<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Dear Yaroslav</span></font></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Woops, that was embarrassing! Thanks for clearing that up. However, I've just spotted another potential problem in my code. I assumed that the experimental design was the same for all runs, because only task001_run001
(in the sub001/BOLD directory) has an attributes.txt file indicating the order of stimulus presentations (unless I'm very much mistaken?) None of the other runs contain this file, so I used...<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span style="font-family: Consolas, Courier, monospace;">targets = SampleAttributes(pjoin('haxby2001, 'sub001', 'BOLD','task001_run001', 'attributes.txt'))['targets']</span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">for every chunk in ds. However, when examining the data loaded in by load_tutorial_data...</p>
<p style="margin-top:0;margin-bottom:0"></p>
<div><br>
</div>
<div>print ds.targets[ds.chunks==0]<br>
> ['scissors' 'scissors' 'scissors'...</div>
<div><span>print ds.targets[ds.chunks==1]</span></div>
<div><span>> ['face' 'face' 'face'....</span><br>
</div>
<p></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">SO I was clearly wrong on that front. Is there a way to access information about the experimental design from the other runs? As I mentioned above, only task001_run001 contains the relevant attributes.txt file, so I'm
rather at a loss as to where the necessary info might be located.<br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<p><span style="color:rgb(0,0,0); font-family:arial,sans-serif; font-size:12.8px">---------------------------------------------------------</span></p>
<span style="color:rgb(0,0,0)"></span>
<p><span style="color:rgb(0,0,0); font-family:arial,sans-serif; font-size:12.8px"><b>Lyam Bailey, B.Sc., M.Sc. </b></span></p>
<p><span style="color:rgb(0,0,0); font-family:arial,sans-serif; font-size:12.8px"></span><span style="font-family:arial,sans-serif; font-size:12.8px">Doctoral Student</span></p>
<span style="color:rgb(0,0,0)"></span>
<div style="color:rgb(136,136,136); font-family:arial,sans-serif; font-size:12.8px">
<span style="color:rgb(0,0,0)">Department of Psychology & Neuroscience</span></div>
<span style="color:rgb(0,0,0)"></span>
<div style="color:rgb(136,136,136); font-family:arial,sans-serif; font-size:12.8px">
<span style="color:rgb(0,0,0)">Dalhousie University</span></div>
<br>
<p></p>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Pkg-ExpPsy-PyMVPA <pkg-exppsy-pymvpa-bounces+lyam.bailey=dal.ca@alioth-lists.debian.net> on behalf of Yaroslav O Halchenko <yoh@onerussian.com><br>
<b>Sent:</b> Wednesday, August 14, 2019 12:25:19 PM<br>
<b>To:</b> pkg-exppsy-pymvpa@alioth-lists.debian.net <pkg-exppsy-pymvpa@alioth-lists.debian.net><br>
<b>Subject:</b> Re: [pymvpa] Loading multiple ROIs with fmri_dataset</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText"><br>
On Wed, 14 Aug 2019, Lyam Bailey wrote:<br>
<br>
> Dear Yaroslav,<br>
<br>
> Thanks so much for the quick reply. I tried implementing this with:<br>
<br>
> fa_fname = {a: "haxby2001/sub001/masks/25mm/%s.nii.gz" % a for a in ["vt,<br>
> hoc"]}<br>
> temp_ds = fmri_dataset(bold_fname, mask=None, targets = targets,<br>
> add_fa=fa_fname, chunks = int(i)-1)<br>
<br>
> The code ran without errors, however when I continued through the example<br>
> RSA script (<a href="http://www.pymvpa.org/examples/rsa_fmri.html">http://www.pymvpa.org/examples/rsa_fmri.html</a>) the<br>
> dissimilarity matrices appeared very different to those generated when<br>
> using load_tutorial_data. I experimented with<br>
> fa_fname = {a: "haxby2001/sub001/masks/25mm/%s.nii.gz" % a for a in<br>
> ["white"]}<br>
<br>
> ...and this turned out to generate exactly the same results. I also get<br>
> the same results with add_fa = None. So I get the feeling that add_fa is<br>
> not actually being implemented. Can you see a problem in the way I've<br>
> called fmri_dataset?<br>
<br>
add_fa just adds those feature attributes. You would still need to<br>
subselect those features if you decide to work with specific ROIs. <br>
<br>
for se3lection could do smth like<br>
<br>
roi_ds = temp_ds[:, temp_ds.fa.vt != 0]<br>
<br>
or am I missing what you are missing? ;)<br>
<br>
-- <br>
Yaroslav O. Halchenko<br>
Center for Open Neuroscience <a href="http://centerforopenneuroscience.org">http://centerforopenneuroscience.org</a><br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
WWW: <a href="http://www.linkedin.com/in/yarik">http://www.linkedin.com/in/yarik</a>
<br>
<br>
_______________________________________________<br>
Pkg-ExpPsy-PyMVPA mailing list<br>
Pkg-ExpPsy-PyMVPA@alioth-lists.debian.net<br>
<a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a></div>
</span></font></div>
</body>
</html>