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Revert doc to 2.1.9 #228

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Jul 6, 2023
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Revert doc to 2.1.9 #228

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13 changes: 6 additions & 7 deletions docs/get-started/install.md
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ name: dcm2bids
channels:
- conda-forge
dependencies:
- python>=3.8
- python>=3.7
- dcm2niix
- dcm2bids
```
Expand Down Expand Up @@ -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
Expand All @@ -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
```
Expand Down Expand Up @@ -342,7 +341,7 @@ containers:
channels:
- conda-forge
dependencies:
- python>=3.8
- python>=3.7
- dcm2niix
- dcm2bids

Expand Down
79 changes: 28 additions & 51 deletions docs/how-to/create-config-file.md
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Expand Up @@ -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"
}
}
Expand Down Expand Up @@ -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` :

Expand All @@ -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`.
Expand All @@ -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

Expand Down
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