Cannot initialize neurosynth database

Software Support
1

Hello all,

I want to decode IC maps with neurosynth and get relevant keywords for each map. However, I cannot initialize neurosynth dataset. I am following the code here (which is the same in many other tutorials): https://github.com/neurosynth/neurosynth/blob/master/examples/create_a_new_dataset_and_load_features.py

I downloaded the “database.txt” and “features.txt” files from neurosynth’s repository.

However, when I run dataset = Dataset('database.txt') command, I receive the following error:

ExpiredDeprecationError: get_header method is deprecated.
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0

I tried to find a workaround but I cannot load the dataset in another way. I tried changing the deprecated command in the script with the suggested one, but it did not work.

Is there any other updated way to initialize the database that I am not aware of? I would also appreciate it if you could help me with the decoding method too.

Many thanks!

2

Hello,

Apologies for the delayed response.

Unfortunately, the neurosynth library is deprecated in favor of NiMare.
The error you are seeing is due to a mismatch between nibabel version and neurosynth. You may be able to get around this by downgrading nibabel.

I would instead suggest using NiMare.

Here is how you load Neurosynth into NiMARE: NiMARE: Neuroimaging Meta-Analysis Research Environment — NiMARE 0.2.1+0.g2b1c23a.dirty documentation

You can then use the the decoding module.

Are you trying to decode a discrete image (i.e. ROI) or a full statistical map?

Here is an example of discrete decoding: NiMARE: Neuroimaging Meta-Analysis Research Environment — NiMARE 0.2.1+0.g2b1c23a.dirty documentation

There is no example yet for continous decoding but it’s possible: NiMARE: Neuroimaging Meta-Analysis Research Environment — NiMARE 0.2.1+0.g2b1c23a.dirty documentation