Spreadsheets
Editing the spreadsheets
DO NOT EDIT THE DIRECTLY IN THE REPOSITORY!!!
Instead edit them on the google drive
and then run type tox run -e update to update all the TSVs in the repository.
The spreadsheets that allow us to generate the different checklists are hosted on this google drive folder and we back them up as TSVs in the main repo of the project.
Available spreadsheets
Apps
Some apps have their entire list of questions into a single spreadsheet.
| web app | reference | spreadsheet | Github repository |
|---|---|---|---|
| eyetracking | link | spreadsheet | github |
| neurovault | link | spreadsheet | github |
| pet | link | spreadsheet | github |
| reexecution | link | spreadsheet | github |
Reproschema "Activities"
Some sections of our checkists are kept in separate google sheets.
They are listed below.
| activity | reference | spreadsheet | Preview |
|---|---|---|---|
| core-behavior | link | spreadsheet | preview |
| core-data_sharing | link | spreadsheet | preview |
| core-participants | link | spreadsheet | preview |
| core-reproducibility | link | spreadsheet | preview |
| meeg-acquisition | link | spreadsheet | |
| meeg-statistical_analysis | link | spreadsheet | |
| meeg-design | link | spreadsheet | |
| meeg-processing | link | spreadsheet | |
| meeg-reporting | link | spreadsheet | |
| mri-acquisition | link | spreadsheet | preview |
| mri-all_sequences | link | spreadsheet | preview |
| mri-connectivity | link | spreadsheet | preview |
| mri-design | link | spreadsheet | preview |
| mri-mass_univariate | link | spreadsheet | preview |
| mri-multivariate | link | spreadsheet | preview |
| mri-preprocessing | link | spreadsheet | preview |
| mri-results | link | spreadsheet | preview |
Preset responses
Some items have a long list of possible responses, or several items may share the same response set.
Those are kept in separate spreadhsheets and turned into ResponseOptions JSON-LD.
| response list | google spreadsheet | jsonld |
|---|---|---|
| amplitude_measurement | spreadsheet | jsonld |
| boolean | spreadsheet | jsonld |
| cost_functions | spreadsheet | jsonld |
| eeg_cap_types | spreadsheet | jsonld |
| eyetracker_model_name | spreadsheet | jsonld |
| eyetracker_preproc_softwares | spreadsheet | jsonld |
| eyetracker_producer | spreadsheet | jsonld |
| filter | spreadsheet | jsonld |
| interpolations | spreadsheet | jsonld |
| latency_measurement | spreadsheet | jsonld |
| linux_version | spreadsheet | jsonld |
| macos_version | spreadsheet | jsonld |
| meeg_acquisition_softwares | spreadsheet | jsonld |
| meeg_amplifier_brands | spreadsheet | jsonld |
| meeg_analysis_softwares | spreadsheet | jsonld |
| meeg_reference_electrodes | spreadsheet | jsonld |
| mri_softwares | spreadsheet | jsonld |
| multiple_comparisons | spreadsheet | jsonld |
| operating_systems | spreadsheet | jsonld |
| spm_version | spreadsheet | jsonld |
| stimulus_presentation_softwares | spreadsheet | jsonld |
| waveform | spreadsheet | jsonld |
| windows_version | spreadsheet | jsonld |
Working with the spreadsheets
Here is a short list of the different things to keep in mind when working on one of the spreadsheet.
Each line must correspond to one checklist item that must have only one unambiguous item with an associated question. Any item that opens the possibility of a response of the form:
If A was used, then list the parameters B, C, D
Then it must be broken down into several questions:
1. Was A used?
2. If so, what parameter was used for B?
3. What parameter was used for C?
...
For each item:
-
make sure it has a name, preferred label, description
-
make sure that there is a clear specific and unambiguous question associated to this item
-
identify the response type expected
-
create a response choice list where needed
-
mark the item as high-priority to be in the next release of the app.
-
assess whether there is way to not expose users to that item (or restrict list of the response choices for that item) if it is not relevant to their use-case
Style guide
Where relevant we try to use snake_case and stick to lower case.
