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miykael / atlasreader

Python interface for generating coordinate tables and region labels from statistical MRI images
BSD 3-Clause "New" or "Revised" License
89 stars 31 forks source link

can not install through pip #83

Closed EhsanTadayon closed 5 years ago

EhsanTadayon commented 5 years ago

Hi,

I'm getting this error while installing through pip:

Collecting atlasreader Could not find a version that satisfies the requirement atlasreader (from versions: ) No matching distribution found for atlasreader

miykael commented 5 years ago

Hi @EhsanTadayon. I'm happy to hear that you want to use atlasreader. We haven't set it up yet, that you can install atlasreader via the web, but if you download the github repo and then run pip install -U . within the main folder, that should work.

Did this solve your issue?

We're planing on making atlasreader pip installable directly from the web until the end of this year.

EhsanTadayon commented 5 years ago

Hi @miykael. Thanks. It is definitely a great tool. I actually went ahead and installed it after cloning it.

I think the main purpose of atlasreader is to annotate statistical maps using an atlas but I used it to annotate several masks. It works great. The only problem is that since these are masks there is no maximum peak. I didn't go through the package to understand how exactly it works, but I assume it finds the center of the mask for annotation?

miykael commented 5 years ago

Hmm.. that's a very good question. I checked the code and it should use center_of_mass from scipy.ndimage (see here).

Does it seem to do the right thing with your masks?

EhsanTadayon commented 5 years ago

It seems right to me. There are two output files: one for clusters ( which has only one row, since it is a mask) and one for peaks. The cluster correctly outputs the structures based on the atlas and as you are saying the peaks output the center of the mask. The annotation for the peak sometimes is not the annotation with the maximum probability ( in clusters file), which makes sense if it is a statistical map but might not be ideal if it is a binary mask. Aside from that, it works perfectly.

miykael commented 5 years ago

Hi @EhsanTadayon, atlasreader can now be installed via pip. Is it alright if I therefore close this issue?

miykael commented 5 years ago

I will close this issue for now. Should it not be resolved, I'm happy to reopen it again.