Comments on: fMRIPrep tutorial: Running the docker image https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/?utm_source=rss&utm_medium=rss&utm_campaign=fmriprep-tutorial-running-the-docker-image Wed, 04 Dec 2024 18:37:40 +0000 hourly 1 https://wordpress.org/?v=6.7.1 By: Wenjun https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-32762 Mon, 14 Mar 2022 13:54:45 +0000 http://reproducibility.stanford.edu/?p=789#comment-32762 Hi,
Thank you for the tutorial. It helped a lot.
I want to konw how to execute with Docker in parallel.
Thank you for your time.
Wenjun

]]> By: Marvin https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-32398 Sun, 27 Feb 2022 22:26:07 +0000 http://reproducibility.stanford.edu/?p=789#comment-32398 Thanks for this helpful tutorial. Can you think of any reason why after running command in Step 3, no directory called “fmriprep” was created? I still get the “sub-/” directory and others but somehow the structure is different.

]]> By: Franklin Feingold https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-17871 Wed, 21 Oct 2020 00:33:47 +0000 http://reproducibility.stanford.edu/?p=789#comment-17871 Hi Matin,

Thank you for your messages. I would suggest asking these over on NeuroStars using the fMRIPrep tag (https://neurostars.org/tags/fmriprep). fMRIPrep experts are on NeuroStars to help answer questions.

Thank you,
Franklin

]]> By: Matin https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-17784 Sat, 17 Oct 2020 10:33:58 +0000 http://reproducibility.stanford.edu/?p=789#comment-17784 And another question I’m asking is how may I modify fMRIPrep for Macaque monkeys brain? I didn’t find any description about this in the prepared docs!

]]> By: Matin https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-17783 Sat, 17 Oct 2020 08:20:39 +0000 http://reproducibility.stanford.edu/?p=789#comment-17783 Hi,
how much does it take usually for the process to be done completely on a single subject? On my local I have 8 cores and 16 GB of RAM. It has been running for more than 5 hours now and it’s not finished yet. Considering I am running fMRIPrep on just one subject!

]]> By: Franklin Feingold https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-9399 Tue, 03 Sep 2019 23:48:15 +0000 http://reproducibility.stanford.edu/?p=789#comment-9399 Hi Sameera,
Thank you for your question! There is not a specific tutorial for Multi-echo data, perhaps on NeuroStars with tag fmriprep (https://neurostars.org/tags/fmriprep), there are useful comments from the community. Please feel free to post your question on NeuroStars, fmriprep experts are on there and able to help!

Thank you,
Franklin

]]> By: Sameera Abeykoon https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-9313 Thu, 29 Aug 2019 19:19:17 +0000 http://reproducibility.stanford.edu/?p=789#comment-9313 Hi,
Thank you for the tutorial. It helped me how to use fmriprep.

Now I need to process Multi-echo data using fMRIprep. Do you have similar type of fMRIPrep tutorial for MUlti-echo data.?

Thank you
Sameera

]]> By: Franklin Feingold https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-7778 Fri, 31 May 2019 17:43:36 +0000 http://reproducibility.stanford.edu/?p=789#comment-7778 Hi Chris,
Thank you for your question. There is not a BIDS formatted version of the tutorial data available. The BIDS tutorial 1B – http://reproducibility.stanford.edu/bids-tutorial-series-part-1b/ – provides the commands to convert and streamline the process. This tutorial only uses a smaller sample of that tutorial to make it easier to get to this stage. Another option is to grab data off of https://openneuro.org/. Datasets need to be BIDS validated, but depending on what options you may be looking to see (i.e. Slice Timing correction, the timing would need to be defined in the json to do the correction). I apologize for the inconvenience.

]]> By: Chris Cox https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-7738 Thu, 30 May 2019 01:09:30 +0000 http://reproducibility.stanford.edu/?p=789#comment-7738 Is there a BIDS formatted version of the tutorial data? I would rather not go through the whole BIDS tutorial just to have a reference dataset as I work on getting fMRI prep and podman properly configured on RHEL.

]]> By: Franklin Feingold https://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/#comment-7013 Tue, 23 Apr 2019 21:20:35 +0000 http://reproducibility.stanford.edu/?p=789#comment-7013 Hi Zhenfu,

Thank you for your question and happy to hear your use of fMRIPrep. There are likely to be recommendations/advice on https://neurostars.org/tags/fmriprep (this is a forum where you may ask questions and read issues other users have flagged). Currently, I am not aware of specific tutorials to interpret the reports.

Thank you,
Franklin

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