1.1 - Upload a DICOM file
Page description for heading and indexes.
2.1 - Connect machines
Page description for heading and indexes.
2.2 - CTP
Page description for heading and indexes.
2.3 - XNat
Page description for heading and indexes.
3.1 - fmriprep
Package Info
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing
pipeline that is designed to provide an easily accessible, state-of-the-art
interface that is robust to variations in scan acquisition protocols and that
requires minimal user input, while providing easily interpretable and comprehensive
error and output reporting. It performs basic processing steps (coregistration,
normalization, unwarping, noise component extraction, segmentation,
skullstripping etc.) providing outputs that can be easily submitted to a variety
of group level analyses, including task-based or resting-state fMRI, graph
theory measures, surface or volume-based statistics, etc.
Optional flags that can be provided to the fmriprep_flags parameter:
[--anat-only] [--boilerplate_only] [--md-only-boilerplate]
[--error-on-aroma-warnings] [-v]
[--ignore {fieldmaps,slicetiming,sbref,t2w,flair} [{fieldmaps,slicetiming,sbref,t2w,flair} ...]]
[--output-spaces [OUTPUT_SPACES [OUTPUT_SPACES ...]]]
[--me-output-echos] [--bold2t1w-init {register,header}]
[--bold2t1w-dof {6,9,12}] [--force-bbr] [--force-no-bbr]
[--medial-surface-nan] [--slice-time-ref SLICE_TIME_REF]
[--random-seed _RANDOM_SEED]
[--use-aroma]
[--aroma-melodic-dimensionality AROMA_MELODIC_DIM]
[--return-all-components]
[--fd-spike-threshold REGRESSORS_FD_TH]
[--dvars-spike-threshold REGRESSORS_DVARS_TH]
[--skull-strip-template SKULL_STRIP_TEMPLATE]
[--skull-strip-fixed-seed]
[--skull-strip-t1w {auto,skip,force}] [--fmap-bspline]
[--fmap-no-demean] [--topup-max-vols TOPUP_MAX_VOLS]
[--use-syn-sdc [{warn,error}]] [--force-syn]
[--no-submm-recon] [--cifti-output [{91k,170k}] | --fs-no-reconall]
[--resource-monitor]
[--reports-only] [--config-file FILE] [--write-graph]
[--stop-on-first-crash] [--notrack]
[--debug {compcor,fieldmaps,all} [{compcor,fieldmaps,all} ...]]
[--sloppy]
Required licenses
| Name | URL | Description |
|---|
| freesurfer | https://surfer.nmr.mgh.harvard.edu/registration.html | fMRIPRep uses FreeSurfer tools, which require a license to run. |
Command
| Key | Value |
|---|
| Task | arcana.bids:bids_app |
| Operates on | session |
| Name | Required data-type | Default column data-type | Description |
|---|
T1w | medimage/nifti-gz-x | medimage/dicom-series | T1-weighted anatomical scan |
T2w | medimage/nifti-gz-x | medimage/dicom-series | T2-weighted anatomical scan |
bold | medimage/nifti-gz-x | medimage/dicom-series | functional MRI |
fmap_magnitude1 | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 1 & 2: magnitude of first echo |
fmap_magnitude2 | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 1 & 2: magnitude of second echo |
fmap_magnitude | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 3: magnitude image used for anatomical reference |
fmap_phasediff | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 1: phasediff image corresponding to the phase-diff map between echo times |
fmap_phase1 | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 2: phase of first echo |
fmap_phase2 | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 2: phase of second echo |
fmap_fieldmap | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 3: directly reconstructed field map |
fmap_epi | medimage/nifti-gz-x | medimage/dicom-series | Field map - BIDS Case 4: Spin Echo EPI scans with different phase encoding directions to estimate the distortion map corresponding to the nonuniformities of the B0 field |
Outputs
| Name | Required data-type | Default column data-type | Description |
|---|
fmriprep | generic/directory | generic/directory | Preprocessed fMRI data |
Parameters
| Name | Data type | Description |
|---|
fmriprep_flags | str | Command line flags passed on directly to fMRIPrep |
json_edits | str | JQ filters (https://devdocs.io/jq/) to apply to JSON side-cars in order to handle special cases where the dcm2niix fails to produce valid a BIDS |
3.2 - mriqc
Package Info
MRIQC extracts no-reference IQMs (image quality metrics) from
structural (T1w and T2w) and functional MRI (magnetic resonance
imaging) data.
Command
| Key | Value |
|---|
| Task | arcana.bids:bids_app |
| Operates on | session |
| Name | Required data-type | Default column data-type | Description |
|---|
T1w | medimage/nifti-gz-x | medimage/dicom-series | T1-weighted anatomical scan |
T2w | medimage/nifti-gz-x | medimage/dicom-series | T2-weighted anatomical scan |
fMRI | medimage/nifti-gz-x | medimage/dicom-series | functional MRI |
Outputs
| Name | Required data-type | Default column data-type | Description |
|---|
mriqc | generic/directory | generic/directory | Generated QC outputs |
Parameters
3.3 - smriprep
Package Info
SMRIPrep: a structural MRI data preprocessing pipeline including Freesurfer
Required licenses
| Name | URL | Description |
|---|
| freesurfer | https://surfer.nmr.mgh.harvard.edu/registration.html | sMRIPRep uses FreeSurfer tools, which require a license to run. |
Command
| Key | Value |
|---|
| Task | arcana.bids:bids_app |
| Operates on | session |
| Name | Required data-type | Default column data-type | Description |
|---|
T1w | medimage/nifti-gz-x | medimage/dicom-series | T1-weighted anatomical scan |
T2w | medimage/nifti-gz-x | medimage/dicom-series | T2-weighted anatomical scan |
Outputs
| Name | Required data-type | Default column data-type | Description |
|---|
smriprep | generic/directory | generic/directory | Preprocessed sMRI data |
Parameters
| Name | Data type | Description |
|---|
smriprep_flags | str | Command line flags passed on directly to sMRIPrep |
json_edits | str | JQ filters (https://devdocs.io/jq/) to apply to JSON side-cars in order to handle special cases where the dcm2niix fails to produce valid a BIDS |