Added bids config file for bids-validator #2
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If you only need to ignore files it would be much simpler to update the validator in this BIDS App and include https://github.com/INCF/bids-validator#bidsignore files in your input datasets. |
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BTW what makes your README files not compliant? Perhaps this is an issue similar to https://neurostars.org/t/how-to-upload-eeg-data/1250/10 ? |
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I didn't know about .bidsignore. I have been using the bids configuration file instead. Using .bidsignore would be easier. I just can't seem to get it to work. Here is the contents of my BIDS directory Can you please tell me what I am doing wrong? Thanks for your help |
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Are you using the latest version of the validation?
Best,
Chris
…On Feb 22, 2018 6:14 AM, "bkraft4257" ***@***.***> wrote:
I didn't know about .bidsignore. I have been using the bids configuration
file instead. Using .bidsignore would be easier. I just can't seem to get
it to work. Here is the contents of my BIDS directory
aging1a ➜ bids ls -a
. .bidsignore~ participants.tsv sub-imove1061 task-rest_acq-pcasl_bold.json
.. CHANGES README sub-imove1071
acrostic.list dataset_description.json sub-imove1011 sub-imove9001
.bids.cfg .heudiconv sub-imove1031 task-rest_acq-epi_bold.json
.bidsignore log_file sub-imove1051 task-rest_acq-mbepi_bold.json
aging1a ➜ bids cat .bidsignore
.*
!/.heudiconv
The syntax of the .bidsignore file is based upon your comments about similar content as .gitignore, which I found here https://stackoverflow.com/questions/8021441/git-how-to-ignore-hidden-directories
aging1a ➜ bids bids-validator $PWD
... (missing text)
1: This file is not part of the BIDS specification, make sure it isn't included in the dataset by accident. Data derivatives (processed data) should be placed in /derivatives folder. (code: 1 - NOT_INCLUDED)
./.bids.cfg
Evidence: .bids.cfg
./.bidsignore
Evidence: .bidsignore
./.bidsignore~
Evidence: .bidsignore~
./.heudiconv/imove1011/ses-1/info/dicominfo_ses-1.csv
Evidence: dicominfo_ses-1.csv
./.heudiconv/imove1011/ses-1/info/dicominfo_ses-1.tsv
Evidence: dicominfo_ses-1.tsv
./.heudiconv/imove1011/ses-1/info/filegroup_ses-1.json
Evidence: filegroup_ses-1.json
... (missing text)
Summary: Available Tasks: Available Modalities:
650 Files, 5.48GB rest T1w
6 - Subjects TODO: full task name for rest T2w
1 - Session dwi
sbref
magnitude1
phasediff
bold
fieldmap
Can you please tell me what I am doing wrong?
Thanks for your help
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I am running bids-validator -v Unfortunately, I couldn't find the current version of the bids-validator on the GitHub page. |
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It's on npm - https://docs.npmjs.com/getting-started/updating-global-packages |
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Chris,
I have used the antsCorticalThickness BIDS app successfully on several of my data sets. Each time I have created a specific BIDS directory with just the T1w images so it passes the bids-validator.
As you know, the code checks that that BIDS directory is valid before proceeding with running antsCorticalThickness. This works well if your BIDS directory is compliant without a configuration file. Unfortunately, for me this is normally not the case. I use the configuration file to avoid certain issues.
For example, when doing the heudiconv conversion the hidden directory .heudiconv is written to the BIDS directory. This directory is not BIDS compliant and the bids-validator will fail if the directory remains. I also like to leave README files within the BIDS directory to explain issues with the data to our group. These README files are not BIDS compliant and the bids-validator will fail. I also like to keep the BIDS validator configuration file in the BIDS directory so people can see what is being ignored during the validation. This file is not BIDS compliant either.
I deal with the above examples by specifying to ignore these files and directories during the BIDS validation. This works great until I try to run antsCorticalThickness BIDS APP because it doesn't use the BIDS configuration file when performing the BIDS validation.
I would like to recommend that either the bids-validator check is removed from the BIDS apps or the bids-validator configuration file is passed in through argparse.
I forked this repository and I made the suggested changes. I was able to some simple testing. However, I am relatively new to python and I am not sure if the subprocess handles the string I am passing it to correctly.
Please consider these simple changes. I believe that it will allow more people to use this BIDS app.
Thanks
Bob