BIDSifying dual echo SWI DATA

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1

Hi,

Could you please explain the folder structure for SWI data in BIDS? I have SWI with dual echoes. I am not sure whether SWI is going into ‘swi’ folder in ses folders. I could not find more information on BIDS. So Could you please have a look at the below and advise me on this?

Error 1: [Code 1] NOT_INCLUDED
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Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.8 files
sub-2010_ses-01B_part-mag_echo-1_GRE.json2.516 KB | application/json
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-mag_echo-1_GRE.json

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-mag_echo-1_GRE.json

sub-2010_ses-01B_part-mag_echo-1_GRE.nii.gz2179.918 KB | application/gzip
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-mag_echo-1_GRE.nii.gz

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-mag_echo-1_GRE.nii.gz

sub-2010_ses-01B_part-mag_echo-2_GRE.json2.515 KB | application/json
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-mag_echo-2_GRE.json

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-mag_echo-2_GRE.json

sub-2010_ses-01B_part-mag_echo-2_GRE.nii.gz2083.313 KB | application/gzip
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-mag_echo-2_GRE.nii.gz

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-mag_echo-2_GRE.nii.gz

sub-2010_ses-01B_part-phase_echo-1_GRE.json2.551 KB | application/json
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-phase_echo-1_GRE.json

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-phase_echo-1_GRE.json

sub-2010_ses-01B_part-phase_echo-1_GRE.nii.gz5966.205 KB | application/gzip
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-phase_echo-1_GRE.nii.gz

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-phase_echo-1_GRE.nii.gz

sub-2010_ses-01B_part-phase_echo-2_GRE.json2.55 KB | application/json
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-phase_echo-2_GRE.json

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-phase_echo-2_GRE.json

sub-2010_ses-01B_part-phase_echo-2_GRE.nii.gz5984.667 KB | application/gzip
Location:
BIDS_dataset/sub-2010/ses-01B/swi/sub-2010_ses-01B_part-phase_echo-2_GRE.nii.gz

Reason:
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

Evidence:
sub-2010_ses-01B_part-phase_echo-2_GRE.nii.gz

Thank you.

Best regards,
Ru

2

Hi @Pradeepa_Ruwan,

As you can see here, the SWI BIDS specification is still being developed, and thus is not included in the validator. You can take a look at the proposal, design your files accordingly, but then include the following line in your .bidsignore file such that the validator does not throw errors:

sub-*/ses*/swi/

Best,
Steven

3

Thank you very much for your prompt response. Will follow this.

Thanks,
Ru

4

Hi Steven,

Now I get this error after adding .bidsignore for SWI.

Error 1: [Code 45] SUBJECT_FOLDERS
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There are no subject folders (labeled "sub-*") in the root of this dataset.

Any clue to fix this? Thank you.

Best regards,
Ruwan

5

Try changing it to sub-*/ses-*/swi/, and are there any other items in the .bidsignore?

6

Hi,

It works for sub-*/ses-*/swi/*

Thank you for your help.

Best regards,
Ruwan

7

Can you please let me know how to include 2 items in .bidsignore? I get an error on the bids validator when I include the second item in .bidsignore.

Thank you.

Best regards,
Ru

8

Each item should be on its own line.

9

Hi.

Thanks, my .bidsignore file looks like this.
.bidsignore

Is something missing there?

Thanks,
Ru

10

No, it looks fine to me, you don’t need the /* at the end though (that is, each item can end with the folder name you want to ignore)

11

Also, angio is an item that goes into anat according to the specification. Is there a reason for making its own folder?

12

Hi,

I checked them after removing /* that does not change anything. I still get the same error [There are no subject folders (labeled “sub-*”) in the root of this dataset.]

Regarding angio, we have PCAs for ICA, MCA for both hemispheres and also phase and magnitude images this makes 12 scans for PCA. I am not sure whether I need to include all of them though, but as we are going to collect a large dataset I wanted to put them together in a folder. What is the best way to organise PCA in BIDS? Please advise me on this.

Thank you.

Best regards,
Ruwan

13

Hi @Pradeepa_Ruwan,

This is starting to stray too far from the original topic, so I am going to close this thread. I encourage you to read through the BIDS specification, and then open a new issue for anything that does not make sense afterwards.

Best,
Steven

14