Not able to convert to BIDS the data downloaded from ADNI

[Joan Carreras Diaz]

Dear Clinica team,

I am experiencing some troubles trying to convert the ADNI data to BIDS using the function convert adni-to-bids.

I have followed the instructions given in the page named "adni-to-bids – Conversion of the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to BIDS"  link: https://aramislab.paris.inria.fr/clinica/docs/public/latest/Converters/ADNI2BIDS/#downloading-adni.

There, I was told to download all the clinical data too.

I downloaded all the CSV files, and I had to change the names manually because they were downloaded with the date on its name.

Once I downloaded all the data, I created the destination folder named BIDS_DIRECTORY. And I applied the function given in the tutorial: "clinica convert adni-to-bids [OPTIONS] DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY BIDS_DIRECTORY", replacing it for my directories: 

clinica \

convert \

adni-to-bids \

--subjects_list my_subject.txt \

/Users/joancarrerasdiaz/Desktop/CARPETES/UdG/Pràctiques/Dades_ADNI/DATASET_DIRECTORY \

/Users/joancarrerasdiaz/Desktop/CARPETES/UdG/Pràctiques/Dades_ADNI/CLINICAL_DATA_DIRECTORY \

/Users/joancarrerasdiaz/Desktop/CARPETES/UdG/Pràctiques/Dades_ADNI/BIDS_DIRECTORY

The results I have obtained are the following ones:

I believe that the results are not the ones I was looking for, these are some tables and some of them are empty.

Note: I am working with only one patient in the DATASET_DIRECTORY. And the folder has the following structure:

I am working with macOS

Thank you,

Joan

[Matthieu Joulot]

Hi Joan,

I'm not sure what your issue is and what your looking for. Could you formulate a question ? You've given great details and it would help me helping you !

However, looking at what you've said, it looks like some of the data you want to convert, is not being converted. If that is the case, can you tell me which sequences these are ? We might not convert them as specified here in the folded items.

Have a good day,

Matthieu

[Joan Carreras Diaz]

Yes, for sure. The main issue is that I would like to follow the steps of this tutorial: "https://carpentries-incubator.github.io/SDC-BIDS-fMRI/aio/index.html". To do that it is important to convert the data downloaded from ADNI to BIDS. However, it seems that when I try to do that, using the function clinica convert-adni-to-bids, it looks like that the data is not properly converted. 

The data downloaded is a .dcm file with brain images meanwhile the results are some tables. 

Sincerely, I do not know if the problem is due to a wrong use of the function convert adni-to-bids or if it is the data downloaded in ADNI.

Thank you vey much!

Joan

[Matthieu Joulot]

There is a bunch of possibilities with what happens:

 - It is possible that the sequences you've downoaded do not meet the criteria we've set for conversion (which you can find here).

 - Maybe the data you've downloaded the wrong way ? It seems strange to me that you would have only one DICOM file and that you'd only have 5 sequences. Did you follow the instructions to download the imaging data as well ? Your folder is supposed to look like this:

On my side, when I convert your subject (002_S_0295), I get this:

I am able to convert T1w and FLAIR images. That being said, I am not sure what it is exactly that you wish to obtain. I'd guess you want to get fMRI images since the tutorial you've sent is oriented towards it, is that it ?

Have a good day,

Matthieu

[Joan Carreras Diaz]

Dear Matthieu,

I have discovered that the problem I had was because I was trying to download the ADNI data in Safari. I have tried with another navigator and now I have achieved your results. However I would like to get results like these 

But the results I have obtained are the following ones:

As you can see, the folder named "func" has not been generated and I believe there is some data missing.

Thank you very much,

Joan

[Joan Carreras Diaz]

I have discovered why the func folder was not being generated. I was not downloading fMRI data. I have downloaded the patient data again applying these filters:

And the results obtained after converting the ADNI data to BIDS are the following ones:

Should I have to add some other filters?

[Matthieu Joulot]

Hi Joan,

On getting something like this (image below): you won't be able to, because this (image below) is a BIDS-derivatives and not a BIDS. The converter generates a BIDS. I do not know the content of your tutorial, but i think you are supposed to obtain this BIDS-derivative by processing the BIDS (which you obtain with the adni-to-bids converter) with fmriprep.

On the data missing: that is absolutely normal and the output you get is correct. We only convert specific sequences (usually the rawest). You can find the details on the choices that have been made here.

On adding more filters: i don't know, depends what you want to get. I've downloaded your subject, and there is not more fmri to be converted. If this answer is not satisfactory, can you please reformulate your question specifying in a very detailed manner what you hope to get as an output of the converter by adding more filters ?

Have a good day,

Matthieu

[Joan Carreras Diaz]

The instructions I have been given are the following ones:

The data needed are the structural matrix (obtained with dMRI, followed by a tractography, the fMRI you already have, and measurements of Amyloid-beta and Tau, both are measured with PET.

Thank you for everything.

[Matthieu Joulot]

No problem ! Feel free to ask if you have any other question !

[Joan Carreras Diaz]

Hi Matthieu,

I am facing some issues trying to convert the BIDS data to fmriprep. At first it did not work properly until I downloaded Docker. Then, once I run the following comand given in the tutorial Executing with Docker:

It appears the following message in the terminal:

And the folder I wanted to send the data preprocessed named DATA_PREP gets the following structure:

I believe that the cause why is not converting properly the folder DATA_PREP is due to the warnings given. The problem is that I do not know how I can solve them.

Thank you,

Joan 

[Matthieu Joulot]

Hi Joan,

You should ask the question related to fMRIPrep to the fMRIPrep community, since we do not process fMRI. Here is a link to their GitHub.

However, it seems you are missing the FreeSurfer License which is required to use your processing.

Have a good day,

Matthieu