Assistance with NIFD to BIDS Conversion

[oumayma soula]

Dear community

PLZ, I am attempting to apply the Conversion of Neuroimaging in Frontotemporal Dementia (NIFD) to BIDS, as I believe it will greatly facilitate the management and processing of my data. I have followed all the steps outlined on the site and in the documents but usually fail. I suspect the problem may lie in my data selection. My dataset contains only T1 and resting-state images. As you know, after downloading this data, it is organized into numerous subfolders.
Could you please clarify whether Clinica supports fMRI data and if there are any issues related to reading these subfolders until finding DICOM images? Additionally, I would appreciate guidance on the exact process for downloading the data, as I am not interested in all modalities. Should I convert all subjects together or separate them into control and patients?

I would also appreciate any suggestions for managing my data, particularly since I need to organize it by visit (M0, M6, M12, and M18) to study disease progression.

Thanks  !

[Alice Joubert]

Hello !

To better assist you with the issues you encounter using the NIFD-to-BIDS converter it would be easier if you could provide the command line you used, on which folder organisation (raw) and what the error is. 

To answer your other questions :

- No, Clinica does not support fMRI data for the NIFD dataset so these images will not be converted. You can find all the supported modalities in the documentation of Clinica if you want to check.

- Could you be more specific when you say you do not want all the modalities ? You can normally select MRI or/and PET images on the site used to download data.

- The way you organize your data depends on what you want to do with it afterwards : you could have them in separate folders between control and patients or have an additional file indicating if subjects are known to be control or patient. It depends on how you process your data.

- If you succeed in converting your NIFD data to BIDS format, your images should be organized by visit at some point so it should be quite practical to study evolution over time.

Hope this helps,

Alice

[oumayma soula]

Thank you very much this is so helpful
the commande i used is: clinica convert nifd-to-bids <dataset_directory> <clinical_data_directory> <bids_directory>
then the error : Error: Invalid value for 'DATASET_DIRECTORY' It seems like the data is not being read that's why i asked about dataset
Note that dcm2niix and the clinical environment are already installed.
okay i understand , noted 

thanks 

[Alice Joubert]

What do you put in the command line instead of dataset_directory ? (You can just copy here the command line you used with your own paths)

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[oumayma soula]

clinica convert nifd-to-bids /home/ouma/Downloads/DATASET_DIRECTORY /home/ouma/Downloads/clinical_data_directory /home/ouma/Downloads/NIFD_BIDS

and this is a screen shot for the error even during the activation clinica-env

[Alice Joubert]

This error occurs when the converter cannot find the metadata stored in a .csv file in the BIDS_DIRECTORY. When you downloaded your raw data, did you also get the csv ?

If you did you just need to place the resulting csv in the BIDS_DIRECTORY folder and the converter should work.

Hope this helps,

Alice

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[oumayma soula]

thanks Alice,

So, the DATASET_DIRECTORY should contain folders of subjects and their CSV file ; if yes, I got this error ( should i  respect a specific file name;)

[Alice Joubert]

Hi ! 

I think you did everything right and the error came from the code itself. I made a modification to adjust to that so if you update Clinica to its latest dev version the conversion should work.

Let me know !

Alice

To view this discussion on the web visit https://groups.google.com/d/msgid/clinica-user/0aec0d25-7de2-485d-81b7-f6e08dad2a9dn%40googlegroups.com.

[oumayma soula]

HI again

I still got the same error. Is Clinica version 0.8.1 the correct one? This is what I got after the update

[Alice Joubert]

Hi ! 

We updated the dev version but not the 0.8.1 yet. We are currently working on it so I will get back to you when it's done !

Alice

To view this discussion on the web visit https://groups.google.com/d/msgid/clinica-user/f76365b9-6e21-4313-af23-6748d11a7adan%40googlegroups.com.

[oumayma soula]

Hi Alice 

To update Clinica to its latest development version, I follow these guidelines (which still are not working for me) . If I'm wrong, please provide the correct link to the GitHub repository or documentation.

[Alice Joubert]

Hello !

Clinica 0.8.2 which contains the fix mentioned above was released today, so there is no need for you to install the dev version anymore. In principle 0.8.2 can be installed with the same command line you used for installing 0.8.1 (here as a reminder) but since you already have the previous version you can just use "pip install --upgrade clinica" in your clinica folder on your device.

Tell me if that helps,

Alice

[oumayma soula]

Hi Alice!

It works now! Thanks a lot for your assistance and kindness. 

Now l should look into fMRI to see how to convert and manage them.

Thanks again !

[Alice Joubert]

No worries. Thanks a lot for reaching out to us, we could fix this issue thanks to you !

Have a good day,

Alice

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