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<p dir="auto">Oula,</p>
<p dir="auto">Thanks for your reply, sorry for my delayed response.</p>
<p dir="auto">So we have a nifti file where simnibs gives "the qform and sform of do not match". This file has a <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">qform_code</code> of <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">NIFTI_XFORM_UNKNOWN</code> (0), and an <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">sform_code</code> of <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">NIFTI_XFORM_SCANNER_ANAT</code> (1).</p>
<p dir="auto">Usually, when you encounter NIFTI_XFORM_UNKNOWN in either the sform or qform, you should ignore it.</p>
<p dir="auto">The <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">--forceqform</code> option is not helpful here because it's the qform that is <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">NIFTI_XFORM_UNKNOWN</code>. There appears to be no way to make SimNIBS use the sform.</p>
<p dir="auto">I would suggest that:</p>
<ol>
<li>SimNIBS should look at the <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">[qs]form_code</code> value and ignore any <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">NIFTI_XFORM_UNKNOWN</code>. If you are then left with only one, there's no need to even check if they match.</li>
</ol>
<p dir="auto">and/or</p>
<ol start="2">
<li>add a <code style="margin: 0 0; padding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">--forcesform</code> option</li>
</ol>
<p dir="auto">Cheers,</p>
<p dir="auto">Sean</p>
<p dir="auto">On 6 Jan 2023, at 9:03, Oula Puonti wrote:</p>
</div><div class="plaintext" style="white-space: normal;"><blockquote style="margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777777; color: #777777;"><p dir="auto">Hi Sean,</p>
<p dir="auto">Techincally they don't have to match, but it that seems different nifti
<br>
readers sometimes use one and sometimes the other, which can cause
<br>
problems. We decided it's best to explicitly "force" the qform to keep
<br>
everything consistent within charm. As the qform should store the
<br>
transformation from voxels to scanner coordinates, i.e., no shears, we
<br>
decided to go with that.</p>
<p dir="auto">Best,
<br>
Oula</p>
<p dir="auto">On Thu, 2023-01-05 at 19:14 -0500, Sean McBride wrote:</p>
<blockquote style="margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777777; border-left-color: #999999; color: #999999;"><p dir="auto">Hi all,</p>
<p dir="auto">I notice here:</p>
<p dir="auto"><a href="https://github.com/simnibs/simnibs/blob/8fe54625a6d5b523456a4bf2efb24b890ee05fdb/simnibs/segmentation/charm_main.py#L661" style="color: #999999;">https://github.com/simnibs/simnibs/blob/8fe54625a6d5b523456a4bf2efb24b890ee05fdb/simnibs/segmentation/charm_main.py#L661</a></p>
<p dir="auto">The error message "The qform and sform of do not match. Please run
<br>
charm with the --forceqform option".</p>
<p dir="auto">Why are the qform and sform expected/required to match?</p>
<p dir="auto">Also: there is a stray "of" in that error message text.</p>
<p dir="auto">Thanks,</p>
<p dir="auto">Sean
<br>
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<blockquote style="margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777777; color: #777777;">
<blockquote style="margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777777; border-left-color: #999999; color: #999999;">
<p dir="auto"><a href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss" style="color: #999999;">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a></p>
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