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help > RE: CONN compatibility with BIDS and fmriprep output
Feb 14, 2019 12:02 PM | Alfonso Nieto-Castanon - Boston University
RE: CONN compatibility with BIDS and fmriprep output
Dear Karolina,
Thank you for your question. Yes, we are also very enthusiastic about BIDS and have been adding a lot of BIDS-compatibility functionality into CONN (and continue doing so). First there is the new Tools.Import.FromBIDS menu in CONN, which allows you to easily import an entire BIDS-structured dataset including original or preprocessed functional/structural files as well as condition/task definitions into CONN. We also partially support the opposite directionality, where you can use the 'Copy to local BIDS folder and import' option in the Setup.Structural/Functional tabs when importing your raw data into CONN and that will internally save your data in a BIDS-compatible format. Then there are several preprocessing and setup steps which can automatically read/interpret BIDS-formatted information (for example you may choose 'BIDS' slice acquisition order, or fieldmap acquisition parameters, or leave empty the TR field, and CONN will then attempt to read the relevant information from your functional data sidecar .json files)
While we have not yet built a specific import functionality for fmriprep output files (this may be built into some of the next few releases) I believe you should currently be able to import fmriprep output files into CONN easily using a combination of the ToolsImport.FromBIDS functionality (this will import task info as well as preprocessed functional and structural files) together with some manual file-selection during Setup (e.g. to import realignment first-level covariate files and Gray/White/CSF tissue ROIs, unless you are planning to run some of these additional preprocessing steps from CONN). I have not tried this myself yet so please feel free to try any of this out and let us know of any issues you may run into and/or any suggestions to help us make this functionality better / more useful in future releases.
Best
Alfonso
Originally posted by Karolina Finc:
Thank you for your question. Yes, we are also very enthusiastic about BIDS and have been adding a lot of BIDS-compatibility functionality into CONN (and continue doing so). First there is the new Tools.Import.FromBIDS menu in CONN, which allows you to easily import an entire BIDS-structured dataset including original or preprocessed functional/structural files as well as condition/task definitions into CONN. We also partially support the opposite directionality, where you can use the 'Copy to local BIDS folder and import' option in the Setup.Structural/Functional tabs when importing your raw data into CONN and that will internally save your data in a BIDS-compatible format. Then there are several preprocessing and setup steps which can automatically read/interpret BIDS-formatted information (for example you may choose 'BIDS' slice acquisition order, or fieldmap acquisition parameters, or leave empty the TR field, and CONN will then attempt to read the relevant information from your functional data sidecar .json files)
While we have not yet built a specific import functionality for fmriprep output files (this may be built into some of the next few releases) I believe you should currently be able to import fmriprep output files into CONN easily using a combination of the ToolsImport.FromBIDS functionality (this will import task info as well as preprocessed functional and structural files) together with some manual file-selection during Setup (e.g. to import realignment first-level covariate files and Gray/White/CSF tissue ROIs, unless you are planning to run some of these additional preprocessing steps from CONN). I have not tried this myself yet so please feel free to try any of this out and let us know of any issues you may run into and/or any suggestions to help us make this functionality better / more useful in future releases.
Best
Alfonso
Originally posted by Karolina Finc:
Dear Alfonso,
Many researchers in the field (including myself) started to use BIDS for formatting and organization their datasets and also fmriprep (https://fmriprep.readthedocs.io/en/stabl...) for data preprocessing. How compatible is CONN with BIDS formatting and fmriprep output?
Is this possible in the future releases of CONN to allow users to load fmriprep output directly into CONN?
Best,
Karolina
Many researchers in the field (including myself) started to use BIDS for formatting and organization their datasets and also fmriprep (https://fmriprep.readthedocs.io/en/stabl...) for data preprocessing. How compatible is CONN with BIDS formatting and fmriprep output?
Is this possible in the future releases of CONN to allow users to load fmriprep output directly into CONN?
Best,
Karolina
Threaded View
| Title | Author | Date |
|---|---|---|
| Karolina Finc | Feb 9, 2019 | |
| Alfonso Nieto-Castanon | Feb 14, 2019 | |
| Karolina Finc | Feb 14, 2019 | |
| padma | Jul 12, 2021 | |
| omaomae | Jul 12, 2021 | |
| padma | Jul 13, 2021 | |
| omaomae | Jul 14, 2021 | |
| padma | Jul 9, 2021 | |
| Harrison Fisher | Mar 13, 2019 | |
| Karolina Finc | Mar 19, 2019 | |
| David Pagliaccio | Mar 18, 2021 | |
| Kylie Isenburg | Jun 11, 2021 | |