- #DESKTOPR MAC OSX#
- #DESKTOPR INSTALL#
- #DESKTOPR REGISTRATION#
- #DESKTOPR LICENSE#
- #DESKTOPR WINDOWS#
If you are on Windows, you may experience this problem for the same reason immediately above.
#DESKTOPR LICENSE#
fMRIPrep requests the FreeSurfer license file, although one is provided.Please make sure you allow Docker to mount folders from the host in your settings. fMRIPrep requires that the original data are “mounted” into the container.
#DESKTOPR WINDOWS#
Mounting drives on Windows: the Docker for Windows Engine does not allow sharing data from the host to make it available within the container. To check/change this we have shown the process below. Please make sure to apply & restart or this change will not have been implemented. We recommend assigning 8GB or more memory to the Docker Engine. Please, check your Docker configuration before running fMRIPrep. #DESKTOPR MAC OSX#
Memory issues: on Windows and Mac OSX systems, the Docker Engine is configured to access 2GB RAM by default. New users may run into two families of problems: Under the “Methods” section of each report, you’ll find a detailed description of the exact processing workflow ready to copy-and-paste into your manuscript, including all pertinent references.īrain mask and brain tissue segmentation of the T1w A careful examination of the report of every subject should be done to assess the quality of the preprocessing results. These reports, written in HTML to be viewed in your web browser (we recommend Chrome or Firefox), will walk you through the preprocessing steps run, and highlights some of the decisions fMRIPrep made along the way. Now we have completed running fMRIPrep on the dataset! What’s Next? After running fMRIPrep we encourage you to open up the generated visual reports (for example, screenshots of the Brain mask and brain tissue segmentation of the T1w, EPI to T1 registration, and the BOLD Summary portions are shown below). tsv file with one confounding time-series per column, from which you can select and use after pertinent orthogonalizations to regress confounds out with their preferred tools. NOTE: fMRIPrep does not run confounds regression or any other filtering. More broadly, the outputs of fMRIPrep conform to the BIDS-Derivatives specification, Release Candidate 1. When fMRIPrep has completed running, the output directory looks like this.Ī detailed description of the fMRIPrep outputs can be found here. For simplicity, we recommend placing the input, output and analysis levels prior to any options.įmriprep-docker /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/Nifti /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/derivatives participant -participant-label 2475376 -fs-license-file /Users/franklinfeingold/freesurfer.txt -ignore slicetiming You may pass additional arguments as you would to fMRIPrep. Please note that the ‘sub-’ prefix is not included. Lastly, we provide the participant label tag to indicate which participant to run. Followed by passing the keyword ‘participant’ as the third argument, which selects the analysis level that will be executed (see the BIDS-Apps specification for further details and possible values in the case of fMRIPrep, only ‘participant’ is available). The next part is providing the output directory. To break down the command: the first argument is providing the input path to the BIDS dataset. The command to execute it is illustrated below. More information regarding this can be found here. We saved our license into a file called /Users/franklinfeingold/freesurfer.txt. Please save this license file to your computer. #DESKTOPR REGISTRATION#
After filling out the registration form, a license file will be sent to the email provided. To get the license and run FreeSurfer, FreeSurfer requires users to register for free, here. Because of this, fMRIPrep requires a FreeSurfer license. fMRIPrep uses FreeSurfer to reconstruct anatomical surfaces of the brain as well as some registration steps. )ģ) Please be cautious running multiple subjects in parallel due to space and memory limits on your machine.
NOTE: Please observe there are a few BIDS validator warnings that may need to be attended to before running fMRIPrep.ġ) To do the susceptibility distortion correction, the IntendedFor metadata keys need to be defined for every field map that is to be applied.Ģ) To do the slice timing correction, the slice timings need to be defined in the BOLD json metadata file (if you want to ignore the slice timing correction, please add the ‐‐ignore slicetiming option, the command to do this is shown below. Please find pictured below our BIDS validated dataset.
We will only be taking sub-2475376 session 1 anatomical and resting state scan at TR=1400ms.
#DESKTOPR INSTALL#
Pip install -user -upgrade fmriprep-dockerįor this tutorial, we will be using the Nathan Kline Institute (NKI) Rockland Sample – Multiband Imaging Test-Retest Pilot Dataset.
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