BIDS vs CAPS for starting folder

[Michael Evans]

Hello,

I am preparing a script to convert some of my patient data (sMRI, fMRI, PET) to BIDS compliance in matlab and I am confused about the difference between BIDS and CAPS.

Does my initial input directory for the t1-freesurfer pipeline require just BIDS? Is the output of this pipeline already going to be in CAPS compliance? 

Assuming my initial directory before running anything needs to be in BIDS and not CAPS, are the "CAPSVersion" and "DatasetType" values required in my dataset_description.json?

Since I am referring to the starting dataset before running any clinica pipelines, I imagine my BIDS dataset's dataset_description.json file should have  "DatasetType" as "raw" and does not need the "CAPSVersion"? Is this right?

Thanks so much,

Michael

[Alice Joubert]

Hello Michael,

First, BIDS is a standard format used in the neuroimaging community. It is well defined with specifications and is versioned. Clinica offers converters from raw format to BIDS for some public datasets (ex ADNI) and uses BIDS as the input for all its processing pipelines. CAPS is a format that looks alike BIDS but is used for outputs of clinica pipelines that need additional files not defined in BIDS specifications. As such, CAPS is specific to Clinica while BIDS is a common standard. If you want to know more, please refer to this page in the documentation. 

In the case of `t1-freesurfer`, you only need to prepare a BIDS. The CAPS you have to indicate in the command line is where you want your output to be. The pipeline will automatically write it in CAPS format. Indeed, the `dataset_description.json` should look like this : 

```

{ "Name": "name identifier for the dataset", "BIDSVersion": "1.7.0", "DatasetType": "raw" }

```

Hope this helps,

Alice

[Michael Evans]

Hi Alice,

Thank you for your help. I have a small sample of 5 patients to test with, each have a t1w MRI and FDG PET scan.

The t1-freesurfer pipeline has just finished succesfully and now we want to run the pet-surface pipeline on the PET scans, which requires us to use the processed MRI scan produced from the t1-freesurfer pipeline.

Since the input to the pet-surface pipeline requires BIDS, and the output from the t1-freesurfer pipeline is CAPS, how should we go about using the original BIDS format directory with the updated MRI from the t1-freesurfer pipeline? Is there just a single file in the CAPS output that we need to replace the orginal BIDS MRI with before running pet-surface ?

Thanks again,

Michael

[Alice Joubert]

Hello Michael,

The BIDS should not have been modified by t1-freesurfer since it is only read in. What is modified is the CAPS. 

As such you can just use your original BIDS as it is and the CAPS you obtained with t1 freesurfer. Pet-surface will read what it needs from both folders and modify the CAPS.

Tell me if this is clear,

Best,

Alice

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