diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md index d0991be72e..d5367cfcdd 100644 --- a/src/appendices/qmri.md +++ b/src/appendices/qmri.md @@ -133,10 +133,13 @@ A guide for using macros can be found at Please visit the [file collections appendix](./file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications. -### Quantitative maps are derivatives +### Outputs are quantitative maps -Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the `derivatives` directory. -For example a `T1map` can be generated from an `MP2RAGE` file collection using either options. +qMRI maps are stored differently depending on the process that generated them. +Pre-generated qMRI maps MAY be stored as part of a raw BIDS dataset, +whereas they MUST be stored in a derivative BIDS dataset if they were post-generated. + +See the example below of a `T1map` generated from an `MP2RAGE` file collection using either option. If the map is post-generated: @@ -151,15 +154,25 @@ A guide for using macros can be found at "qMRI-software-name": { "sub-01": { "anat": { - "sub-01_T1map.nii.gz": "", + "sub-01_T1map.nii.gz": " # --> T1 map in a derivative dataset", "sub-01_T1map.json": "", - "sub-01_UNIT1.nii.gz": "", + "sub-01_UNIT1.nii.gz": " # --> UNI T1 in a derivative dataset", "sub-01_UNIT1.json": "", - }, }, }, }, }, + "sub-01": { + "anat": { + "sub-01_inv-1_part-mag_MP2RAGE.nii.gz":"", + "sub-01_inv-1_part-phase_MP2RAGE.nii.gz":"", + "sub-01_inv-1_MP2RAGE.json":"", + "sub-01_inv-2_part-mag_MP2RAGE.nii.gz":"", + "sub-01_inv-2_part-phase_MP2RAGE.nii.gz":"", + "sub-01_inv-2_MP2RAGE.json":"", + }, + }, + }, } ) }} @@ -172,25 +185,30 @@ A guide for using macros can be found at {{ MACROS___make_filetree_example( { "ds-example": { - "derivatives": { - "Siemens": { - "sub-01": { - "anat": { - "sub-01_T1map.nii.gz": "", - "sub-01_T1map.json": "", - "sub-01_UNIT1.nii.gz": "", - "sub-01_UNIT1.json": "", - }, - }, - }, + "sub-01": { + "anat": { + "sub-01_inv-1_part-mag_MP2RAGE.nii.gz":"", + "sub-01_inv-1_part-phase_MP2RAGE.nii.gz":"", + "sub-01_inv-1_MP2RAGE.json":"", + "sub-01_inv-2_part-mag_MP2RAGE.nii.gz":"", + "sub-01_inv-2_part-phase_MP2RAGE.nii.gz":"", + "sub-01_inv-2_MP2RAGE.json":"", + "sub-01_T1map.nii.gz": " # --> T1 map in a raw dataset", + "sub-01_T1map.json": "", + "sub-01_UNIT1.nii.gz": " # --> UNI T1 in a raw dataset", + "sub-01_UNIT1.json": "", }, }, + } } ) }} -Note: Even though the process from which pre-generated qMRI maps are obtained (vendor pipelines) is not known, -vendors generally allow exporting of the corresponding input data. -It is RECOMMENDED to share them along with the vendor outputs, whenever possible for a qMRI method supported by BIDS. +!!! note "Sharing of vendor outputs" + + Even though the process from which pre-generated qMRI maps are obtained (vendor pipelines) is not known, + vendors generally allow exporting of the corresponding input data. + It is RECOMMENDED to share them along with the vendor outputs, + whenever possible for a qMRI method supported by BIDS. ### Example datasets @@ -326,7 +344,7 @@ A guide for using macros can be found at `dataset_description.json`: -```text +```json { "Name": "qMRLab Outputs", "BIDSVersion": "1.5.0", @@ -526,12 +544,13 @@ as an input to offline calculation of a `T1map` using a dictionary lookup approa provided by the stock sequence. Instead, the `magnitude` and `phase` images are exported. Please see the relevant discussion at [qMRLab issue #255](https://github.com/qMRLab/qMRLab/issues/255). -Therefore, the `UNIT1` image provided by the scanner is RECOMMENDED to be stored under the `anat` -raw dataset directory along with the `MP2RAGE` file collection and to be used as the primary input -for quantifying a `T1map`. +Therefore, the `UNIT1` image provided by the scanner +SHOULD be stored under the `anat` in a raw BIDS dataset +along with the `MP2RAGE` file collection +and to be used as the primary input for quantifying a `T1map`. -If an additional `UNIT1` image is calculated offline, then the output is to be stored in the -`derivatives` directory with necessary provenance information. +If an additional `UNIT1` image is calculated offline, +then the output MUST be stored in a derivative BIDS dataset with necessary provenance information. ##### `NumberShots` metadata field