ADNI converter not able to convert T1 images

[Kang Liu]

Dear Clinica team,
I have been facing conversion problems with ADNI images when using the converter (Clinica Version 0.7.7 and  dcm2niiX (v1.0.20190902)  ).  My command was:
clinica -v convert adni-to-bids DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY ADNI_converted -m T1.

However, I'm still encountering the following error, and I've been struggling with it for days now.
2023-12-01 15:50:42,517:INFO:Creating sessions files...
2023-12-01 15:50:42,866:INFO:Clinical dataframe extracted from ADNIMERGE.csv is empty after filtering.
2023-12-01 15:50:42,979:INFO:Clinical dataframe extracted from CDR.csv is empty after filtering.
2023-12-01 15:50:43,219:INFO:Clinical dataframe extracted from NEUROBAT.csv is empty after filtering.
2023-12-01 15:50:43,273:INFO:Clinical dataframe extracted from ADASSCORES.csv is empty after filtering.
2023-12-01 15:50:43,306:INFO:Clinical dataframe extracted from CCI.csv is empty after filtering.
2023-12-01 15:50:43,399:INFO:Clinical dataframe extracted from ECOGPT.csv is empty after filtering.
2023-12-01 15:50:43,485:INFO:Clinical dataframe extracted from ECOGSP.csv is empty after filtering.
2023-12-01 15:50:43,536:INFO:Clinical dataframe extracted from FCI.csv is empty after filtering.
2023-12-01 15:50:43,621:INFO:Clinical dataframe extracted from GDSCALE.csv is empty after filtering.
2023-12-01 15:50:43,693:INFO:Clinical dataframe extracted from MODHACH.csv is empty after filtering.
2023-12-01 15:50:43,804:INFO:Clinical dataframe extracted from MOCA.csv is empty after filtering.
2023-12-01 15:50:43,969:INFO:Clinical dataframe extracted from NPI.csv is empty after filtering.
2023-12-01 15:50:44,038:INFO:Clinical dataframe extracted from NPIQ.csv is empty after filtering.
2023-12-01 15:50:44,056:INFO:Clinical dataframe extracted from BHR_EVERYDAY_COGNITION.csv is empty after filtering.
2023-12-01 15:50:44,119:INFO:Clinical dataframe extracted from BHR_BASELINE_QUESTIONNAIRE.csv is empty after filtering.
2023-12-01 15:50:44,152:INFO:Clinical dataframe extracted from BHR_LONGITUDINAL_QUESTIONNAIRE.csv is empty after filtering.
2023-12-01 15:50:44,241:INFO:Clinical dataframe extracted from MEDHIST.csv is empty after filtering.
Traceback (most recent call last):
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/bin/clinica", line 8, in
sys.exit(main())
^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/clinica/cmdline.py", line 92, in main
cli()
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py", line 79, in cli
adni_to_bids.convert_clinical_data(
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py", line 145, in convert_clinical_data
adni_utils.create_adni_sessions_dict(
File "/lyceum/kl2y21/miniconda3/envs/clinicaEnv/lib/python3.11/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 971, in create_adni_sessions_dict
raise ValueError("Empty dataset detected. Clinical data cannot be extracted.")
ValueError: Empty dataset detected. Clinical data cannot be extracted.

And this is my datasets:

The clinical data is:

I believe I followed the instructions in the documentation to download the data and use the commands. I really don't understand why this error occurred, and I would be extremely grateful for any help you can provide.

Kang

[Kang Liu]

I noticed that the documentation for ADNI to BIDS does not mention ADNI4, so I downloaded ADNI1, 2, GO, and 3, and used the same command with data from two patients to run it again. However, the type of error I encountered was exactly the same, leaving me really unsure of what to do next. I've been stuck on this for a week now, and I'm unclear about where the problem lies. Could this be a bug in Clinica?
warm regards,

kang

[Matthieu Joulot]

Hi Kang,

Can you tell me which sequences you have downloaded ? I think the problem may be linked to this. Clinica only converts specific sequences, which are detailed here in the folded items.

Have a good day,

Matthieu

[Kang Liu]

Dear Matthieu,

Thank you for your reply.

Firstly, i have used pip install --upgrade dcm2niix, conda install -c conda-forge dcm2niix, and
I can't upgrade dcm2niix any further; the final version remains v1.0.20190902.

Secondly, i just download the datasets images, just like that , and all the clinical data, which is like that

And what is the meaning of sequences? is it withing  the clinical data?

warm regards,

kang

[Matthieu Joulot]

Hi Kang,

You can find the latest versions here. Do tell me if you're able to install it.

And for the sequences, no it is not a csv file. The sequence is a the image. So if you open the directory of your subject, you should have something like this:

The title of the directory is the sequence (for instance Axial_DTI). Can you give tell me which one you want to convert ? And show me the sequences you have ?

And we only convert some of them as detailled in these criteria items (see image below) which you can find here. 

[Kang Liu]

Thank you very much for your patient reply.

i have downloaded the latest version of dcm2niix, which is 1.0.20230411

 

and need i configure the environment? Could you tell me where I can find instructions for configuring environment variables?

My sequence is below image(I only use two subject):

I am looking to get the T1-weighted MRI, and the conversion command I used is clinica -v convert adni-to-bids DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY ADNI_converted -m T1

[Matthieu Joulot]

Hi Kang,

Sorry I was misleading. You'll need to follow the instructions here, or the ones right above to install using pip or conda. It would be better if you could install it using pip or conda of course, as it is simpler. your version of conda and python might not be compatible with the latest dcm2niix version so I suggest you update your conda environment and use python3.10.

I'll try to replicate your issue on my side.

Have a a good day,

Matthieu

[Kang Liu]

okay, i have installed another conda and python just now, so my python is 3.11.5 and conda is 23.10.0

[Kang Liu]

Dear Matthieu,

Is it possible that I have too few subjects, and none of them have T1-MRI (Does every subject in the ADNI dataset have T1-MRI?)? However, the error reported is 'Clinical dataframe extracted from xxx.csv is empty after filtering', which seems unrelated to the number of subjects.

Warm regards,

Kang

[Matthieu Joulot]

After looking into the subjects you are trying to use, it turns out they are not in the file ADNIMERGE.csv, which we need to to the conversion. This data is unfortunately missing and the converter will not be able to convert it.

If it is not paramount that you use these two subjects, I would try others.

Were you able to install the right dcm2niix version ?

Have a good day,

Matthieu

[黄锦泰]

Hi,

I'm facing the same problem, while my data search criteria are like this:

Then, the clinical data is the same as instructed in the tutorial documentation: "Select ALL tabular data (csv format)".

And I followed the instruction to use the corresponding command: clinica convert adni-to-bids ADNI_DIRECTORY CLINICAL_DATA_DIRECTORY BIDS_DIRECTORY -m T1.

After running it, I got the same error. I really don't know how to fix this. I've been stuck here for a week now. I'll be grateful if someone can help.

The version I used are the latest version: Clinica Version 0.7.7 and  dcm2niiX (v1.0.20230411) 

Best regards,

Harry

[Matthieu Joulot]

Hi Harry,

Can you give a copy of the error you get ? That would be very helpful, thanks. Also, are trying to convert a specific subject ?

Have a good day,

Matthieu

[黄锦泰]

Hi Matthieu,

Thank you for your reply.

The error I got was like this:

Also, I tried to convert a specific subject whose ID is 002_S_0413. Here is the search process:

However, I still got the same error and don't know what's wrong.

Best regards,

Harry