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Added rules for naming files from different samples
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@ayendiki
ayendiki authored Dec 24, 2024
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Expand Up @@ -39,8 +39,8 @@ dandi download https://lincbrain.org/dandiset/101010/draft
The above example will create a directory called `/path/to/my/staging/area/101010` with a file called `dandiset.yaml` in it. Any data files that you want to upload to your new lincbrain.org dataset have to first be saved here, and organized according to the [Brain Imaging Data Structure (BIDS)](https://bids-specification.readthedocs.io/).

## Organize your data
An example from a (fictional) dataset that includes dMRI and histology data from two brains is shown below, and can be used as a guide for organizing your own data. A few things to watch out for:
1. If you are creating a new dataset, you have to create a `dataset_description.json` file.
An example from a (fictional) dataset that includes dMRI and histology data from two brains is shown below. This can be used as a guide for organizing your own dataset. A few things to watch out for:
1. If you are creating a new dataset, you have to create the `dataset_description.json` file.
1. If you are adding data from a new subject to an existing dataset, you have to add an entry with the new subject's information to the `participants.tsv` file.
1. If you are adding data from a new sample (part of the brain) to an existing dataset, you have to add an entry with the new sample's information to the `samples.tsv` file.
1. Any data files that you add must go under:
Expand All @@ -52,15 +52,15 @@ An example from a (fictional) dataset that includes dMRI and histology data from
101010/
dataset_description.json
participants.tsv
samples.tsv
rawdata/
sub-Ken1/
dwi/
sub-Ken1_acq-DSI_dwi.bval
sub-Ken1_acq-DSI_dwi.bvec
sub-Ken1_acq-DSI_dwi.json
sub-Ken1_acq-DSI_dwi.nii.gz
sub-Ken1_sample-brain_acq-DSI_dwi.bval
sub-Ken1_sample-brain_acq-DSI_dwi.bvec
sub-Ken1_sample-brain_acq-DSI_dwi.json
sub-Ken1_sample-brain_acq-DSI_dwi.nii.gz
micr/
samples.tsv
sub-Ken1_sample-slice0001_photo.json
sub-Ken1_sample-slice0001_photo.tif
sub-Ken1_sample-slice0001_stain-Nissl_BF.json
Expand All @@ -79,16 +79,15 @@ An example from a (fictional) dataset that includes dMRI and histology data from
sub-Ken1_sample-slice0010_stain-LY_DF.tif
sub-Ken2/
dwi/
sub-Ken2_acq-DSI_dwi.bval
sub-Ken2_acq-DSI_dwi.bvec
sub-Ken2_acq-DSI_dwi.json
sub-Ken2_acq-DSI_dwi.nii.gz
sub-Ken2_acq-MulShellMulTE_dwi.bval
sub-Ken2_acq-MulShellMulTE_dwi.bvec
sub-Ken2_acq-MulShellMulTE_dwi.json
sub-Ken2_acq-MulShellMulTE_dwi.nii.gz
sub-Ken2_sample-brain_acq-DSI_dwi.bval
sub-Ken2_sample-brain_acq-DSI_dwi.bvec
sub-Ken2_sample-brain_acq-DSI_dwi.json
sub-Ken2_sample-brain_acq-DSI_dwi.nii.gz
sub-Ken2_sample-brain_acq-MulShellMulTE_dwi.bval
sub-Ken2_sample-brain_acq-MulShellMulTE_dwi.bvec
sub-Ken2_sample-brain_acq-MulShellMulTE_dwi.json
sub-Ken2_sample-brain_acq-MulShellMulTE_dwi.nii.gz
micr/
samples.tsv
sub-Ken2_sample-slice0001_photo.json
sub-Ken2_sample-slice0001_photo.tif
sub-Ken2_sample-slice0001_stain-Nissl_BF.json
Expand Down Expand Up @@ -136,8 +135,31 @@ sub-Ken1 43 M healthy
sub-Ken2 61 M hypertension
```

### samples.tsv
This text file is [described in detail in the BIDS specification](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#samples-file). For this dataset, the `samples.tsv` would look like this:

```
participant_id sample_id sample_type
sub-Ken1 sample-brain tissue
sub-Ken1 sample-slice0001 tissue
sub-Ken1 sample-slice0002 tissue
sub-Ken1 sample-slice0009 tissue
sub-Ken1 sample-slice0010 tissue
sub-Ken2 sample-brain tissue
sub-Ken2 sample-slice0001 tissue
sub-Ken2 sample-slice0002 tissue
sub-Ken2 sample-slice0003 tissue
sub-Ken2 sample-slice0009 tissue
sub-Ken2 sample-slice0010 tissue
sub-Ken2 sample-slice0011 tissue
```

Label the sample as `brain` if the whole brain was imaged. Label it as `lefthemi` or `righthemi` if a whole hemisphere was imaged.

### rawdata
This directory contains one subdirectory for each brain, which contain one subdirectory for each modality, which in turn contain raw image data files named according to the BIDS specification.
This directory contains one subdirectory for each brain, which contains one subdirectory for each modality, which in turn contains raw image data files named according to the BIDS specification.

The name every image or data file under `rawdata/` must start with a prefix that contains its subject and sample label, e.g., `sub-Ken1_sample-brain_*.nii.gz`, `sub-Ken2_sample-slice0001_*.json`, etc.

### dwi
This directory contains dMRI data files [as described in detail in the BIDS specification](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#diffusion-imaging-data).
Expand Down Expand Up @@ -166,20 +188,6 @@ index name
...
```



### samples.tsv
This text file is [described in detail in the BIDS specification](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#samples-file). For Ken1, the `samples.tsv` would look like this:

```
participant_id sample_id sample_type
sub-Ken1 sample-slice0001 tissue
sub-Ken1 sample-slice0002 tissue
sub-Ken1 sample-slice0009 tissue
sub-Ken1 sample-slice0010 tissue
```


## Upload your data
Upload the data from your local machine to lincbrain.org:

Expand Down

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