Hidden columns
If some columns do not appear, it is possible that they have been hidden by someone else. You will simply have to click on the double black arrow at the limit between columns to display them back.
Filtering
If you want to only see certain rows, it is better to filter them rather than hide them.
The column headers can be used to filter which item to display:
for example, the activity_name column can be filtered using the arrow in the top cell in order
to see only the items corresponding to one or more main sections
(e.g., "Acquisition", "Experimental design", "Preprocessing", etc.).
Spreadsheet content
The description of the columns common to all spreadsheet is described in the data dictionary.
Each column is described by an element in the JSON data dictionarry.
"column_name": {
"LongName": "",
"VariableName": "name of the corresponding variable, if relevant, in the conversion scripts",
"Description": "",
"Levels": "describes the different possibilities in this column"
}
| Column name | Description | Requirement level |
|---|---|---|
| UUID | Unique identifier of the item. | OPTIONAL |
| activity_order | position in which the activity is supposed to be presented in a protocol | OPTIONAL |
| activity_pref_label | preferred label of the activity | REQUIRED |
| bids_file | list the bids file in which the item can be found | OPTIONAL |
| bids_key | list the json key corresponding to this item in the bids json file | OPTIONAL |
| bids_key_for_unit | OPTIONAL | |
| bids_status | list if the item can be found in a BIDS (Brain Imaging Data Structure) dataset | OPTIONAL |
| choices | List of possible responses. Options are separated by a pipe ' | '. For integers, floats, and sliders, the values represent min |
| details | Some questions might require some additional information to be understandable by all users, so any extra information to be displayed to the users should be put the detail column. | RECOMMENDED |
| duplicate | reports the number of items that have the same name in this spreadsheet | OPTIONAL |
| field_type | type of response expected | REQUIRED |
| fsl_default | default value for FSL | OPTIONAL |
| in_Carp_2012 | name of the item in the literature review of Carp, 2012 | OPTIONAL |
| include | Whether the item should be generated and included in the activity. | REQUIRED |
| item | name of the item | REQUIRED |
| item_description | description of the item | RECOMMENDED |
| item_order | Position in which the item is supposed to be presented in the activity. | REQUIRED |
| item_pref_label | preferred label of the item | RECOMMENDED |
| mandatory | whether an answer to the item is required | RECOMMENDED |
| meta-analysis_comment | Comment for inclusion in a meta-analysis. | OPTIONAL |
| mri_type | Mention the type of MRI this item is applicable to. | OPTIONAL |
| neurovault | refers to the name of this item in a Neurovault collection | OPTIONAL |
| nidm_results | Mention where information this item can be found in an NIDM results package. | OPTIONAL |
| percent_of_studies | Percent of studies reporting the item in Carp, 2012. If the number is in bold, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article). | OPTIONAL |
| percent_of_studies_anat | Percent of studies reporting this item in for the anatomical data in the papers reviewed by Carp, 2012. If the number is in bold, it was approximately extracted from one of the figures of the paper (because it was not reported in the text of the article). | OPTIONAL |
| percent_reported | Frequency at which items are present in the eyetracking literature (see the preprint) | OPTIONAL |
| preamble | introductory text to the activity | RECOMMENDED |
| question | question corresponding to the item | REQUIRED |
| spm_default | default value for SPM | OPTIONAL |
| unit | unit of the item | OPTIONAL |
| use_case_meta-analysis | Whether the item could be important to evaluate studies for a meta-analysis. | OPTIONAL |
| validation | Extra validation to perform on the item value. For example, item_1 > item_2, Item 1 must be less then item 2. means that the alert 'Item 1 must be less then item 2.' will be displayed if item_1 > item_2. Comma act as separator between the cvheck to perform and alert to display. |
OPTIONAL |
| visibility | Lists the conditions that have to be fulfilled for each item to be displayed to the user. By default, an item will be displayed. Other it will only be shown if a specific answer has been given to a previous item: in this case the expression in this cell must be a valid javascript expression like: 'previousItem === 1' | REQUIRED |