One directory per modality

[tsalo]

It would be logical that the directory structure of the subject-level derivatives would reflect the structure of the raw data. Therefore, we may need to think the structure of the raw data with a bit more attention to general aspects of the processing. Joining modalities that may need completely different analysis under same the folder (anat, func and dwi) may end up generating problems. Not only derivatives can be overwritten but also having many different modalities in the same directory can be rather confusing (Not to speak about the problem of modalities like DfMRI (If someone manages to make it real) or future modalities we have not even heard about).

The way to go may be be one folder per modality, rather than one per scan.

• All T1ws in the T1w directory.
• All DWIs in the dMRI directory.
• All task fMRIs in the tfMRI directory.
• All resting fMRIs in the rfMRI directory.
• All T2ws in the T2w directory.
• All ASL in the ASL directory.
• All FLAIR in the FLAIR directory.
• All SWIs in the SWI directory.
• Etc.

At the end, we would end with 10/12 directories at most, but probably better organised.

Original authors: Unknown

[tsalo]

@Athanasiamo wrote:

I think this is an excellent idea. I think it is preferable to have more folders to allow easy overview of the existing data, rather than fewer which entails having to look through so many files within the folders to find what you are looking for. And it's a good point regarding the derivatives, it is definitely worth trying to create a structure where as much as possible is the same in the raw and derivatives structures.

[tsalo]

@spinicist wrote:

I like this idea. I have essentially adopted it in my own processing pipelines already

[tsalo]

Robert Welsh wrote:

• All DWIs in the dMRI directory.

How to handle phase encode polarity reverse for the DWI data?

And what of the raw data for phase reversal for the create of effective field maps for distortion correction of BOLD/EPI data?

[tsalo]

@spinicist wrote:

How to handle phase encode polarity reverse for the DWI data?

And what of the raw data for phase reversal for the create of effective field maps for distortion correction of BOLD/EPI data?

Filename suffix?