diff --git a/questions/general_bep.question.md b/questions/general_bep.question.md index ec2f2eff..117e95c9 100644 --- a/questions/general_bep.question.md +++ b/questions/general_bep.question.md @@ -47,8 +47,9 @@ but this gives a little extra flexibility. - BEP034: [Computational modeling](https://bids.neuroimaging.io/bep034) - BEP035: [Modular extensions for individual participant data mega-analyses with non-compliant derivatives](https://bids.neuroimaging.io/bep035) - BEP041: [Statistical Model Derivatives](https://bids.neuroimaging.io/bep041) +- ### metadata - - BEP028: [Provenance](https://bids.neuroimaging.io/bep028) - BEP034: [Computational modeling](https://bids.neuroimaging.io/bep034) +- ### file format diff --git a/questions/general_convert_nifti.question.md b/questions/general_convert_nifti.question.md new file mode 100644 index 00000000..cdad7e08 --- /dev/null +++ b/questions/general_convert_nifti.question.md @@ -0,0 +1,57 @@ +--- +title: "General: I only have nifti files and no dicom. Can I still create a BIDS dataset?" +--- + +In theory yes, but it is possible that you will be missing some metadata that is required by the BIDS specification. + +A couple of BIDS converters can work with nifti files: + +- bidscoin +- bidsme +- explore asl +- data2bids + +See the list of converters [here](https://bids.neuroimaging.io/benefits.html#mri-and-pet-converters). + +**However**... + +- They may not work with the datatype you have + (for example not sure that explore ASL can deal with `func` data). +- Many of them still expect that you have a json side car for each nifti + (BIDSme for example - from the top of my head). +- They may expect a certain input structure to work efficiently, + so we may have to move files around. + + + +### Regarding the "missing" JSON files + +Depending on the datatype you are dealing with this can be more of less annoying. + +2 examples: + +For the most typical `anat` files, +they don't have any REQUIRED metadata, +so you could have just the data files without any accompanying JSON. +If you get into more exotic anat files (like for quantitative MRI) +then this may become a problem. + +For `func` files you only need `TaskName` and `RepetitionTime` +and the former you can decide what it is and the latter should be in the Nifti header. +So you should be OKish there too. + +Obviously you will be missing some metadata that would be required +for some type of preprocessing (like slice timing info). + +### Tips + +- If you have the PDF with the details of acquisition sequence or a method section + from a paper with that data, you could "recover" some extra metadata. +- SPM dicom import tool usually leaves a couple of metadata in a description field of the nifti header. + That can be a problem for data anonymisation but may help you in your case if this is the tool that was used. + See an example [here](https://github.com/PeerHerholz/BIDSonym/issues/41#issue-768636869) +- If you have to script tings manually rather than using a converter, + remember to use pybids [path construction tools](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#path-construction) or the [bids matlab equivalent](https://github.com/bids-standard/bids-matlab/blob/master/examples/03_BIDS-Matlab_filenames_and_metadata.ipynb) to make your life easier when constructing bids valid filenames. diff --git a/src/FAQ.md b/src/FAQ.md index 24aea053..16af4668 100644 --- a/src/FAQ.md +++ b/src/FAQ.md @@ -198,6 +198,61 @@ If you deal with EEG data, you may want to read this as well before considering combining recordings acquired on different occasions within the same `session` folder. +## General: I only have nifti files and no dicom. Can I still create a BIDS dataset? + +In theory yes, but it is possible that you will be missing some metadata that is required by the BIDS specification. + +A couple of BIDS converters can work with nifti files: + +- bidsme +- explore asl +- data2bids + +See the list of converters [here](https://bids.neuroimaging.io/benefits.html#mri-and-pet-converters). + +**However**... + +- They may not work with the datatype you have + (for example not sure that explore ASL can deal with `func` data). +- Many of them still expect that you have a json side car for each nifti + (BIDSme for example - from the top of my head). +- They may expect a certain input structure to work efficiently, + so we may have to move files around. + + + +### Regarding the "missing" JSON files + +Depending on the datatype you are dealing with this can be more of less annoying. + +2 examples: + +For the most typical `anat` files, +they don't have any REQUIRED metadata, +so you could have just the data files without any accompanying JSON. +If you get into more exotic anat files (like for quantitative MRI) +then this may become a problem. + +For `func` files you only need `TaskName` and `RepetitionTime` +and the former you can decide what it is and the latter should be in the Nifti header. +So you should be OKish there too. + +Obviously you will be missing some metadata that would be required +for some type of preprocessing (like slice timing info). + +### Tips + +- If you have the PDF with the details of acquisition sequence or a method section + from a paper with that data, you could "recover" some extra metadata. +- SPM dicom import tool usually leaves a couple of metadata in a description field of the nifti header. + That can be a problem for data anonymisation but may help you in your case if this is the tool that was used. + See an example [here](https://github.com/PeerHerholz/BIDSonym/issues/41#issue-768636869) +- If you have to script tings manually rather than using a converter, + remember to use pybids [path construction tools](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#path-construction) or the [bids matlab equivalent](https://github.com/bids-standard/bids-matlab/blob/master/examples/03_BIDS-Matlab_filenames_and_metadata.ipynb) to make your life easier when constructing bids valid filenames. + ## General: Is there a machine readable version of the BIDS specification? Yes. The BIDS specification exist as a schema.