Comments on: BIDS Tutorial Series: HeuDiConv Walkthrough https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/?utm_source=rss&utm_medium=rss&utm_campaign=bids-tutorial-series-part-2a Fri, 26 Mar 2021 21:47:38 +0000 hourly 1 https://wordpress.org/?v=6.7.1 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

]]> 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

]]> By: Franklin Feingold https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-15547 Wed, 08 Jul 2020 17:41:21 +0000 http://reproducibility.stanford.edu/?p=536#comment-15547 Hi Simon,
Good to hear this was resolved! This case may be something the HeuDiConv team could provide guidance on.

Thank you,
Franklin

]]> By: Simon THIBAULT https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-15096 Fri, 19 Jun 2020 10:02:19 +0000 http://reproducibility.stanford.edu/?p=536#comment-15096 It ‘s has been solved after rebooting my computer but I did not understand the reason …

]]> By: Simon THIBAULT https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-15094 Fri, 19 Jun 2020 08:09:52 +0000 http://reproducibility.stanford.edu/?p=536#comment-15094 Hi,
Thank you for this tutorial.
I am getting an error that I am struggling to understand. Yesterday, it worked perfectly until step 4.
However, today it’s more difficult because I have an issue “INFO: Need to process 0 study sessions”.
I already had this issue at the beginning but I did not really understand how I solved it .
Did I miss an important step before applying step 2 ? Something about re-initialisation or something similar ?
Best,
Simon

]]> By: Franklin Feingold https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-10350 Thu, 24 Oct 2019 01:36:36 +0000 http://reproducibility.stanford.edu/?p=536#comment-10350 Thank you for your question! This appears to be an issue with the mounting of directories and HeuDiConv not reading them. This is seen from the message `INFO: Need to process 0 study sessions`. Confirming the paths to the files and the subject and session keys.

]]> By: RB https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-10223 Tue, 15 Oct 2019 01:34:46 +0000 http://reproducibility.stanford.edu/?p=536#comment-10223 Thank you for this great tutorial. I am following the steps on the example dataset, however I can not create .tsv file. when i run step 2, i get this –
INFO: Running heudiconv version 0.6.0.dev1
INFO: Need to process 0 study sessions
and there is nothing in output folder.

]]> By: Mingwen https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-7066 Fri, 26 Apr 2019 18:58:45 +0000 http://reproducibility.stanford.edu/?p=536#comment-7066 @Brian Odegaard I encountered into the same error and used the following command to make it work `docker pull nipy/heudiconv:debian`

]]> By: Franklin Feingold https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-6686 Wed, 03 Apr 2019 01:57:43 +0000 http://reproducibility.stanford.edu/?p=536#comment-6686 Hi Brian,

Thank you for your question. By chance was docker running when you received this error? I have found this error is typically associated with docker not running with trying to use docker. The pip error is interesting – it could be worth raising it on their github: https://github.com/nipy/heudiconv.

Thank you,
Franklin

]]> By: Brian Odegaard https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/#comment-6651 Mon, 01 Apr 2019 21:13:40 +0000 http://reproducibility.stanford.edu/?p=536#comment-6651 Hi –

Very basic question: step 1 in this tutorial yields the following error for me:

docker pull nipy/heudiconv:latest
Error response from daemon: manifest for nipy/heudiconv:latest not found

I tried installing HeuDiConv with pip, which worked fine, and then tried to avoiding the :latest tag in other steps, but it looks like it’s automatically built in even when not explicitly included, so it kept giving the same error. Any advice?

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