<div dir="ltr">Hi Richard,<div><br></div><div>Thank you so much for the help, I am surprised you have this down to memory —as is, your example runs perfectly with the trained 'thr' object as all that is needed. </div><div><br></div><div>One last question for you, or anyone who may know - is there a way to use the AttributePermutator in a way that maintains the same label shuffling across subjects? Even with cross-validation? I have read several sources saying this should be done for several reasons, eg, discussion here:</div><div><br></div><div><a href="http://mvpa.blogspot.com/2012/10/permuting-searchlight-maps-stelzer.html">http://mvpa.blogspot.com/2012/10/permuting-searchlight-maps-stelzer.html</a></div><div><br></div><div>Thank you again for any help, this has been immense.</div><div><br></div><div>Best,</div><div>Ryan<br><br><br><div class="gmail_quote"><div dir="ltr">On Sun, Feb 26, 2017 at 7:02 AM <<a href="mailto:pkg-exppsy-pymvpa-request@lists.alioth.debian.org">pkg-exppsy-pymvpa-request@lists.alioth.debian.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pkg-ExpPsy-PyMVPA mailing list submissions to<br class="gmail_msg">
<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" class="gmail_msg" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br class="gmail_msg">
<br class="gmail_msg">
To subscribe or unsubscribe via the World Wide Web, visit<br class="gmail_msg">
<a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" rel="noreferrer" class="gmail_msg" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br class="gmail_msg">
<br class="gmail_msg">
or, via email, send a message with subject or body 'help' to<br class="gmail_msg">
<a href="mailto:pkg-exppsy-pymvpa-request@lists.alioth.debian.org" class="gmail_msg" target="_blank">pkg-exppsy-pymvpa-request@lists.alioth.debian.org</a><br class="gmail_msg">
<br class="gmail_msg">
You can reach the person managing the list at<br class="gmail_msg">
<a href="mailto:pkg-exppsy-pymvpa-owner@lists.alioth.debian.org" class="gmail_msg" target="_blank">pkg-exppsy-pymvpa-owner@lists.alioth.debian.org</a><br class="gmail_msg">
<br class="gmail_msg">
When replying, please edit your Subject line so it is more specific<br class="gmail_msg">
than "Re: Contents of Pkg-ExpPsy-PyMVPA digest..."<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
Today's Topics:<br class="gmail_msg">
<br class="gmail_msg">
1. Re: GroupClusterThreshold data / attributes (Richard Dinga)<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
----------------------------------------------------------------------<br class="gmail_msg">
<br class="gmail_msg">
Message: 1<br class="gmail_msg">
Date: Sat, 25 Feb 2017 19:52:11 +0100<br class="gmail_msg">
From: Richard Dinga <<a href="mailto:dinga92@gmail.com" class="gmail_msg" target="_blank">dinga92@gmail.com</a>><br class="gmail_msg">
To: Development and support of PyMVPA<br class="gmail_msg">
<<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" class="gmail_msg" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br class="gmail_msg">
Subject: Re: [pymvpa] GroupClusterThreshold data / attributes<br class="gmail_msg">
Message-ID:<br class="gmail_msg">
<CABbjURCstmE8TgKQ8Qw=uYQSb52zm=<a href="mailto:sxDhGoNy1xR-chAZTOSQ@mail.gmail.com" class="gmail_msg" target="_blank">sxDhGoNy1xR-chAZTOSQ@mail.gmail.com</a>><br class="gmail_msg">
Content-Type: text/plain; charset="utf-8"<br class="gmail_msg">
<br class="gmail_msg">
Hi,<br class="gmail_msg">
I am sorry, my python is bit rusty by now, and I don't have a data set<br class="gmail_msg">
ready to give you an reproducible example. However I think that once you<br class="gmail_msg">
train your GroupClusterThreshold object, then the all cluster sizes from<br class="gmail_msg">
your bootstraps should be in _null_cluster_sizes attribute. Then your<br class="gmail_msg">
p-value for your arbitrary cluster is just a it's percentile in that array.<br class="gmail_msg">
<br class="gmail_msg">
You can also use methods get_cluster_pvals or _transform_to_pvals from the<br class="gmail_msg">
GroupClusterThreshold class to do it for you. Somehow :)<br class="gmail_msg">
