Nosetests fail because sample dataset is outdated

[larsoner]

Would it be possible to add a link to the newest version of the sample dataset in the development section? I just downloaded the one that is linked on the FTP server, and I keep getting errors/warnings like this in nosetests:

UserWarning: Sample dataset (version 0.3) is older than mne-python (version 0.4.git). If the examples fail, you may need to update the sample dataset by using force_update=True

No such file or directory: '/home/larsoner/custombuilds/mne-python/mne/simulation/tests/../../../examples/MNE-sample-data/MEG/sample/labels/Aud-lh.label'

I got errors of this sort even when I ran this from scratch (without downloading from the FTP site). I'm also not sure where I can set force_update=True to get it to download the newest version, but having a link would be preferable for me in any case.

[agramfort]

we'll have to wait for @mluessi who takes care of it now. He is away for a couple of weeks.

[mluessi]

The sample dataset has been updated to 0.4 on the FTP :)

@agramfort: don't forget to update the one at Neurospin

[larsoner]

Hey @mluessi, while we're at it (sorry for not suggesting this earlier), it would be excellent if we could add distance info to the source space so I can add a nosetest for that at some point. I used a call like this:

mne_add_patch_info --dist 7 --src sample-oct-6-src.fif --srcp sample-oct-6-src.fif

And uploaded the resulting file here:

http://faculty.washington.edu/larsoner/sample-oct-6-src.fif

Could you swap that one in? It should be the same as the old one, but with distances up to 7mm included. I checked to make sure swapping that into examples/MNE-sample-data/subjects/sample/bem/ didn't break any nosetests. If you're up for adding this, I'll put in a basic nosetest to ensure that reading in distances works.

[larsoner]

Also, for some reason mne_analyze can't get the coordinate transform right for the subject "sample". If you open mne_analyze, load "sample", and do View->Show Coordinates, you'll see that the MNI coordinates are not listed, and there's an error in the terminal of:

Adding Talairach transforms...[failed]
Warning : Transform file not present in these MRI data

I'm not sure why this error happens, but it would be good if we could fix it so I can make my nosetests better for vertex_to_mni(). It doesn't seem like mne_analyze should be failing, since "mri/transforms/talairach.xfm" exists. Perhaps @mshamalainen would know why mne_analyze can't get the MNI coordinate transforms for "sample"...?

[mluessi]

@Eric89GXL can you make a PR for mne-scripts to add the patch info? I will update the sample data again when mne-python 0.5 is released, the current version works with 0.4. Updating the sample data every time we add something to the git version creates to much overhead.

[larsoner]

I could do that...but where are mne-scripts? Are those the ones in mne-python/bin/?

[mluessi]

The scripts are here: https://github.com/mne-tools/mne-scripts

[agramfort]

hum I've never used "show coordinates" and on my box it says "nothing
yet"... is it a mac issue?

can you send me a screen shot of what you see?

[larsoner]

After that window pops up saying nothing yet, click on some location on the
brain and it should calculate the position in MNI coordinates. Note that it
does for fsaverage, but not for sample.

[agramfort]

problem reproduced.

@mshamalainen if you have time to take a look it would be great.

[larsoner]

It would be good for us to know if mne_analyze has a good reason for rejecting the talairach.xfm for "sample", since in the python code it currently uses it as though it's correct.

[agramfort]

I tried changing the sample talairach.xfm with the fsaverage one and it is
not working either.
The problem is somewhere else.