<p dir="ltr">Thank you very much, I'll try these methods tomorrow. </p>
<p dir="ltr">Balázs </p>
<div class="gmail_quote">2013.08.07. 20:01, "Tim Mullen" <<a href="mailto:mullen.tim@gmail.com">mullen.tim@gmail.com</a>> ezt írta:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>Hi Balazs,</div><div><br></div><div>First, just to be clear, you pruned the set of components using pop_subcomp (which will ensure a consistent dataset with proper dimensions for .icawinv and equal number of dipoles to components)?</div>
<div><br></div><div>If so, I suspect you ran SIFT once before for this dataset before pruning. In this case the pre-processing function would have retrieved the default value for ComponentsToKeep from the currently stored value in EEG.CAT.curComponentNames -- i.e. the last set of components you selected in SIFT before you pruned the dataset. This would explain why the default list of components is set to 1:16. BrainMovie3D uses the list in EEG.CAT.curComponentNames to plot labels at each node location. If the length of this list exceeds the actual number of nodes (components) an error will occur. </div>
<div><br></div><div>However, the fix is simple.</div><div><br></div><div>The cleanest, failsafe, solution is just to remove the 'CAT' field from the EEG structure...</div><div><font face="courier new, monospace" color="#0000ff">EEG = rmfield(EEG,'CAT');</font></div>
<div><font face="courier new, monospace" color="#0000ff">ALLEEG(CURRENTSET) = EEG;</font></div><div>...and then run the SIFT pipeline again. This will clear all SIFT usage history (note this will also clear any previous SIFT result you had). </div>
<div><br></div><div>If you want to preserve your previously calculated results, then you *should* only need to fix the .curComponentNames, and .curComps lists by typing:</div>
<div><font face="courier new, monospace" color="#0000ff">EEG.CAT.curComponentNames = strtrim(cellstr(num2str((1:9)'))');</font></div><div><font face="courier new, monospace" color="#0000ff">EEG.CAT.curComps = 1:9;</font></div>
<div><font face="courier new, monospace" color="#0000ff">ALLEEG(CURRENTSET) = EEG:</font></div><div><br></div><div>The BrainMovie should now work properly.</div><div>
<br></div><div>A tip: in many cases there is automatic "sanity checking" of default options, but in some cases these checks may not be present. So always make sure that default options -- such as the range of components -- match your expectations before proceeding to the next step in processing. In releases of SIFT prior to 1.0b, it's also important not to run pre-processing twice on the same dataset.</div>
<div><br></div><div>Cheers,</div><div>Tim <br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 6, 2013 at 9:20 AM, boglyas <span dir="ltr"><<a href="mailto:kamanbalazs@gmail.com" target="_blank">kamanbalazs@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hy there,</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">I tried to remove components from EEG data set for better results, but I cannot use the 3D brain movie in SIFT after that,because it gives an error "Index exceeds matrix dimensions".</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Basically it was a 61 channel recording with 60 (or 61) components, but I had a data set that was already pruned, it had only 16 components/dipoles. Some of the dipoles from the 16 were not in the cortex, they were deep inside the brain (eg. thalamus), so I decided to remove those in order to have better results later. After removing these components, if i check the plotting in the EEGlab, or the EEG <1x1 struct> in MATLAB, it all says that it has 9 components left.</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">At the same time, if I try to run SIFT, every tool thinks that i have 16 components (and not 9). Even in pre-processing, the default "components to keep" goes like: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16;</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><div style="font-family:arial,sans-serif;font-size:13px">Meanwhile it doesn't give error during the pre-pocessing or the model fitting, and the validation also seems ok. I can visualize the connectivity result in a Time-Frequency grid (and it only plots 9 x 9 figure), but when I try to visualize in BrainMovie3D, it crashes, error messages, and so on.<br>
<br>What should I do, or what did I do wrong?<br><br>Thanks,<br>Balazs</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/8/6 boglyas <span dir="ltr"><<a href="mailto:kamanbalazs@gmail.com" target="_blank">kamanbalazs@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hy there,</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">I tried to remove components from EEG data set for better results, but I cannot use the 3D brain movie in SIFT after that,because it gives an error "Index exceeds matrix dimensions".</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Basically it was a 61 channel recording with 60 (or 61) components, but I had a data set that was already pruned, it had only 16 components/dipoles. Some of the dipoles from the 16 were not in the cortex, they were deep inside the brain (eg. thalamus), so I decided to remove those in order to have better results later. After removing these components, if i check the plotting in the EEGlab, or the EEG <1x1 struct> in MATLAB, it all says that it has 9 components left.</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">At the same time, if I try to run SIFT, every tool thinks that i have 16 components (and not 9). Even in pre-processing, the default "components to keep" goes like: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16;</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><div style="font-family:arial,sans-serif;font-size:13px">Meanwhile it doesn't give error during the pre-pocessing or the model fitting, and the validation also seems ok. I can visualize the connectivity result in a Time-Frequency grid (and it only plots 9 x 9 figure), but when I try to visualize in BrainMovie3D, it crashes, error messages, and so on.<br>
<br>What should I do, or what did I do wrong?<br><br>Thanks,<br>Balazs</div></div>
</div></div></blockquote></div><br></div>
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