numpy & pandas non-compatibility?

[hollysully]

Hi--thanks for creating this software--it is awesome!

I am getting this error when I try to run randomise_summary.py
TypeError: Cannot interpret '<attribute 'dtype' of 'numpy.generic' objects>' as a data type

The link below discusses that this error is due to non-compatibility between some versions of numpy & pandas:
https://stackoverflow.com/questions/66563463/how-to-treat-attribute-dtype-of-numpy-generic-objects-error

Could you please tell me which versions of numpy & pandas you are currently using that do not produce this error? (I have tried downgrading pandas to -0.25.3 but it did not resolve the issue)

Thanks!
Holly

[kcho]

Hi @hollysully,

Thanks! I noticed that pandas was updated and removed pd.Panel, which broke the statsmodels version that I was using. Updatingstatsmodels to 0.13.2 resolved this issue for me and I'm wondering if it is the same issue raising the error for you.

Could you try updating statsmodels and paste here the whole error message if you still get them after the update please?

Thanks!

[hollysully]

Thank you for the suggestion! pnl_randomise seems to be installed now and started to run but I got this error message:

FileNotFoundError: [Errno 2] No such file or directory: '/data/pnl/soft/pnlpipe3/tbss/data/enigmaDTI/ENIGMA_DTI_FA_skeleton_mask.nii.gz'

The script seems to think my FA_skeleton_mask will have a different name?

Attached is the full error message. Any thoughts?

[kcho]

I'm glad that it's running, at least to the next error🙈 Which template did you use, when you ran your tbss?

The current version of randomise_summary, by default, looks for ENIGMA skeleton files, under /data/pnl/soft/pnlpip3/tbss/data/enigmaDTI/ENIGMA_DTI_FA_skeleton_mask.nii.gz. From the screenshot that you shared above, I'll have to edit the code to make it more flexible to accept non-enigma skeleton masks from the user. I'll get to it soon.

If you want to apply a quick fix, you could change the line raising FileNotFoundError to the path of your skeleton mask and re-try it?

[hollysully]

In the randomise_summary.py script, I changed the template to mean_FA.nii.gz and now I am getting a new error. Any thoughts on what this error means?

[anarfouto]

Hi! I am having the same error message, can you give updates on this issue? Thanks!