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BrkRaw / brkraw

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
https://brkraw.github.io
GNU General Public License v3.0
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[bids converter] Remove .bamt files in bids output #58

Closed ycAbout closed 2 years ago

ycAbout commented 3 years ago

BIDS standard does not support .bmat file, and there is no plan for them to support the type given that, BIDS already supports bval & bvec files and these two and .bmat are same thing. (Are they the same thing?)

See also issue https://github.com/bids-standard/bids-specification/issues/770

gdevenyi commented 3 years ago

Notes on file formats, http://brainsuite.org/processing/diffusion/file-formats/

dvm-shlee commented 3 years ago

@ycAbout @gdevenyi Hi, thank you for pointing out. Actually, I'm not familiar with the DTI preprocessing, so just added all function to extract all possible parameter from the header that I can search from google. BTW, I doubt the code I wrote whether it could correctly generate the bval and bvec. Could you provide some sample DTI data (raw data) with an ideally converted nifti file with the bval, bvec? Some gradient direction and animal orientation-related things were not clear to me when I coded that.

gdevenyi commented 3 years ago

Could you provide some sample DTI data (raw data) with an ideally converted nifti file with the bval, bvec?

Do you mean some human data?

dvm-shlee commented 3 years ago

Could you provide some sample DTI data (raw data) with an ideally converted nifti file with the bval, bvec?

Do you mean some human data?

Oh no, any data collected from Bruker scanner? Just in case if you have any. Just want to check if the bval and bvec converted with this module present the same value as expected.

gdevenyi commented 3 years ago

I think there's a set in what I sent you ☺️

ycAbout commented 3 years ago

If this also helps: For a couple bids output files such as ****run-02_dwi.nii.gz it does not pass the bids validator with the following error: The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

dvm-shlee commented 3 years ago

@ycAbout does it the one converted from the test dataset you had shared to me? I will take a look.

ycAbout commented 3 years ago

I think @gdevenyi send you a dataset, it might be the same but I'm not sure. I think this issue is the blocker for output a valid bids dataset now. All the other issue seems been fixed with the PR's.

gdevenyi commented 3 years ago

@ycAbout is working with the same files I sent to you @dvm-shlee

dvm-shlee commented 2 years ago

patched on de6cb1e69bc10d101db0fcabe88179ede778335b