adni-to-bids T1 files, scaled images are being selected?

[Pauline Amrouche]

Hello Clinica team,

I am using the adni-to-bids pipeline for T1 files and I am unsure about what files are selected by the converter. 

Indeed the documentation specifies that when preprocessed files are available, the converter will look for the file that has been "Scaled" (i.e. fully preprocessed) and then use the "N3" image (the preprocessed image not scaled). This explains why the "Image_ID" column in t1_paths.tsv can refer to the scaled image while the "Sequence" column refers to the N3-image (as explained in the documentation). Explicitly wanting to select the N3-image (not scaled) has been confirmed in this GitHub Issue, and this post on the forum. So I would expect the converter to select the image based on the information in the "Sequence" column to select the N3-image.

However the  _find_path_single_image function uses the "Image_ID" column to select the image files (in this line). Therefore it seems that the scaled image, to which the image id refers, is actually converted to BIDS instead of the N3-image.

Did I understand the code correctly? And do you confirm that the N3 image should be used instead of the scaled image?

If so, then I think the _find_path_single_image function should use the "Sequence" column to select the file rather than "Image_ID".

Thanks,

Best regards,

Pauline

[Alice Joubert]

Hello Pauline,

Thanks for reaching out to us. I need to investigate before replying. I will report back to you once I know more, hopefully next week maximum.

Best,

Alice

[Pauline Amrouche]

Hello Alice,

For my specific usecase I've ended up forking Clinica's GitHub and modify it to find the actual image ID corresponding to the N3 corrected not scaled images.

Here is my fork: https://github.com/pauline-amrouche/clinica . If you think this could be helpful, I'm happy to submit a PR. Please note that this solution requires to download a list of images and their image ID from the LONI interface to match images names with their correct id.

Best regards,

Pauline

[Alice Joubert]

Hello Pauline,

Thanks for offering your work ! We are considering using Scaled images actually after seeing the recommendations of ADNI experts. In your use case, would you specifically need not scaled images ?

Best,

Alice