Skip to content

Commit

Permalink
Merge d134642 into 5c59781
Browse files Browse the repository at this point in the history
  • Loading branch information
@mariehbourget
mariehbourget committed Nov 16, 2022
2 parents 5c59781 + d134642 commit faec040
Show file tree
Hide file tree
Showing 6 changed files with 77 additions and 56 deletions.
12 changes: 0 additions & 12 deletions docs/source/tutorials/two_class_microscopy_seg_2d_unet.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,18 +57,6 @@ microscopy segmentation training.
"path_data": ["data_axondeepseg_sem"]
- ``loader_parameters:bids_config``: Location of the custom BIDS configuration file required for microscopy
file indexing.

.. note::

You will need to update the value ``"ivadomed/config/config_bids.json"`` to
``"<PATH_TO_IVADOMED>/ivadomed/config/config_bids.json"``

.. code-block:: xml
"bids_config": "<PATH_TO_IVADOMED>/ivadomed/config/config_bids.json"
- ``loader_parameters:target_suffix``: Suffix of the ground truth segmentations. The ground truths are located
under the ``data_axondeepseg_sem/derivatives/labels`` folder. In our case, the suffix are ``_seg-axon-manual``
and ``_seg-myelin-manual``:
Expand Down
73 changes: 61 additions & 12 deletions ivadomed/config/config_bids.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,10 @@
"name": "staining",
"pattern": "[_/\\\\]+stain-([a-zA-Z0-9]+)"
},
{
"name": "tracer",
"pattern": "[_/\\\\]+trc-([a-zA-Z0-9]+)"
},
{
"name": "reconstruction",
"pattern": "[_/\\\\]+rec-([a-zA-Z0-9]+)"
Expand All @@ -42,7 +46,7 @@
},
{
"name": "run",
"pattern": "[_/\\\\]+run-0*(\\d+)",
"pattern": "[_/\\\\]+run-(\\d+)",
"dtype": "int"
},
{
Expand Down Expand Up @@ -99,7 +103,7 @@
},
{
"name": "datatype",
"pattern": "[/\\\\]+(anat|beh|dwi|eeg|fmap|func|ieeg|meg|perf|micr|ct)[/\\\\]+"
"pattern": "[/\\\\]+(anat|beh|dwi|eeg|fmap|func|ieeg|meg|micr|perf|pet|ct)[/\\\\]+"
},
{
"name": "extension",
Expand All @@ -110,24 +114,69 @@
"default_path_patterns": [
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{suffix<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{suffix<epi|m0scan>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func|meg|beh>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",
"sub-{subject}[/ses-{session}]/[{datatype<func|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>|.tsv.gz}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<meg>}{extension}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<channels>}{extension<.tsv|.json>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<coordsystem>}{extension<.json>|.json}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<photo>}{extension<.jpg>|.jpg}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<coordsystem>}{extension<.json>|.json}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<headshape>}{extension<.pos>|.pos}",
"sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_acq-{acquisition<calibration|crosstalk>}_{suffix<meg>|meg}{extension<.fif|.dat>}",
"sub-{subject}[/ses-{session}]/{datatype<eeg>|eeg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<eeg>}{extension<.edf|.vhdr|.vmrk|.eeg|.set|.fdt|.bdf|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<ieeg>|ieeg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<ieeg>}{extension<.mefd/|.json|.edf|.vhdr|.eeg|.vmrk|.set|.fdt|.nwb|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<eeg|ieeg>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<channels|events>}{extension<.tsv|.json>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<eeg|ieeg>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}]_{suffix<coordsystem>}{extension<.json>|.json}",
"sub-{subject}[/ses-{session}]/{datatype<eeg|ieeg>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}]_{suffix<electrodes>}{extension<.tsv|.json>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<eeg|ieeg|meg>}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<photo>|photo}{extension<.jpg>}",
"sub-{subject}[/ses-{session}]/{datatype<eeg>|eeg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_recording-{recording}]_{suffix<physio>}{extension<.tsv.gz|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<micr>|micr}/sub-{subject}[_ses-{session}]_sample-{sample}[_acq-{acquisition}][_stain-{staining}][_run-{run}][_chunk-{chunk}]_{suffix<TEM|SEM|uCT|BF|DF|PC|DIC|FLUO|CONF|PLI|CARS|2PE|MPE|SR|NLO|OCT|SPIM>}{extension<.png|.tif|.ome.tif|.ome.btf|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<micr>|micr}/sub-{subject}[_ses-{session}]_sample-{sample}[_acq-{acquisition}]_{suffix<photo>|photo}{extension<.jpg|.png|.tif|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_echo-{echo}[_part-{part<mag|phase|real|imag>}]_{suffix<MEGRE|MESE