Merge pull request #166 from Remi-Gau/update_readme_template

Update readme template

Author: Remi-Gau

manualTests/dummyData/README

@@ -1 +1,157 @@
-# README
+# README
+
+(template copied from the BIDS starter kit: 
+https://github.com/bids-standard/bids-starter-kit)
+
+The README is usually the starting point for researchers using your data
+and serves as a guidepost for users of your data. A clear and informative
+README makes your data much more usable.
+
+In general you can include information in the README that is not captured by some other
+files in the BIDS dataset (dataset_description.json, events.tsv, ...).
+
+It can also be useful to also include information that might already be 
+present in another file of the dataset but might be important for users to be aware of 
+before preprocessing or analysing the data.
+
+If the README gets too long you have the possibility to create a `/doc` folder
+and add it to the `.bidsignore` file to make sure it is ignored by the BIDS validator.
+
+More info here: https://neurostars.org/t/where-in-a-bids-dataset-should-i-put-notes-about-individual-mri-acqusitions/17315/3
+
+## Details related to access to the data
+
+- [ ] Data user agreement
+
+If the dataset requires a data user agreement, link to the relevant information.
+
+- [ ] Contact person
+
+Indicate the name and contact details (email and ORCID) of the person responsible for additional information.
+
+- [ ] Practical information to access the data
+
+If there is any special information related to access rights or 
+how to download the data make sure to include it. 
+For example, if the dataset was curated using datalad, 
+make sure to include the relevant section from the datalad handbook:
+http://handbook.datalad.org/en/latest/basics/101-180-FAQ.html#how-can-i-help-others-get-started-with-a-shared-dataset
+
+## Overview
+
+- [ ] Project name (if relevant)
+
+- [ ] Year(s) that the project ran
+
+If no `scans.tsv` is included, this could at least cover when the data acquisition 
+starter and ended. Local time of day is particularly relevant to subject state.
+
+- [ ] Brief overview of the tasks in the experiment
+
+A paragraph giving an overview of the experiment. This should include the 
+goals or purpose and a discussion about how the experiment tries to achieve
+these goals.
+
+- [ ] Description of the contents of the dataset
+
+An easy thing to add is the output of the bids-validator that describes what type of 
+data and the number of subject one can expect to find in the dataset. 
+
+- [ ] Independent variables
+
+A brief discussion of condition variables (sometimes called contrasts
+or independent variables) that were varied across the experiment.
+
+- [ ] Dependent variables
+
+A brief discussion of the response variables (sometimes called the
+dependent variables) that were measured and or calculated to assess
+the effects of varying the condition variables. This might also include
+questionnaires administered to assess behavioral aspects of the experiment.
+
+- [ ] Control variables
+
+A brief discussion of the control variables --- that is what aspects 
+were explicitly controlled in this experiment. The control variables might 
+include subject pool, environmental conditions, set up, or other things 
+that were explicitly controlled.
+
+- [ ] Quality assessment of the data
+
+Provide a short summary of the quality of the data ideally with descriptive statistics if relevant
+and with a link to more comprehensive description (like with MRIQC) if possible.
+
+## Methods  
+
+### Subjects
+
+A brief sentence about the subject pool in this experiment.
+
+Remember that `Control` or `Patient` status should be defined in the `participants.tsv`
+using a group column.
+
+- [ ] Information about the recruitment procedure
+- [ ] Subject inclusion criteria (if relevant)
+- [ ] Subject exclusion criteria (if relevant)
+ 
+### Apparatus
+
+A summary of the equipment and environment setup for the
+experiment. For example, was the experiment performed in a shielded room
+with the subject seated in a fixed position.
+
+### Initial setup
+
+A summary of what setup was performed when a subject arrived.
+
+### Task organization
+
+How the tasks were organized for a session.
+This is particularly important because BIDS datasets usually have task data
+separated into different files.) 
+
+- [ ] Was task order counter-balanced?
+- [ ] What other activities were interspersed between tasks?  
+
+- [ ] In what order were the tasks and other activities performed? 
+
+### Task details
+
+As much detail as possible about the task and the events that were recorded. 
+
+### Additional data acquired
+
+A brief indication of data other than the
+imaging data that was acquired as part of this experiment. In addition
+to data from other modalities and behavioral data, this might include
+questionnaires and surveys, swabs, and clinical information. Indicate
+the availability of this data.
+
+This is especially relevant if the data are not included in a `phenotype` folder.
+https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#phenotypic-and-assessment-data
+
+### Experimental location
+
+This should include any additional information regarding the 
+the geographical location and facility that cannot be included
+in the relevant json files.
+
+### Missing data
+
+Mention something if some participants are missing some aspects of the data.
+This can take the form of a processing log and/or abnormalities about the dataset. 
+
+Some examples:
+
+- A brain lesion or defect only present in one participant
+- Some experimental conditions missing on a given run for a participant because
+  of some technical issue.
+- Any noticeable feature of the data for certain participants
+- Differences (even slight) in protocol for certain participants.
+
+### Notes
+
+Any additional information or pointers to information that
+might be helpful to users of the dataset. Include qualitative information 
+related to how the data acquisition went.
+