Import/Export BIDS database

ftadel commented 3 years ago

Import from BIDS-manager database:

Anatomy files: all supported imaging modalities (T1, T2, FLAIR, CT, PET), pre/post/postop
FreeSurfer segmentation: from /derivatives/freesurfer
GADO true = presence of the tag ce-GADOLINIUM in the T1 filenames

Export to BIDS-database:

Selected solution: Two electrodes.tsv files directly in the raw acquisition folders, intranat specified with the tag acq-intranat
- T1pre scanner-based space: /sub-XXXX/ses-YYYY/ieeg/sub-XXXX_ses-YYYY_acq-intranat_space-Other_electrodes.tsv
- SPM12 MNI space: /sub-XXXX/ses-YYYY/ieeg/sub-XXXX_ses-YYYY_acq-intranat_space-IXI549Space_electrodes.tsv
Alternative solution rejected: saving the .tsv in the derivatives derivatives / intranat/ sub-<label> / [ses-<label>] / anat / sub-<label>[_ses-<label>][_space-<label>]_electrodes.tsv

Reference: https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/04-intracranial-electroencephalography.html#electrode-description-_electrodestsv

Modifications to ImageImport:

Add user preference: Linked BIDS database path: Done
Add button to import a list of subjects from the BIDS database automatically: Done
Remove the validation of the center of the head: Done (uses now by default the center of the image)

ftadel commented 3 years ago

CHUGA BIDS database – data description

Directory tree

root/
.. dataset_description.json
.. participants.tsv 
.. sourcedata/
.. derivatives/
.. code/
.. sub-<chuga_id>/
…. ses-<inclusion_year>/ 
…. sub-<chuga_id>_ses-<inclusion_year >_scans.tsv
...... ieeg/
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_ieeg.vhdr
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_ieeg.vmrk
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_ieeg.eeg
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_ieeg.json
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_events.tsv
…….. sub-<chuga_id>_ses-<inclusion_year >_task-<ieeg_task>_acq-<ieeg_acquisition>_run-<run>_proc-<ieeg_proc>_channels.tsv
…… anat/
…….. sub-<chuga_id>_ses-<inclusion_year>_acq-<imaging_acquisition>_run-<run>_T1w.nii
…….. sub-<chuga_id>_ses-<inclusion_year>_acq-<imaging_acquisition>_run-<run>_T2w.nii
…….. sub-<chuga_id>_ses-<inclusion_year>_acq-<imaging_acquisition>_run-<run>_FLAIR.nii
…….. sub-<chuga_id>_ses-<inclusion_year>_acq-<imaging_acquisition>_run-<run>_CT.nii
…… pet/
…….. sub-<chuga_id>_ses-<inclusion_year>_acq-<imaging_acquisition>_run-<run>_PET.nii

Complementary information on file formats and file-internal data structures: • Tab-Separted Value format (tsv): labels in first row; data of same type in columns • JavaScript Object Notation (json): 1D (non-nested) key-value pairs • Neuroimaging Informatics Technology Initiative (nii): native space, unprocessed data • Brain Vision (vhdr, vmrk, eeg): unprocessed SEEG data

Directory	Description
sub-/	BIDS subject. Subject directory
ses-/	BIDS session. Session directory
sourcedata/	BIDS sourcedata. Contains raw/source data. Follows BIDS folder structure (Empty)
derivatives/	BIDS derivatives. Processing pipeline outputs. Follows BIDS folder structure (Empty)
code/	BIDS code. Source code of scripts used to prepare the data (Empty)

Files

File	Description
dataset_description.json	short description of the dataset
participants.tsv	subjects clinical/demographic data
*._scans.tsv	subject/session file listing with acquisition time
*._ieeg.vhdr	Brain Vision. text file. header
*._ieeg.vmrk	Brain Vision. text file. events
*._ieeg.eeg	Brain Vision. binary file. voltage values
*._ieeg.json	BIDS acquisition infos. e.g. task, stimulation parameters, recording mode
*._events.tsv	BIDS event infos. e.g. onset, duration, type
*._channels.tsv	BIDS channel infos. e.g. name, type, sampling frequency
*._T1w.nii	T1 weighted MRI
*._T2w.nii	T2 weighted MRI
*._FLAIR.nii	FLAIR MRI
*._CT.nii	Computerized tomography
*._PET.nii	Positron emission tomography

BIDS entities/pairs

Key	Values
	Unique subject identifier
	2000, 2001, 2003…
_	CCEP1Hz, Interictal, Seizure, ConfiDecid, Localizer, Switch
	preRFTC, postRFTC, sleepPreRFTC, awakePreRFTC, sleepPostRFTC, awakePostRFTC, bloc, stim, training, arfa, audi, comp, lec2, mcse, visu
	Unique. Only apply to ConfiDecid iEEG task.
	post, postop, pre
	01, 02, 03…

ftadel commented 3 years ago

@AnthonyUGA FYI

ftadel commented 3 years ago

Updated to-do list:

Import BIDS: all supported imaging modalities
Export BIDS .tsv: Will be done ON TOP of the currently generated files, because they are ALL in use.

sub-test_electrodes.tsv: Patient space based on the T1 (equivalent de space-scanner)

name, x, y, z, size (required)
GreyWhite
MarsAtlas
MarsAtlasFull => eg. [[u'R_ITCm', 79.56989247311827]]
Destrieux
DKT
HCP-MMP1
Lausanne2008-33
Lausanne2008-60
Lausanne2008-125
Lausanne2008-250
Lausanne2008-500

sub-test_space-IXI549Space_electrodes.tsv: SPM12 MNI space

name, x, y, z, size (required)
MarsAtlas
MarsAtlasFull
FreeSurfer
DKT
HCP-MMP1
Lausanne2008-33
Lausanne2008-60
Lausanne2008-125
Lausanne2008-250
Lausanne2008-500
AAL
AALDilate
AAL2018
AAL2
AAL3
Brodmann
BrodmannDilate
Hammers
AICHA
JulichBrain => v2.5 from EBRAINS

Reference: https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html

ftadel commented 3 years ago

Import BIDS: DONE

Add BIDS database path in the preferences: https://github.com/ftadel/IntrAnat/commit/423f029515fe4bb8a6c14f13d6a1acee53c8afa3
Add button to import BIDS database: https://github.com/ftadel/IntrAnat/commit/003ce386344c89eacfba07f2ecb24bbc0a0cef64 https://github.com/ftadel/IntrAnat/commit/9081914c8b72a9d0c27e0ab5b4a2c6c89fc1dbac
Import FreeSurfer from BIDS database (/derivatives/freesurfer/sub-xxxx_ses-yyyy): https://github.com/ftadel/IntrAnat/commit/f688fc8ef192b958963112fd22982de7ef3ef953

ftadel commented 3 years ago

Export as BIDS TSV: https://github.com/ftadel/IntrAnat/commit/1899aa7700b4284676e53ca8fe6088f4e181875e https://github.com/ftadel/IntrAnat/commit/c4be735390253dab96a4bd5e9faa85ef2b78a554

Examples of files generated: ieeg_electrodes_tsv.zip

ftadel / IntrAnat