Hi Mark, <br>
<br>
,Thanks for the feeback. I&#39;m new to FSL and was unaware of the purpose
of the corrections file, but it was my hunch that there might be a size
problem. The orginal problem of not generating the copes occured when a
temporal derivative was applied to the EV&#39;s. I have been able to
generate a limited amount of cope images (three)&nbsp; when I do not input a
temporal derivative to the EV&#39;s. Following this temporary success I
reasoned that the design I was modelling became unstable when the
events were shifted slightly in time. I reasoned that this made sense
given some of my events are sometimes within 2000ms. I feel this is a
bit of an odd explanation given that I never received any indication my
design was rank deficient. Does this reasoning make sense? However, when I input all the contrasts I
intend to use (20) without the temporal derivativer, again there are no
copes. Is this what I should expect to occur given space limitations? <br><br>Thanks<br>Nick<br><br><div><span class="gmail_quote">On 1/4/07, <b class="gmail_sendername">Mark Woolrich</b> &lt;<a href="mailto:[log in to unmask]">
<a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0701%26L%3DFSL%26E%3D7bit%26P%3D107586%26B%3D------%253D_Part_15148_12064589.1167938899924%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">Hi Nicholas,<div><br></div><div>The problem is likely to be the size of the corrections file in the stats directory. The&nbsp;corrections file is related to the correlation matrix of the PEs, 
i.e. its size is a function of the number of brain voxels and (number of EVs)^2, and is needed to compute the statistics for your chosen contrasts. With 24 EVs you are quite likely to be running out of disk space.</div><div>
<div><div><br></div><div>Cheers, Mark.</div></div></div><br><div> <span style="border-collapse: separate; border-spacing: 0px; 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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
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<div style="margin: 0px;">----</div><div style="margin: 0px;">Dr Mark Woolrich</div><div style="margin: 0px; min-height: 14px;">EPSRC Advanced Research Fellow&nbsp;University Research Lecturer</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">Oxford University Centre for Functional MRI of the Brain (FMRIB),</div><div style="margin: 0px;">John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">Tel: (+44)1865-222782 Homepage: <a href="http://www.fmrib.ox.ac.uk/%7Ewoolrich" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.fmrib.ox.ac.uk/~woolrich
</a></div><div><br></div><div><br></div><br></span></span></span></span> </div><div><span class="e" id="q_10fecbd787d0c32b_1"><br><div><div>On 1 Jan 2007, at 22:29, Christian Beckmann wrote:</div><br><blockquote type="cite">
<div style="margin: 0px;">Hi,</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">this is virtually impossible to sort out without additional information,, is it possible that your design is rank deficient? Please check the FAQ (particularly point 2) and provide the relevant information. You might also want to upload the 
feat.fsf file, the reports, an ls -ltR of the feat directory and all the design.* files in a single tar file to <a href="http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi</a></div><div style="margin: 0px;">and then email the upload ID.</div><div style="margin: 0px;">cheers</div><div style="margin: 0px;">christian</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">On 1 Jan 2007, at 22:11, Nicholas Wymbs wrote:</div><div style="margin: 0px; min-height: 14px;"><br></div> <blockquote type="cite"><div style="margin: 0px;">Hi all,</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">I&#39;m having some difficulty getting FEAT to output cope images along with other stat images. It</div><div style="margin: 0px;">appears to run smoothly and strangely no error message is generated. The only images that FEAT
</div><div style="margin: 0px;">sends to the stats directory are the<span>&nbsp; </span>partial error images, &#39;corrections&#39;, &#39;threshac&#39;, and</div><div style="margin: 0px;">&#39;sigmasquareds&#39;. Has anyone seen this general problem?
</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">I believe the source of my problem is with the model I&#39;m using but can&#39;t really understand why. I</div><div style="margin: 0px;">
have 24 EV&#39;s which are inputted using a set of custom 3-column stimulus files. I have selected the</div><div style="margin: 0px;">orthogonalise option along with a temporal derivative and temporal filtering.</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">I&#39;ve avoided the problem by running with less, say 6. What&#39;s odd is that I&#39;ve encountered the error</div><div style="margin: 0px;">when inputting 12 EV&#39;s in the orginal full model order but not when I selected a different group of
</div><div style="margin: 0px;">12 EV&#39;s.</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">Sorry this is a bit vague, any help in solving this mystery is welecomed!</div><div style="margin: 0px; min-height: 14px;">
<br></div><div style="margin: 0px;">Cheers and Happy New Year</div><div style="margin: 0px;">Nicholas</div> </blockquote><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">--</div><div style="margin: 0px;">
<span>&nbsp;</span>Christian F. Beckmann</div><div style="margin: 0px;"><span>&nbsp;</span>Oxford University Centre for Functional</div><div style="margin: 0px;"><span>&nbsp;</span>Magnetic Resonance Imaging of the Brain,</div><div style="margin: 0px;">
<span>&nbsp;</span>John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK</div><div style="margin: 0px;"><span>&nbsp;</span>Email: <a href="mailto:[log in to unmask]" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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<span>&nbsp;</span>Phone: +44(0)1865 222551 Fax: +44(0)1865 222717</div> </blockquote></div><br></span></div></div>
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