Comments for Stanford Center for Reproducible Neuroscience https://reproducibility.stanford.edu Wed, 04 Dec 2024 18:37:40 +0000 hourly 1 https://wordpress.org/?v=6.7.1 Comment on BIDS Tutorial Series: Introductory Walkthrough by Anonymous https://reproducibility.stanford.edu/bids-tutorial-series-part-1a/#comment-33187 Fri, 01 Apr 2022 15:55:25 +0000 http://reproducibility.stanford.edu/?p=335#comment-33187 Hi, all

I fixed the problem above

Best,
Wenjun

]]> Comment on BIDS Tutorial Series: Introductory Walkthrough by Anonymous https://reproducibility.stanford.edu/bids-tutorial-series-part-1a/#comment-33181 Fri, 01 Apr 2022 12:23:25 +0000 http://reproducibility.stanford.edu/?p=335#comment-33181 Hi, all
Thank you for the tutorial! I wonder if I get a longitudinal structral MRI data(and I just have structral MRI data without dwi or fmri data), how should I organized? treat the second longitudinal structral MRI data as another subject? (I have put my second longitudinal structral MRI into ses-2 folder, but got an error)

please give me some advice!
Many thanks!
Best,
Wenjun

]]> Comment on fMRIPrep tutorial: Running the docker image 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

]]> Comment on fMRIPrep tutorial: Running the docker image 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.

]]> Comment on BIDS Tutorial Series: HeuDiConv Walkthrough by Franklin Feingold https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-22838 Fri, 26 Mar 2021 21:42:46 +0000 http://reproducibility.stanford.edu/?p=536#comment-22838 Hi Carina,

Thank you for your message and I apologize for my very delayed reply. If you may please direct questions over to NeuroStars (https://neurostars.org/tag/bids) with the “bids” tag. That is a more active platform for supporting the community to adopt BIDS.

Thank you,
Franklin

]]> Comment on BIDS Tutorial Series: Introductory Walkthrough by Franklin Feingold https://reproducibility.stanford.edu/bids-tutorial-series-part-1a/#comment-22837 Fri, 26 Mar 2021 21:39:33 +0000 http://reproducibility.stanford.edu/?p=335#comment-22837 Hi Donna,

I apologize for my very delayed reply. If you may you please direct questions over to NeuroStars (https://neurostars.org/tag/bids) with the “bids” tag. That is an active platform for supporting the community adopting BIDS.

Thank you,
Franklin

]]> Comment on BIDS Tutorial Series: HeuDiConv Walkthrough by Carina Forster https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-19128 Sun, 29 Nov 2020 10:33:37 +0000 http://reproducibility.stanford.edu/?p=536#comment-19128 Thank you for the great tutorial.

If I want to validate session 5 I get the following error:
JSON_SCHEMA_VALIDATION_ERROR
sub-01_ses-005_task-rest_run-001_bold.json43.582 KB

Location:
Nifti/sub-01/ses-005/func/sub-01_ses-005_task-rest_run-001_bold.json

Reason:
Invalid JSON file. The file is not formatted according the schema.

Evidence:
.CogAtlasID should match format “uri”

task-rest_bold.json43.631 KB
Location:
Nifti/task-rest_bold.json

Reason:
Invalid JSON file. The file is not formatted according the schema.

Evidence:
.CogAtlasID should match format “uri”

I am not sure how to solve that issue?

Thank you again for your help.

Carina

]]> Comment on BIDS Tutorial Series: Introductory Walkthrough by Donna Gift Cabalo https://reproducibility.stanford.edu/bids-tutorial-series-part-1a/#comment-18821 Thu, 19 Nov 2020 13:09:09 +0000 http://reproducibility.stanford.edu/?p=335#comment-18821 Hello.

Thanks for the tutorial! I have T1 and resting state fmri dataset (just one session) that I am attempting to convert. While my anat folder is a valid data set, I am getting an error the following error on the func folder:
Error 1: [Code 50] TASK_NAME_MUST_DEFINE
Click here for more information about this issue
I renamed the converted files like the following and transferred them inside the func folder but to no avail.
sub-275679_task-rest_bold.nii
sub-275679_task-rest_bold.json
What could be causing this?

]]> Comment on fMRIPrep tutorial: Running the docker image 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

]]> Comment on fMRIPrep tutorial: Running the docker image 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!

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