Actual code that computes the p-values for clusters is:<br class="gmail_msg">
cluster_probs_raw = _transform_to_pvals( area, self<br class="gmail_msg">
._null_cluster_sizes.astype('float'))<br class="gmail_msg">
so MAYBE this will work for you<br class="gmail_msg">
cluster_probs_raw = GroupClusterThreshold._transform_to_pvals(<br class="gmail_msg">
np.array([40. 60, 80]), thr._null_cluster_sizes.astype('float'))<br class="gmail_msg">
<br class="gmail_msg">
On Thu, Feb 9, 2017 at 10:40 PM, Ryan Stolier <<a href="mailto:ryan.m.stolier@gmail.com" class="gmail_msg" target="_blank">ryan.m.stolier@gmail.com</a>><br class="gmail_msg">
wrote:<br class="gmail_msg">
<br class="gmail_msg">
> Hi all,<br class="gmail_msg">
><br class="gmail_msg">
> I recently implemented GroupClusterThreshold() based on help I found in<br class="gmail_msg">
> this thread: <a href="https://lists.alioth.debian.org/pipermail/pkg-" rel="noreferrer" class="gmail_msg" target="_blank">https://lists.alioth.debian.org/pipermail/pkg-</a><br class="gmail_msg">
> exppsy-pymvpa/2015q3/003202.html<br class="gmail_msg">
><br class="gmail_msg">
> I was able to execute everything properly and get back results. However, I<br class="gmail_msg">
> am curious if there is a way to access data used along the way in the<br class="gmail_msg">
> algorithm and figure out corrected significance levels of *any* size<br class="gmail_msg">
> cluster, rather than only the clusters in my real (non-permuted) data. Ie,<br class="gmail_msg">
> can I access the table of cluster sizes from the 100000 bootstraps of the<br class="gmail_msg">
> permutation maps used to determine the significance levels of clusters in<br class="gmail_msg">
> my real data? Say I wanted to find out the hypothetical significance level<br class="gmail_msg">
> of clusters sized: 40, 60, 80 given everything besides the 'mean_map' input<br class="gmail_msg">
> in the email exchange in the listserv above. Does that make sense? Also, I<br class="gmail_msg">
> suppose the data used at steps 6/7 here: <a href="http://mvpa.blogspot" rel="noreferrer" class="gmail_msg" target="_blank">http://mvpa.blogspot</a>.<br class="gmail_msg">
> com/2012/10/permuting-searchlight-maps-stelzer.html<br class="gmail_msg">
><br class="gmail_msg">
> Thank you so much for any assistance!<br class="gmail_msg">
> Ryan<br class="gmail_msg">
><br class="gmail_msg">
> _______________________________________________<br class="gmail_msg">
> Pkg-ExpPsy-PyMVPA mailing list<br class="gmail_msg">
> <a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" class="gmail_msg" target="_blank">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br class="gmail_msg">
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" rel="noreferrer" class="gmail_msg" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br class="gmail_msg">
><br class="gmail_msg">
-------------- next part --------------<br class="gmail_msg">
An HTML attachment was scrubbed...<br class="gmail_msg">
URL: <<a href="http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/attachments/20170225/69ca5c95/attachment-0001.html" rel="noreferrer" class="gmail_msg" target="_blank">http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/attachments/20170225/69ca5c95/attachment-0001.html</a>><br class="gmail_msg">
<br class="gmail_msg">
------------------------------<br class="gmail_msg">
<br class="gmail_msg">
Subject: Digest Footer<br class="gmail_msg">
<br class="gmail_msg">
_______________________________________________<br class="gmail_msg">
Pkg-ExpPsy-PyMVPA mailing list<br class="gmail_msg">
<a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" class="gmail_msg" target="_blank">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br class="gmail_msg">
<a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" rel="noreferrer" class="gmail_msg" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br class="gmail_msg">
<br class="gmail_msg">
------------------------------<br class="gmail_msg">
<br class="gmail_msg">
End of Pkg-ExpPsy-PyMVPA Digest, Vol 107, Issue 6<br class="gmail_msg">
*************************************************<br class="gmail_msg">
</blockquote></div></div></div>