Road map for projects at CIR

The purpose of CIR is to make sophisticated imaging methods available for researchers with different backgrounds and level of experience. To this end CIR and/or KI core facility staff is available for supporting researchers throughout a project. Below are some useful checkpoints to keep track of during a project together with a summary of what level of support can be provided at each stage.

 

* Support can be provided by CIR or imaging core facility staff.

First step

  • Formulate an idea - Formulate and idea from your previous research, or gaps i knowledge in your field.
     
  • Research relevant literature - Search the literature for what has been done and what imaging experiments can produce new knowledge.
     
  • Develop research question compatible for imaging* - Imaging at CIR can be used for a wide variety of research questions. Reach out to CIR or staff at the different imaging facilities to get expert advice on how to best approach your research topic with imaging tools.

Initiate project

  • Form a team* - It is useful to early on plan who will be responsible for the different parts of a project. This is a required part of registering a new project with CIR. Depending on scope of project and experience within a research group, different levels of involvement and support from CIR may be needed and must be clarified before initiating a project.
     
  • Ethical approval* - It is the responsibility of the project’s PI to ensure that ethical approval has been granted for the project, as specified in the user agreement, and that it is adhered to throughout the project. CIR and imaging core facility staff can provide support in describing the general risks and benefits of the different imaging modalities and methodologies used.
     
  • Register project - Register a new project with CIR. It is the responsibility of the projects Principal Investigator (PI) that the registration is correct and complete.
     
  • Facility access and training* - Some imaging facilities can be "self-use" by researchers or students for data collection after training. Make sure the researchers intended for this sign up for a drivers license course and register for door access as needed. Scheduling of core facilities at KI is done in iLab - apply for access to be able to check availability and book facilities yourself. 
     
  • Data access* - In general, data generated at CIR is uploaded to the Share Platform for Imaging in the CIR Environment (SPICE). A project folder is created for you when you register your project and all imaging data is collected here. Request a new user account at SPICE using this web form. The CIR-wiki pages give detailed instructions on how to connect to SPICE.

Set up for imaging

  • Develop experiment* - Any experimental conditions you plan, e.g. sensory stimulation (presenting images or sounds) or auxiliary measurements (eye-tracking, skin conductance, etc.) take time to develop, calibrate and test. Usually experiments are run using PsychoPy, Matlab or NeuroObs Presentation. General experimental paradigms are available and can often be easily modified. CIR or imaging facility staff can support you in setting up and test your experiments but the ultimate responsibility lays with the individual researcher. It is good practice to document and share experimental paradigms (e.g. on github and the CIR-wiki pages) to ensure your experiment is transparent and reproducible.
     
  • Technical piloting* - A project involving development of new methods (e.g. custom MEG sensor arrays or MRI-sequences) may require involvement of CIR or imaging facility staff for technical developments. Schedule this part of your project together with the parties concerned.
     
  • Pilot experiment/protocol - A lot of pieces tend to fall into place during pilot measurements. When possible - pilot early and account for time to modify your protocol and experiment based on lessons learned from piloting.
     
  • Finalize experiment - Finalize you experiment/protocol based on experience from piloting and feedback from the ethical committee.
     
  • Pre-register your research - Pre-registering your study (e.g., with AsPredicted or the Center for Open Science) is considered good scientific practice and provides a record showing that you completed the project as planned.  

Execute project 

  • Archive pilot data and related documentation - Make sure your protocol and experimental paradigm is well documented and shared with your group. This way, the success of the project is not dependent on single individuals and methods are transparent and reproducible.
     
  • Schedule lab time for measurements* - Scheduling of core facilities at KI is done in iLab. Projects that need specific or consistent times for imaging (e.g. for pre- and post measures) can contact the facility they plan to use to make a few preliminary bookings of necessary time-slots.
     
  • Perform measurements* - Finally - it is time to collect your data! Depending on the facilities you are using, this may be done by you or with support from core facility staff as documented in your user agreement.
     
  • Preprocess your data continuously - As your data is collected, organize it in the standard BIDS format, run preprocessing (e.g. motion correction and artefact removal). This allows continuous quality control of collected data and greatly reduce time to publication after data collection is completed.
     
  • Build an analysis pipeline - Don't wait until all your data is collected before designing an analysis pipeline. Start building a framework already using your pilot data. This will allow you to perform quality assurance of data as it is collected and will minimize delay to publish. Seven quick tips for analysis scripts in neuroimaging is an excellent resource for how to organize your analysis. It is strongly recommended you track your analysis scripts in a version control system (like git) and share it (e.g. on github). There are plenty of resources for getting in to version control using git, e.g. from coderefinery and doing so is time well invested. 

After data collection

  • Organize data in project folder* - As you collect data it will land in your projects folder on SPICE. As data collection concludes it is recommended to keep your raw data in BIDS format as a final, read-only data set and use it to create traceable derivatives in your analysis. CIR and core facility staff can support you in organizing your data in BIDS format. 
     
  • Archive data - Note that the server SPICE is offered as an analysis space for active projects, but is not backed-up long term storage. It is the responsibility of each projects PI to ensure data is backed-up and archived, KI offer different solutions for this purpose. [WIP: Link here to wiki on data transfer]
     
  • Analyze data* - Analyze your imaging data according to answer the research questions posed in the project. CIR or core facility staff can offer support with standard analysis tools and methods.
     
  • Write manuscript* - Write and submit a manuscript including any co-authors that have been involved in your projects according to the user agreement authorship guidelines. Depending on the involvement of CIR or core facility staff in your project, your team can support you in writing or reviewing your manuscript.
Niklas Edvall
24-10-2025