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Dear Jamie,<div><br></div><div>For me it is not exactly clear what you want to do. In an earlier message you referred to our paper using a permutation test to test for a significant difference in coherence between conditions (Maris et al 2007). Essentially, as described, this is a test which is performed within each subject allowing you to do statistical inference about the potential difference between two conditions. As such this is the type of test indepsamplesZcoh can perform, if properly used (see below). Yet, you describe using two subjects as an input. This to me sounds rather that you would like to do statistics across subjects (although 2 subjects of course is a rather low number). This is NOT something indepsamplesZcoh can do for you. In general it is possible to test for a significant difference between two conditions across a population of subjects, but this would require a different approach. Rather than shuffling single observations across conditions PRIOR TO COMPUTING THE COHERENCE DIFFERENCE (sorry about the capitals but this is essential for what is to follow below), one would swap the sign of the Z-transformed coherence difference for a random subset of subjects prior to averaging.</div><div>It seems as if you computed coherence spectra between all unique pairs of channels (4x5)/2 and used this as an input to freqstatistics. Yet, for single subject statistics this does not make sense, because indepsamplesZcoh expects fourier-spectra in the input. Within the function Z-transformed coherence difference will be computed between all pairs of input channels (in your case this would be (9x10)/2 (even though the function does not know you provide it with the wrong input), and multiplying this number with 52 would give your 'magical' 2340).</div><div>So, indeed you should either format your data in a different way using single subject fourier spectra in two conditions as an input to freqstatistics, or using a different statistical test to test for differences across subjects.</div><div><br></div><div>Yours,</div><div><br></div><div>Jan-Mathijs</div><div><br></div><div><br></div><div> <br><div><div>On May 3, 2009, at 7:00 PM, Jamie Johnston wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi all <o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I am trying to run a<span class="Apple-converted-space"> </span><span class="SpellE">monte</span><span class="Apple-converted-space"> </span><span class="SpellE">carlo</span><span class="Apple-converted-space"> </span><span class="Apple-converted-space"> </span><span class="SpellE">indepsamplesZcoh</span><span class="Apple-converted-space"> </span> cluster on my data using<span class="Apple-converted-space"> </span><span class="SpellE">freqstatistics</span>.<span class="Apple-converted-space"> </span><span> </span>I input two data files into<span class="Apple-converted-space"> </span><span class="SpellE">freqstatistics</span><span class="Apple-converted-space"> </span>with the<span class="Apple-converted-space"> </span><span class="SpellE">cohspctrm</span><span class="Apple-converted-space"> </span>having dimensions 2 (subjects) x 10 (channels, # of coherence spectra) x 52 (frequencies).<span> <span class="Apple-converted-space"> </span></span>I run into a dimension mismatch in the function<span class="Apple-converted-space"> </span><span class="SpellE">clusterstat</span>.<span> <span class="Apple-converted-space"> </span></span>If I run any other statistic (i.e.,<span class="Apple-converted-space"> </span><span class="SpellE">indepsamplesT</span>) it runs fine.<span class="Apple-converted-space"> </span><span> </span>When running the<span class="Apple-converted-space"> </span><span class="SpellE">indepsamplesT</span>,<span class="Apple-converted-space"> </span><span class="SpellE">clusterstat</span><span class="Apple-converted-space"> </span>receives two inputs:<span class="Apple-converted-space"> </span><span class="SpellE">statobs</span><span class="Apple-converted-space"> </span>(520x1) and<span class="Apple-converted-space"> </span><span class="SpellE">statrnd</span><span class="Apple-converted-space"> </span>(520x100). These dimensions make sense to me.<span> <span class="Apple-converted-space"> </span></span>However, when running<span class="Apple-converted-space"> </span><span class="SpellE">indepsamplesZcoh</span>these two variables have dimensions 2340x1 and 2340x100, respectively.<span> <span class="Apple-converted-space"> </span></span>This happens around lines 104-108 in<span class="Apple-converted-space"> </span><span class="SpellE">indepsamplesZcoh.m</span><span class="Apple-converted-space"> </span>with computation of the variables <span class="SpellE">chancmbsel</span> and <span class="SpellE">nnewsamples</span>.<span> <span class="Apple-converted-space"> </span></span>Im not understanding what these variables do, but my guess is that I need to setup my data files differently in the beginning.<span> <span class="Apple-converted-space"> </span></span>My understanding of what this analysis protocol does is compute the z-statistic on each channel of coherence data (10 for each data file) and then find the difference between the z-statistic for each channel across the data files.<span> </span>Once this is complete it runs the permutations to determine the significance.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Please verify that what I have done is correct and any help with the error I am getting would be greatly appreciated.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Jamie<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>_______________<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Jamie Johnston, Ph.D.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Assistant Professor<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Faculty of Kinesiology<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>University of Calgary<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>2500 University Dr. NW<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Calgary, AB<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>T2N 1N4<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Phone: +1 (403) 220-3649<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>Fax: +1 (403) 284-3553<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>email: <a href="mailto:johnston@kin.ucalgary.ca">johnston@kin.ucalgary.ca</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span>website: <a href="http://www.kin.ucalgary.ca/wcm/knes/johnston.html">http://www.kin.ucalgary.ca/wcm/knes/johnston.html</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><p>----------------------------------</p><p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p><p><a href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a></p><p><a href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a></p></span></blockquote></div><br></div></body></html><p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>