Where can I find the complete raw connectome datasets used in the conn2res toolbox?

[jiedia]

Dear conn2res team,

I have been working with the conn2res toolbox and noticed that the datasets provided are pre-processed versions. I am specifically interested in obtaining the complete raw connectome datasets that were used as the basis for these pre-processed datasets.

Could you please provide information on where I can access the original, unprocessed connectome data? It would be incredibly helpful to have access to the full raw datasets for my research.

Thank you for your help and I look forward to your response!

Best regards,
Peter

[jiedia]

Additionally, I’m mainly looking for the complete raw connectome datasets for mice or rats, as this is the focus of my project. Any links or resources would be really helpful!

[kaurao]

I am running into error for similar reason when trying to run the tutorial:
FileNotFoundError: [Errno 2] No such file or directory: '[PATH_TO]/envs/conn2res/lib/python3.8/site-packages/examples/data/human/connectivity.npy'

this originates at the following line:
conn = Conn(subj_id=0)

I can send the full stack if needed.

Thanks!

[jiedia]

I am running into error for similar reason when trying to run the tutorial: FileNotFoundError: [Errno 2] No such file or directory: '[PATH_TO]/envs/conn2res/lib/python3.8/site-packages/examples/data/human/connectivity.npy'

this originates at the following line: conn = Conn(subj_id=0)

I can send the full stack if needed.

Thanks!

Thank you for your response. I greatly appreciate your time and assistance.

I am specifically looking for the complete raw connectome datasets for mice, as this is the primary focus of my project. If it is possible for your team to provide access to these datasets, it would be immensely helpful for my research. Alternatively, if you could point me to resources or links where I might obtain the raw connectome data for mice, I would be very grateful.

Thank you again for your help, and I look forward to your response!

Best regards,
Peter

[kaurao]

Found the connectomes here: https://zenodo.org/records/10205004
This is linked in the tutorial.

[fmilisav]

Hi @jiedia,

Sorry for the late reply. For the mouse and rat connectomes, we directly used the pre-processed aggregated connectomes from the following publications: https://doi.org/10.1073/pnas.1420315112 (mouse) and https://doi.org/10.1073/pnas.1504394112 (rat). Both used publicly available data for reconstruction: BAMS (https://bams1.org/) for rat and the Allen Mouse Brain Connectivity Atlas (https://connectivity.brain-map.org/). You can refer to the original publications for more details.

Best,
Filip

[zmiller22]

I am running into error for similar reason when trying to run the tutorial: FileNotFoundError: [Errno 2] No such file or directory: '[PATH_TO]/envs/conn2res/lib/python3.8/site-packages/examples/data/human/connectivity.npy'

this originates at the following line: conn = Conn(subj_id=0)

I can send the full stack if needed.

Thanks!

@kaurao I had the same issue which I was able to fix. I also thought it was due to missing data at first, but further investigation revealed that it actually had to do with the use of a virtual environment when following the installation instructions.

If you followed the README instructions and ran pip install . while inside a virtual environment, conn2res is installed as a python package inside your virtual environment (the same as other python packages like NumPy). That is why the file not found error is looking for the data inside your env site-packages in the error message you posted--from the perspective of the running file, the relative path is to the virtual environment not the repo (just as it would be for NumPy and other Python packages installed in your virtual environment). But if you followed the README instructions, you will have installed the data folder from Zenodo in the examples folder of the cloned repo which is different than the virtual environment path (which is intended... the virtual environment path is meant to be where your Python packages live not where you are actively developing code). Also note that this process installed conn2res as a static package... so any edits you make in your repo are not going to show up in the package.

There are a few different ways to fix this. For me, I created a new virtual environment and reinstalled conn2res using the command pip install -e . This installs the package in "editable mode" which has two effects:

• First, it registers the path of the package to the path of the repo rather than to site-packages inside your virtual environment
• Second, it allows you to make edits to the module files that will actually take effect when you run the code

I suspect that for most users, pip install -e . is the intended usage model.