diff --git a/docs/upload.md b/docs/upload.md index 254fea8..ad18644 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -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: @@ -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 @@ -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 @@ -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). @@ -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: