Subsections of Using TRR379 Tools

Subsections of Submit to the Knowledge Pool

Create your contributor profile

TRR379 contributor profiles are automatically updated on the main website based on the knowledge pool. Follow these steps to create and/or edit your own profile, including uploading a portrait photo.

  1. Navigate to the knowledge pooling tool.

  2. Log in using your associated TRR379 hub account.
    • Click the “Login” (human silhouette) button.
    • Select the “Login with TRR379 hub” option.
    • Read the disclaimer, and if you agree, select “Authorize Application”.
    • A checkmark will appear on to the “Login” (human silhouette) button if you were successfully logged in.

  3. Select the “Person” Data Type on the left side of the page.

  4. Create a new record by clicking the + (plus) button, or edit an existing record by clicking the pencil icon.

Screenshot showing the add- and edit-buttons for a person record Screenshot showing the add- and edit-buttons for a person record

  1. To add a portrait photo, click the “Upload a depiction” Wizard button (person silhouette icon). Click the file attachment button (paperclip icon), and select the portrait image with your file browser. Wait for the green checkmark confirmation of a successful upload, and then click “SAVE”.
Important

Image requirements:

  • Contributor portraits: maximum 400 pixels wide
  • Page thumbnails: minimum 320 by 240 pixels, aspect ratio 4:3
  • A single image can serve as both portrait and thumbnail if the face is centered
  1. Proceed to add relevant information to complete your contributor profile as follows:
ORCID identifier
  • Within the “Identifiers” box, select “ADD NEW ITEM” and then “ORCID” from the dropdown menu.
  • Under “Notation”, enter your ORCID in the format “XXXX-XXXX-XXXX-XXXX”.
  • Under “Creator”, start typing “ORCID” and select the “ORCID” organization when it appears in the dropdown menu.
  • Click “SAVE” in the top-right corner to save the ORCID record.
Description
  • Within the “Description” box, type a short biography, which can include (but is not limited to) information such as your affiliation(s), professional expertise/interests, and your role within TRR379.
  • The “Description” field supports Markdown formatting. To preview how your description will render, select the small Markdown logo (capital “M” with a downward-facing arrow) to enter the Markdown editor.
Name(s)
  • Enter the relevant family name(s), given name(s), honorifics, etc. in the respective text boxes.
Affiliation(s)
  • Within the “Delegated by” box, select “Organization” from the dropdown menu.
  • A new box will appear just below “Organization”. Search for your affiliated organization by starting to type its name, and select the appropriate organization when it appears in the dropdown menu.
    • TIP: Organizations might exist in the pool in a language different to what you are searching for, or might not be searchable based on their abbreviations. Try searching keywords in the organization name that do not translate in different languages before adding a new organization. For example, you may want to search “Jülich” instead of “Research Centre Jülich”, “Forschungszentrum Jülich”, or “FZJ”.
  • To add additional affiliations, select the + (plus) button to the right of the “Delegated by” boxes.
  1. Once all relevant information has been entered, click “SAVE” in the top-right corner to save the Person record.
  2. Click the “Submit” button (cloud icon, top-right), which should show a green notification dot to indicate changes are ready to be submitted.
Important note about saving versus submitting

The pool has two separate actions: saving and submitting. Saving stores your work in the browser only! It does not submit the record to the server for use by the consortium workflows. To submit, click the Submit button (cloud icon, top-right corner) when there is a green notification dot indicating records are ready for submission. Do not close your browser tab before submitting, or your data will be lost.

  1. The interface will list all records you are about to submit. For a contributor profile with a profile photo, you should see three records: a File, a Depiction, and a Person.
  2. Click “Submit”. A confirmation message will appear when submission is successful. If an error occurs, note the message and retry. If it persists, you may wish to review common error messages or reach out for help via the resources on the Support page.

Screenshot showing the form submit button with a summary of the saved and to-be submitted records. Screenshot showing the form submit button with a summary of the saved and to-be submitted records.

Report publications

Note

Every member is responsible for submitting their own publications. Do not wait for someone else to add your work. If a publication is not in the pool, it will not appear in the consortium publication overview on the website.

  1. Navigate to the knowledge pooling tool.

  2. Log in using your associated TRR379 hub account.
    • Click the “Login” (human silhouette) button.
    • Select the “Login with TRR379 hub” option.
    • Read the disclaimer, and if you agree, select “Authorize Application”.
    • A checkmark will appear on to the “Login” (human silhouette) button if you were successfully logged in.

  3. Select the “Publication” Data Type on the left side of the page.

  4. Select the “Import a publication via DOI” button (square icon with right-facing arrow, just to the right of the + plus button).

Screenshot showing the button for importing a publication via its DOI Screenshot showing the button for importing a publication via its DOI

  1. Enter the DOI, and select “IMPORT”. A new section should appear showing the imported metadata. If you receive an error message that the record already exists, follow the instructions to edit the existing record instead of importing a new one.
Note

Enter just the DOI without the URL part (i.e., 10.1016/j.neubiorev.2025.106386 and not https://doi.org/10.1016/j.neubiorev.2025.106386)

  1. Confirm, add, or edit the Title, Abstract, and Authors as necessary. For authors that are not automatically linked upon import to Person records in the pool, you can click and search directly in the “Linked Record” column to find a corresponding Person record in the pool; if no linked record is selected, a new Person record will be created for that author. Click “SAVE” when everything looks correct.

Screenshot showing the Imported metadata panel while selecting a Linked Record for a co-author Screenshot showing the Imported metadata panel while selecting a Linked Record for a co-author

  1. Navigate to your new Publication record in the pool’s Publication records list, and click the pencil icon to edit it.

Screenshot highlighting the edit button to edit an existing Publication record Screenshot highlighting the edit button to edit an existing Publication record

  1. For publications to make the best impressions and live up to their fullest metadata potential, proceed to add relevant information to complete the Publication record as follows:
Publication type
  • Within the “Publication type” box, select the appropriate type (e.g., “Academic article”) from the dropdown menu.
Topic(s)
  • Within the “Topic(s)” box, browse and select topics relevant to the publication from the dropdown menu.
  • To add additional topics, select the + (plus) button to the right of the “Topic(s)” box.
Publication journal and date
  • Within the “Generated by” box, select “Activity” from the dropdown menu.
  • A new box will appear just below “Activity”. Select “Publishing process” from the dropdown menu.
  • Click the pencil icon to add qualifying information (i.e., publication time and location).
  • Add the publication date to the “At time” box in the format, YYYY-MM-DD. Alternatively, you can click the calendar icon to select the date.
  • Add the publication venue/journal by searching its name within the “At location” box, and selecting the correct name when it appears in the dropdown menu. Alternatively, you can search the journal’s ISSN. Wait a few seconds for choices to populate before creating a new record; search results may take time to load.
  • Click “SAVE” in the top-right corner to save the publication journal and date information.
Associated project(s)
  • Within the “Generated by” box, select “Project” from the dropdown menu.
  • A new box will appear just below “Project”. Browse and select a TRR379 project associated with the publication from the dropdown menu.
  • To add additional projects, select the + (plus) button to the right of the “Generated by” box.
License
  • If the publication has a particular license (e.g., within the Creative Commons suite), select the appropriate license from the dropdown menu within the “Rules” box.
Funding acknowledgment
  • At the very bottom of your Publication record editing screen, toggle the “All fields” option to on (indicated in blue).
  • Within the “Annotations” box, search “TRR funding” and select whether TRR funding is or is NOT acknowledged in the publication.
  1. Once all relevant information has been entered, click “SAVE” in the top-right corner to save the Publication record. After saving, a well-curated publication record links to its authors, topics, and projects.
  2. Click the “Submit” button (cloud icon, top-right), which should show a green notification dot to indicate changes are ready to be submitted.

Screenshot showing an annotated Publication record and highlighting the submission button Screenshot showing an annotated Publication record and highlighting the submission button

Important note about saving versus submitting

The pool has two separate actions: saving and submitting. Saving stores your work in the browser only! It does not submit the record to the server for use by the consortium workflows. To submit, click the Submit button (cloud icon, top-right corner) when there is a green notification dot indicating records are ready for submission. Do not close your browser tab before submitting, or your data will be lost.

  1. The interface will list all records you are about to submit. You should see your Publication record here.
  2. Click “Submit”. A confirmation message will appear when submission is successful. If an error occurs, note the message and retry. If it persists, you may wish to review common error messages or reach out for help via the resources on the Support page.

Document instruments and questionnaires

TRR379 uses the knowledge pool to document research instruments and questionnaires, and to provide standardized identifiers that can be used when harmonizing data across sites.

You can document an instrument at different levels. In particular, questionnaires can be documented as:

  • the original instrument or questionnaire,
  • a TRR379-specific version or variant,
  • individual questionnaire items, and
  • where useful, site-specific versions of an instrument or item.

These records can be linked to one another to expose the relationships between the original instrument, TRR379 versions, and individual questionnaire items.

You do not need to complete every level or every metadata field at once. Instrument documentation is an iterative process. A basic record with a clear identifier and name is already useful and can be expanded later.

Document an instrument

If you have an instrument that is used in TRR379, start by creating an Instrument record in the knowledge pool. At a minimum, give the instrument a meaningful name and a persistent identifier.

If you know the description, instrument type, source publication, or relationships to other records, add those as well. You can always add additional information later.

  1. Navigate to the knowledge pooling tool.

  2. Log in using your associated TRR379 hub account.
    • Click the “Login” (human silhouette) button.
    • Select the “Login with TRR379 hub” option.
    • Read the disclaimer, and if you agree, select “Authorize Application”.
    • A checkmark will appear on to the “Login” (human silhouette) button if you were successfully logged in.

  3. Select the “Instrument” Data Type on the left side of the page.

  4. Create a new record by clicking the + (plus) button, or edit an existing record by clicking the pencil icon.

Screenshot showing the add- and edit-buttons for an instrument record Screenshot showing the add- and edit-buttons for an instrument record

  1. Click the “Edit PID manually” button (pencil icon to the right of “Persistent identifier”) and edit the random identifer according to the following naming convention:
trr379:instruments/<original_instrument>-<trr379_variant_and_version>-<item_or_subscale_name>

Click the “Persistent identifer” pencil icon again to lock the PID editor.

Important information about PIDs

PIDs should be human-readable and should be sufficient for a knowledgeable human to understand what content is likely contained in that record. These PIDs will end up as column header values in pertinent data tables. The prefix, trr379: expands to https://trr379.de/ns/, and can be left out in any TRR379 internal usage. Within the scope of a data table, the instrument identifier can be further shorted by stripping trr379:instruments/, leaving, for example, lha-trr379-q01-item1 as an item identifier (e.g., as a column header value).

  1. Within the “Name” box, enter a human-readable name for the content in your Instrument record. As is relevant, this might take the format: <original_instrument_name>, <subscale_name> (<trr379_variant>), or for a specific questionnaire item it would simply be the text for that question.
  2. Add whatever metadata you have available (see also Relationships and Additional metadata).

Screenshot showing the “Edit PID manually” button, “Name” box, and additional metadata (i.e., “Description”) Screenshot showing the “Edit PID manually” button, “Name” box, and additional metadata (i.e., “Description”)

  1. Once all relevant information has been entered, click “SAVE” in the top-right corner to save the Instrument record.
  2. Click the “Submit” button (cloud icon, top-right), which should show a green notification dot to indicate changes are ready to be submitted.

Screenshot showing an annotated Instrument record and highlighting the submission button Screenshot showing an annotated Instrument record and highlighting the submission button

Important note about saving versus submitting

The pool has two separate actions: saving and submitting. Saving stores your work in the browser only! It does not submit the record to the server for use by the consortium workflows. To submit, click the Submit button (cloud icon, top-right corner) when there is a green notification dot indicating records are ready for submission. Do not close your browser tab before submitting, or your data will be lost.

  1. The interface will list all records you are about to submit. You should see your Instrument record here.
  2. Click “Submit”. A confirmation message will appear when submission is successful. If an error occurs, note the message and retry. If it persists, you may wish to review common error messages or reach out for help via the resources in the Support page.
Tip

At a minimum:

  • Use a meaningful, human-readable PID.
  • Give the record a meaningful name.
  • Save and submit the record.

Everything after that is a (welcomed) bonus.

Document a questionnaire

Questionnaires can be represented at several levels.

Original instrument
    │
    └─ TRR379 variant
          │
          ├─ Item 1
          ├─ Item 2
          ├─ Item 3
          └─ ...

Original questionnaire

If the original instrument/questionnaire is known, create a record for it, give it a PID in the format, trr379:instruments/<original_instrument> (e.g., trr379:instruments/lha) and, where possible, link it to its source publication or other canonical documentation.

Example of an annotated original instrument, highlighting the PID and links to source documentation Example of an annotated original instrument, highlighting the PID and links to source documentation

TRR379 questionnaire variant

TRR379-specific versions take on the PID format, trr379:instruments/<original_instrument>-<trr379_variant_and_version> (e.g., trr379:instruments/lha-trr379-q01). This is where you should document meaninful differences from the original questionnaire, including:

  • translation
  • modified wording
  • different item selection
  • coding differences
  • particular TRR379 projects using the variant

Example of an annotated variant, highlighting the PID and links to the original instrument Example of an annotated variant, highlighting the PID and links to the original instrument

Questionnaire items

If the individual questionnaire subscales and/or items (i.e., questions) are known, create a separate Instrument record for each item. For LHA, for example:

trr379:instruments/lha-trr379-q01-subscale-aggression
trr379:instruments/lha-trr379-q01-subscale-consequences
trr379:instruments/lha-trr379-q01-subscale-selfdirected
trr379:instruments/lha-trr379-q01-item1
trr379:instruments/lha-trr379-q01-item2
...

Item-level identifiers allow sites to refer to the same questionnaire items consistently when preparing standardized datasets.

For each item, be sure to include:

  • Name: the actual question/item text
  • part of: the questionnaire/variant it belongs to

Example of an annotated subscale, highlighting the PID and links to the relevant questionnaire Example of an annotated subscale, highlighting the PID and links to the relevant questionnaire

When available, this also where value encodings for answer options may be recorded.

Example of an annotated questionnaire item, highlighting the value encodings Example of an annotated questionnaire item, highlighting the value encodings

Relationships

Relationships are useful when you know how the record relates to another instrument or questionnaire.

RelationshipUse when…Example
part ofAn item/subscale belongs to a questionnaireThere are 11 individual items that are part of the LHA
alternate ofTwo records represent alternative versions of the same instrumentA TRR379 variant may be an alternate of the original instrument
derived fromA version was created from an earlier/original instrumentA TRR379 questionanire might be derived from the original instrument through the “Activity”, “Translation”
revision ofA new version revises an earlier versionA second version of a TRR379 questionnaire is a revision of the first version of that TRR379 questionnaire

Additional metadata

For instruments to live up to their fullest metadata potential, proceed to add relevant information as you are able. For example:

Description
  • Within the “Description” box, enter any information that is pertinant to understand what content is contained in your Instrument record. For example, this may be a description/abstract taken directly from an original instrument’s documentation or related publication, or this could include details on how a TRR379 variant was changed (or not) from the original form (e.g., translations, item coding, which TRR379 projects use the variant, etc.)
Instrument type
  • Within the “Instrument type” box, select the appropriate type from the dropdown menu.
  • For questionnaires and their items, relevant types might include (but are not limited to): Psychological Assessment, Clinical or Research Assessment Subscale, Clinical or Research Assessment Question
Topic(s)
  • Within the “About” box, select the “FILTER DATA” button and make sure only “Topic” is checked to browse and select from the dropdown menu topics relevant to your Instrument record.
  • To add additional topics, select the + (plus) button to the right of the “About” box.
Relationship(s)
  • Within the relevant “Part of”, “Alternate of”, and/or “Specialization of” boxes, select the linked Instrument record from the dropdown menu. For example, a TRR379 questionnaire variant may be an alternate of the original instrument, a subscale may be part of a TRR379 variant, and a questionnaire item may be part of a TRR379 variant, as well as a subscale.
  • To add additional links, select the + (plus) button to the right of the “Part of”, “Alternate of”, and/or “Specialization of” boxes.
Provenance

Where known, record where an instrument or questionnaire variant came from, and how it relates to previous versions.

  • Add source documentation and contributors: Within the “Attributed to” box, select “Person” from the dropdown menu. Search for or add the author that contributed to the Instrument you are documenting. You can additiomal link the source documentation by adding to the “Characterized box” a new item with the Predicate, “is described by”, and the Object linking to the relevant Publication.
  • Add derivations for variants: Within the “Derived from” box, select the linked Instrument record from the drop down menu. Click the pencil icon to the right of the box to add the “Generated by” relationship. For example, a TRR379 questionnaire might be derived from the original instrument through the “Activity”, “Translation”. Click “SAVE” in the top-right corner to save the derivation information.
  • Add revisions for different versions: Within the “Revision of” box, select “ADD NEW ITEM”. Within the “Entity” box, select the instrument your record is a revision of. For example, a second version of a TRR379 questionnaire is a revision of the first version of that TRR379 questionnaire. Click “SAVE” in the top-right corner to save the revision information.
Value encodings
  • For counts, select the “Count” Concept within the “About” box’s dropdown menu and “range (value type): nonNegativeInteger” from the “Characterized by” box’s dropdown menu.
  • For categorical values, select “ADD NEW ITEM” within the “Attributes” box. At a minimum enter the “Value” and its “Description”. Select “assumes values specified by” within the “Predicate” box. Optionally, you can add semantics for “Defined by” and “Value type (range)” when appropriate.

Work with raw MRI data

Magnetic resonance imaging is an essential data acquisition method for TRR379. Four sites acquire such data. Each site has (different) established routines and conventions. This documentation collects resources and best practices that can be adopted by TRR379 members.

Subsections of Work with raw MRI data

BIDS conversion

Converting the heterogeneous, site-specific raw MRI data acquisitions into a standardized dataset is an essential precondition for the collaborative work in TRR379. It readies the data for processing with established pipelines, and applies a pseudonymization as a safeguard for responsible use of this personal data.

TRR379 uses the Brain Imaging Data Structure (BIDS) as the standard for its datasets.

Conversion to BIDS

The conversion of raw MRI data in DICOM format to a BIDS-compliant dataset is a largely automated process. The recommended software to be used for conversion is heudiconv. Heudiconv uses dcm2niix as the actual DICOM→NIfTI converter. Heudiconv tutorials further illustrate how the software works.

Heudiconv performs the task of mapping DICOM series to BIDS entities (ie. determining BIDS-compliant file names). A key heudiconv concept is a heuristic: a Python program (function) which receives the DICOM series properties and matches them with a file naming pattern. A heuristic typically relies on DICOM series naming (set at the scanner console), but it can also use other properties such as number of images or acquisition parameters.

Heudiconv workflows have been implemented at each MRI acquisition site, and reuse shared components.

Shared Resources

Important

Each site maintains its own copy of the heuristic (as part of the site-specific DICOM superdataset) to account for site-specific differences.

Details

Modular datasets

A DataLad dataset containing a BIDS dataset will typically have these subdatasets. Subdatasets help in recording provenance while enabling different access scopes for different components:

  • code/heudiconv: heudiconv container (q02/heudiconv-container)
  • code/rdmtools: optional, shared scripts for data curation tasks (q02/rdmtools)
  • sourcedata/dicoms: a site-specific DICOM dataset, itself containing one subdataset per session
  • .heudiconv: heudiconv cache / intermediate outputs are stored in a separate dataset to avoid including DICOM information in the BIDS dataset

Submit Annual DFG Survey

The 2025 survey is closed

Access the survey app to participate.

Need help?

I am having issues with the survey form.

If there are issues with the form, they can be submitted on the TRR379 collaboration hub at https://hub.trr379.de/q02/dfg-cp-survey-ui/issues (requires an account), or emailed to trr379@lists.fz-juelich.de.

I need a personalized access token.

As a member of the TRR379, you should receive an individual access token via email. If you have not received one, please email Michael Hanke with a request.

Background

The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) gathers information from its funded projects on an annual basis. Some information is collected from all members of a coordinated programme, such as a collaborative research centre (CRC).

The data are used to produce statistical reports and provide answers to statistical queries. In addition, the data serve as the basis for statistical evaluations, which the DFG uses to comply with its reporting obligations to financial backers, the federal government and the state governments.

For more information, please refer to the information on data protection in relation to DFG research funding (see point 10 under Research Funding question IV), which can be accessed at https://www.dfg.de/privacy_policy.

TRR379 approach

The TRR379 collects the DFG survey data using the same infrastructure that is employed for research metadata collection and management, rather than the PDF-form based approach suggested by the DFG.

This offers the following advantages:

  • members only have to enter their details in the first survey, and can efficiently resubmit updated records in subsequent years
  • members can consent to having a subset of their information be used to create and update a profile page on their person on the TRR379 website with no additional effort
  • members can consent to having basic information (e.g., name, ORCID) on them be made available in other TRR379 services, for example for reporting publications, or data annotation, to avoid repeated, manual information entry

Collected information is submitted to a TRR379-dedicated virtual server hosted at Forschunsgzentrum Jülich (operated by the Q02 project via an encrypted connection. Individual person records are only accessible via a personalized link with an individual access token. Members receive this access information via email.

This service is opt-in. Members who do not wish to have their data submitted and kept in the described way can follow the standard DFG-procedure and send the PDF-form available at https://www.dfg.de/resource/blob/203580/questionnaire-sfb-grk-fip-2025-en.pdf to the TRR379 management team.

Submit data

The electronic survey form is provided at https://dfg-cp-survey.trr379.de

Members receive a personalized access link via email. Only with this link is it possible to see one’s personal record and to submit information.

Tip

It is highly recommended to use this webform with a desktop browser; the form offers rich contextual information that is hard to access on mobile devices.

Create or edit a record

If no record on a person already exists, a new record must be created. This is done by clicking on the + button in the “Person” category.

Screenshot showing the add-button for a person record Screenshot showing the add-button for a person record

Alternatively, if a previous record already exist, it can be loaded by clicking on the “Edit” button (pencil icon).

Screenshot showing the edit-button for a person record Screenshot showing the edit-button for a person record

Fill the form

Context help is provided for every form filed. This information is accessible by hovering the mouse pointer over the field title.

Screenshot showing where to hover to access the context help Screenshot showing where to hover to access the context help

For some fields (e.g., prior workplace, area of study) one or more choices have to be selected. The selector offers type-ahead search of choices. The selection is constrained to choices matching the entered text in their label.

Screenshot showing the item selector and constrained search Screenshot showing the item selector and constrained search

When no adequate choice exists, a new item can be created by clicking the “Add New Item” button.

Save and submit the form

There are two different save actions: local saves and submitting to the server.

Save form sections (local save)

Whenever a form (or sub-form) is completed, it must be saved by clicking the “Save” button. You must do this for each section you complete.

Screenshot showing the form save button Screenshot showing the form save button

Important

Saving only stores the information in the local browser session! It does not submit the form to the server.

Final submission to server

When the person record is complete and is saved, the record can be submitted to the server by clicking the “Submit” button (cloud icon with up arrow).

Screenshot showing the form submit button Screenshot showing the form submit button

Submission is only possible with a valid access token. If the form was accessed via the personalized link, this token is already in place. If the form was accessed by other means, the token can be entered via the “Key” button. The token is embedded in the access link received via email.