a/docs/get-started/install.md b/docs/get-started/install.md
@@ -189,7 +189,7 @@ name: dcm2bids
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8
+  - python>=3.7
   - dcm2niix
   - dcm2bids
 ```
@@ -277,7 +277,7 @@ usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c
                 [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
 Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-dcm2bids 3.0.0
+dcm2bids 2.1.7
 
 options:
   -h, --help            show this help message and exit
@@ -292,14 +292,13 @@ options:
   -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                         Output BIDS directory, Default: current directory
                         (/home/sam/dcm2bids-proj)
-  --auto_extract_entities If set, it will automatically try to extract entity information [task, dir, echo]
-                          depending on the suffix and datatype. [False]
-  --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
-                        bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
   --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
   --clobber             Overwrite output if it exists
   -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                         Set logging level
+  -a, --anonymizer      This option no longer exists from the script in this
+                        release. See:https://github.com/unfmontreal/Dcm2Bids/blob/m
+                        aster/README.md#defaceTpl
 
             Documentation at https://github.com/unfmontreal/Dcm2Bids
 ```
@@ -342,7 +341,7 @@ containers:
             channels:
                 - conda-forge
             dependencies:
-                - python>=3.8
+                - python>=3.7
                 - dcm2niix
                 - dcm2bids
 

diff --git a/docs/how-to/create-config-file.md b/docs/how-to/create-config-file.md
@@ -6,54 +6,52 @@
 {
   "descriptions": [
     {
-      "datatype": "anat",
-      "suffix": "T2w",
+      "dataType": "anat",
+      "modalityLabel": "T2w",
       "criteria": {
         "SeriesDescription": "*T2*",
         "EchoTime": 0.1
       },
-      "sidecar_changes": {
+      "sidecarChanges": {
         "ProtocolName": "T2"
       }
     },
     {
-      "id": "task-rest",
-      "datatype": "func",
-      "suffix": "bold",
-      "custom_entities": "task-rest",
+      "dataType": "func",
+      "modalityLabel": "bold",
+      "customLabels": "task-rest",
       "criteria": {
         "ProtocolName": "func_task-*",
         "ImageType": ["ORIG*", "PRIMARY", "M", "MB", "ND", "MOSAIC"]
       }
     },
     {
-      "datatype": "fmap",
-      "suffix": "fmap",
-      "intendedFor": "task_rest",
+      "dataType": "fmap",
+      "modalityLabel": "fmap",
+      "intendedFor": 1,
       "criteria": {
         "ProtocolName": "*field_mapping*"
       }
     },
     {
-      "id": "id_task_learning",
-      "datatype": "func",
-      "suffix": "bold",
-      "custom_entities": "task-learning",
+      "dataType": "func",
+      "modalityLabel": "bold",
+      "customLabels": "task-learning",
       "criteria": {
         "SeriesDescription": "bold_task-learning"
       },
-      "sidecar_changes": {
+      "sidecarChanges": {
         "TaskName": "learning"
       }
     },
     {
-      "datatype": "fmap",
-      "suffix": "epi",
+      "dataType": "fmap",
+      "modalityLabel": "epi",
       "criteria": {
         "SeriesDescription": "fmap_task-learning"
       },
-      "IntendedFor": "id_task_learning",
-      "sidecar_changes": {
+      "IntendedFor": 2,
+      "sidecarChanges": {
         "TaskName": "learning"
       }
     }
@@ -100,7 +98,7 @@ subject to change depending on the dcm2niix version in use.
 You can enter several criteria. **All criteria must match** for a description to
 be linked to a sidecar.
 
-## datatype
+## dataType
 
 It is a mandatory field. Here is a definition from `bids v1.2.0` :
 
@@ -110,12 +108,12 @@ It is a mandatory field. Here is a definition from `bids v1.2.0` :
 > field maps), anat (structural imaging such as T1, T2, etc.), meg
 > (magnetoencephalography), beh (behavioral).
 
-## suffix
+## modalityLabel
 
 It is a mandatory field. It describes the modality of the acquisition like
 `T1w`, `T2w` or `dwi`, `bold`.
 
-## custom_entities
+## customLabels
 
 It is an optional field. For some acquisitions, you need to add information in
 the file name. For resting state fMRI, it is usually `task-rest`.
@@ -126,40 +124,19 @@ specifications][bids-spec].
 For a longer example of a Dcm2Bids config json, see
 [here](https://github.com/unfmontreal/Dcm2Bids/blob/master/example/config.json).
 
-Note that the different bids labels must come in a very specific order to be bids valid filenames. 
-If the custom_entities fields that are entered that are in the wrong order,
-then dcm2bids will reorder them for you.
-
-For example if you entered:
-
-```json
-"custom_entities": "run-01_task-rest"
-```
-
-when running dcm2bids, you will get the following warning:
-
-```bash
-WARNING:dcm2bids.structure:✅ Filename was reordered according to BIDS entity table order:
-                from:   sub-ID01_run-01_task-rest_bold
-                to:     sub-ID01_task-rest_run-01_bold
-```
-
-custom_entities could also be combined with extractors. 
-See [custom_entities combined with extractors](./use-advanced-commands.md#custom_entities-combined-with-extractors)
-
-
-## sidecar_changes
+## sidecarChanges
 
 Optional field to change or add information in a sidecar.
 
-## id and intendedFor
+## intendedFor
 
-Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. 
-You will need to set an id to the corresponding description and put the same id in the `IntendedFor` field.
+Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. Just
+put the index or a list of indices of the description(s) that's intended for.
 
-Fo example, **`task_rest`** means it is intended for `task-rest_bold` 
-and **`id_task_learning`** is intended for `task-learning` which will be
-renamed to only `learning` because of the `"sidecar_changes": { "TaskName": "learning" }` field.
+Python index begins at `0` so in the example, **`1`** means it is intended for
+`task-rest_bold` and **`2`** is intended for `task-learning` which will be
+renamed to only `learning` because of the
+`"sidecarChanges": { "TaskName": "learning" }` field.
 
 ## Multiple config files