update FAQ with convert from nifti only (#349)

* update FAQ with convert from nifti only

* Update questions/general_convert_nifti.question.md

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

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.
+
+<!-- Not played with it but, from the README, data2bids sounds pretty flexible
+but may require you to play with python and json files for configuration.
+
+https://github.com/SIMEXP/Data2Bids -->
+
+### 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.

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.
+
+<!-- Not played with it but, from the README, data2bids sounds pretty flexible
+but may require you to play with python and json files for configuration.
+
+https://github.com/SIMEXP/Data2Bids -->
+
+### 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.