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_flip-{flip}[_part-{part<mag|phase|real|imag>}]_{suffix<VFA>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_inv-{inv}[_part-{part<mag|phase|real|imag>}]_{suffix<IRT1>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_flip-{flip}]_inv-{inv}[_part-{part<mag|phase|real|imag>}]_{suffix<MP2RAGE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_flip-{flip}_mt-{mt<on|off>}[_part-{part<mag|phase|real|imag>}]_{suffix<MPM|MTS>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_mt-{mt<on|off>}[_part-{part<mag|phase|real|imag>}]_{suffix<MTR>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_{suffix<T1map|T2map|T2starmap|R1map|R2map|R2starmap|PDmap|MTRmap|MTsat|UNIT1|T1rho|MWFmap|MTVmap|PDT2map|Chimap|S0map|M0map>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_flip-{flip}[_inv-{inv}][_part-{part<mag|phase|real|imag>}]_{suffix<TB1DAM>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_echo-{echo}_flip-{flip}[_inv-{inv}][_part-{part<mag|phase|real|imag>}]_{suffix<TB1EPI>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_flip-{flip}][_inv-{inv}][_part-{part<mag|phase|real|imag>}]_{suffix<TB1AFI|TB1TFL|TB1RFM|RB1COR>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_flip-{flip}_inv-{inv}[_part-{part<mag|phase|real|imag>}]_{suffix<TB1SRGE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_{suffix<TB1map|RB1map>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<pet>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_recording-{recording}_{suffix<blood>}{extension<.tsv|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}]_task-{task}[trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}{extension<.tsv|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<asl|m0scan>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<aslcontext>}{extension<.tsv|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_run-{run}]_{suffix<asllabeling>}{extension<.jpg>}",
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_recording{recording}]_{suffix<physio|stim>}{extension<.tsv|.json>}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][mod-{modality}_]{suffix<defacemask>}{extension<.json>|.json}",
"task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}{extension<.json>|.json}",
"[acq-{acquisition}_]{suffix<dwi>}{extension<.json>|.json}",
"[acq-{acquisition}_][dir-{direction}_][run-{run}_]{fmap<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.json>|.json}",
"[acq-{acquisition}_][dir-{direction}_][run-{run}_]{suffix<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{suffix<epi|m0scan>}{extension<.json>|.json}",
"task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.json>|.json}",
"task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>}"
"task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>}",
"sample-{sample}[_acq-{acquisition}][_stain-{stain}][_run-{run}][_chunk-{chunk}]_{suffix<TEM|SEM|uCT|BF|DF|PC|DIC|FLUO|CONF|PLI|CARS|2PE|MPE|SR|NLO|OCT|SPIM>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_]echo-{echo}[_part-{part<mag|phase|real|imag>}]_{suffix<MEGRE|MESE>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_]flip-{flip}[_part-{part<mag|phase|real|imag>}]_{suffix<VFA>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_]inv-{inv}[_part-{part<mag|phase|real|imag>}]_{suffix<IRT1>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_][flip-{flip}_]inv-{inv}[_part-{part<mag|phase|real|imag>}]_{suffix<MP2RAGE>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_]flip-{flip}_mt-{mt<on|off>}[_part-{part<mag|phase|real|imag>}]_{suffix<MPM|MTS>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_]mt-{mt<on|off>}[_part-{part<mag|phase|real|imag>}]_{suffix<MTR>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_]{suffix<T1map|T2map|T2starmap|R1map|R2map|R2starmap|PDmap|MTRmap|MTsat|UNIT1|T1rho|MWFmap|MTVmap|PDT2map|Chimap|S0map|M0map>}{extension<.json>|.json}",
"[task-{task}_][trc-{tracer}_][rec-{reconstruction}_][run-{run}_]{suffix<pet>}{extension<.json>|.json}",
"[task-{task}_][trc-{tracer}_][rec-{reconstruction}_][run-{run}_]recording-{recording}_{suffix<blood>}{extension<.json>|.json}",
"task-{task}[_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}{extension<.json>|.json}",
"[task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>|.json}",
"[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_]{suffix<asl|m0scan>}{extension<.json>|.json}",
"[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_]{suffix<aslcontext>}{extension<.json>|.json}",
"[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_][recording-{recording}_]{suffix<physio|stim>}{extension<.json>|.json}"
]
}
Loading

0 comments on commit faec040

Please sign in to comment.