Comments (8)
@eugenegkim That's just a bug because I haven't had enough test case for that.
Could you provide the dataset that causes the issue? then I can fix it for the next update.
Thank you!
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Yeah! Seems like ages ago. Hope you and all your loved ones are doing well.
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@eugenegkim Oh BTW, could you let me know if it just flipped or rotated 180 degrees so that the left and right are also flipped?
If you are urgent to access the data and If you are familiar with python, you can easily correct that with python API.
For example. as below.
import numpy as np
import nibabel as nib
import brkraw as br
from brkraw.lib.utils import apply_rotate
raw = br.load('<your raw data path>')
old_nii = raw.get_niftiobj(<scan_id>, <reco_id>)
new_affine = apply_rotate(old_nii.affine, rad_y=np.pi)
new_nii = nib.Nifti1Image(old_nii._dataobj, affine=new_affine, header=old_nii._header)
new_nii.to_filename('<new filename>')
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Oh good point. It looks like it's rotated 180 degrees. I use an in-house converter, so it's not urgent. But I'm looking into making all my data BIDS-compliant. I'll send you the dataset in a moment. Thanks!
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@eugenegkim Oh BTW, have we meet at the Bruker sequence programming course? Your name is familiar 😃
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@eugenegkim Thanks for sharing the data. I will update the code once I clarify the issue. Regarding the BIDS, there is something I haven't documented yet (for JSON), so if you experiencing any issue, please let me know.
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@eugenegkim I found using your dataset that Bruker does internal correction for the position, so actually no need additional correction, but my code originally did. It has been removed now. It will work without issue from v0.3.3 released version.
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Thanks!
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Related Issues (20)
- add some style guide lines HOT 1
- duplicate "contributing" file
- automate the build of the docker image HOT 1
- use a citation.cff file to keep track of metadata to be ingested by zenodo upon release
- Sourcery refactoring suggestions HOT 1
- consider moving the doc within package repo HOT 1
- Fails conversion with tonii_all HOT 7
- Jupyter notebook tutorial gives FileNotValid error HOT 2
- Convert specific file via CLI HOT 4
- The `--output` parameter cannot control the file name (additional elements get auto-added so you need to concatenate with mv to actually get the filenames you want...) HOT 1
- Bids_helper quits when method file is missing HOT 1
- Upcoming Major Update 0.4.0: Scheduled for Mid May 2024 HOT 1
- Regular Bruker recon tools from raw fid HOT 2
- Compressed Sensing Reconstruction for Undersampled Cartesian Sequences PV360.3.3<
- GUI Unable to open PV7 and PV360 zip files HOT 6
- Streamlining Data Operations in Brkraw: Introducing 'PvScan' and 'PvReco' for Enhanced Raw Data Management. HOT 1
- Integration of Brkraw into Neurodesktop HOT 3
- Brkraw CLI for bruker recon of simple cartesian sequences (FLASH, MGE, RARE) HOT 5
- Missing buttons and image preview display when running in Apptainer HOT 5
- Simplifying and Reducing brkrecon submodule HOT 2
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