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Hi JT,
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<div class="">You’d first need to ensure that ‘mri_realigned’ is correctly realigned. Since the resliced MRI image is upside down, this suggests that the coordinate system information that is used by FieldTrip (i.e. the mri_realigned.coordsys -> it looks like
‘ctf’ ) is not compatible with what’s in the data.</div>
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<div class="">If you search the documentation for coordinate systems I think there should be plenty of information that will get you on the road.</div>
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<div class="">Best wishes,</div>
<div class="">JM</div>
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<div class="">On 30 Mar 2022, at 05:45, JT Galla via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<span style="caret-color: rgb(0, 0, 0);" class="">Hello!</span>
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<div class="" style="caret-color: rgb(0, 0, 0);">I am trying to reslice my MRI image for the purposes of EEG Source Reconstruction using the following code:</div>
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<pre class="highlight" style="box-sizing: border-box; font-family: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; font-size: 13.2px; margin-top: 0px; margin-bottom: 0px; overflow: auto; color: rgb(33, 37, 41); background-color: rgb(240, 240, 240); font-variant-ligatures: normal; orphans: 2; widows: 2; text-decoration-thickness: initial;"><code class="" style="box-sizing: border-box; font-family: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; font-size: inherit; color: inherit; word-break: normal;"><span class="n" style="box-sizing: border-box;">cfg</span> <span class="o" style="box-sizing: border-box; color: rgb(102, 102, 102);">=</span> <span class="p" style="box-sizing: border-box;">[];</span>
<span class="n" style="box-sizing: border-box;">mri_resliced</span> <span class="o" style="box-sizing: border-box; color: rgb(102, 102, 102);">=</span> <span class="n" style="box-sizing: border-box;">ft_volumereslice</span><span class="p" style="box-sizing: border-box;">(</span><span class="n" style="box-sizing: border-box;">cfg</span><span class="p" style="box-sizing: border-box;">,</span> <span class="n" style="box-sizing: border-box;">mri_realigned</span><span class="p" style="box-sizing: border-box;">);</span></code></pre>
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<div class="" style="caret-color: rgb(0, 0, 0);">However, when I go to view the output of this command I see that the reslice method has completely removed axial slices and has inverted coronal and sagittal slices. This is, of course, ruining subsequent head
model generations so any guidance that could be provided on why this might be happening and how to fix it would be greatly appreciated. Attached is a screenshot of what my replaced image looks like.</div>
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<div class="" style="caret-color: rgb(0, 0, 0);"><span id="cid:DF98F78D-F6AE-4658-AC9E-D5A8944051B6"><Screen Shot 2022-03-29 at 11.38.25 PM.png></span></div>
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<span style="caret-color: rgb(0, 0, 0);" class="">Thank you for your time!</span><br class="" style="caret-color: rgb(0, 0, 0);">
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<b class="">JT Galla</b>
<div class="">Duke University c/o ’23</div>
<div class="">Neuroscience Major, Chemistry & Computational Biology Minor</div>
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