bids2nda error message

[neggink]

Hello,

I am getting the following error:

pni-17c02tw0zmg8wl:desktop neggink$ bids2nda ~/desktop/openneuro/conreact/ ~/desktop/openneuro/GUID_mapping ~/desktop/openneuro/conreact_NDA
Traceback (most recent call last):
File "/Users/neggink/anaconda/bin/bids2nda", line 11, in
load_entry_point('BIDS2NDA==0.1.0', 'console_scripts', 'bids2nda')()
File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 316, in main
run(args)
File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 207, in run
image_unit4 = units_dict[nii.header.get_xyzt_units()[1]]
KeyError: 'unknown'

Thanks,
Neggin

[chrisgorgo]

Does your input dataset pass the validator? https://github.com/INCF/bids-validator

…

On Fri, May 11, 2018 at 7:31 AM Neggin ***@***.***> wrote: Hello, I am getting the following error: pni-17c02tw0zmg8wl:desktop neggink$ bids2nda ~/desktop/openneuro/conreact/ ~/desktop/openneuro/GUID_mapping ~/desktop/openneuro/conreact_NDA Traceback (most recent call last): File "/Users/neggink/anaconda/bin/bids2nda", line 11, in load_entry_point('BIDS2NDA==0.1.0', 'console_scripts', 'bids2nda')() File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 316, in main run(args) File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 207, in run image_unit4 = units_dict[nii.header.get_xyzt_units()[1]] KeyError: 'unknown' Thanks, Neggin — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp0lABmeTUNBEC4ZyIVKVXzAeve9sks5txaCigaJpZM4T7jdz> .

[neggink]

Yes, it did

[chrisgorgo]

It seem that you have 4D files in your dataset that do not have the units for the fourth dimension defined. This is unexpected. Usually only _bold files are 4D and should define (in the nifti header) what is the unit of the 4th dimension (seconds or milliseconds).

[leej3]

I have come across this problem too. I think it can be avoided by using dcm2niix for conversion from dicom to nifti. If that is not possible you'll have to modify the nifti header. The xyzt_units encodes both spatial and time dimensions as described here: https://brainder.org/2012/09/23/the-nifti-file-format/

So for a scan using mm (2) and seconds (8) the xyzt would be 2 +8 =10

In python:

import nibabel as nb
nii_path = 'path_to_scan'
img = nb.load(nii_path)
 img.header['xyzt_units'] = 10
img.to_filename(nii_path)

If something so fundamental is broken in the nifti you should strongly consider converting to nifti with dcm2niix though. If that doesn't solve the issue it should be fixed there.

[neggink]

Hello,
Thank you for all your help, that error was fixed but now I am getting this one:

Traceback (most recent call last):
File "/Users/neggink/anaconda/bin/bids2nda", line 11, in
load_entry_point('BIDS2NDA==0.1.0', 'console_scripts', 'bids2nda')()
File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 316, in main
run(args)
File "/Users/neggink/anaconda/lib/python3.6/site-packages/bids2nda/main.py", line 159, in run
dict_append(image03_dict, 'scan_type', suffix_to_scan_type[suffix])
KeyError: 'FLASH'

[neggink]

The NDA has added FLASH files to the 'scan_type' column of their Image03 specification: (https://ndar.nih.gov/data_structure.html?short_name=image03) as "MR structural (FLASH)". Can the converter be modified to include this?

Thanks!

[chrisgorgo]

I don't have time to perform this modification myself, but if you send a pull request I would be happy to merge it

[leej3]

I can help if you want @neggink . I've done that before

[neggink]

That would be great @leej3 ! Thank you!!

[leej3]

Ok I've edited the code. so in an environment that doesn't already contains bids2nda install my code:

git clone https://github.com/leej3/BIDS2NDA.git
cd BIDS2NDA
git checkout add_flash_scantype
pip install -e .

Then try running it on your data and report back. If it works I'll submit it as a pull request.

[neggink]

It works! Thank you

[leej3]

Great. Happy uploading.

…

On Tue, Jul 24, 2018 at 3:09 PM, Neggin ***@***.***> wrote: It works! Thank you — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFKsqI2BLNF3eWeYKqI437NcN-Lu7UpYks5uJ3DMgaJpZM4T7jdz> .

[ebarrick]

Hello,

I'm getting the following error:

from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "/anaconda2/bin/bids2nda", line 11, in
sys.exit(main())
File "/anaconda2/lib/python2.7/site-packages/bids2nda/main.py", line 317, in main
run(args)
File "/anaconda2/lib/python2.7/site-packages/bids2nda/main.py", line 154, in run
description = suffix + " " + metadata["TaskName"]
KeyError: 'TaskName'

But I'm unsure why this error is occurring.

Thanks!
E