<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div>Hi Don,<div class=""><br class=""></div><div class="">You can read the fif file mne_make_cor_set made in mrilab and do the coordinate transformation there as you have used to and produce a new fif file where the transformation is in place.</div><div class="">This does not deal with the different coordinate systems between the one derived from the DICOM files and the mgz files, though.</div><div class=""><br class=""></div><div class="">- Matti</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Apr 18, 2016, at 11:31 AM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu" class="">kriegerd@upmc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">This is a follow-on to a previous post to which Jon Houck helpfully suggested using mne_make_cor_set.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am using this to convert .mgz files to .fif .<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I normally start with the original dicom set and convert them to .fif using ELEKTA’s dicom_access.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">But for these MEG data sets, I only have a defaced (via freesurfer) .mgz files.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">In either case I then use the .fif files to do MEG coregistration with ELEKTA’s Mrilab tool.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Using Mrilab is part of my standard pipeline and I would like to stick with that if possible.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">When I convert a standard dicom scan series to fif using ELEKTA’s dicom_access, the .fif is in MR RAS coordinates.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">But a .fif file obtained by conversions from .mgz with mne_make_cor_set appears to be in tkr RAS coordinates instead.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">So the transform matrix that I get when I do the coregistration is: Head<span class="Apple-converted-space"> </span><span style="font-family: Wingdings;" class="">à</span><span class="Apple-converted-space"> </span>tkrRAS rather than Head<span class="Apple-converted-space"> </span><span style="font-family: Wingdings;" class="">à</span><span class="Apple-converted-space"> </span>RAS .<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I tried spoofing mne_make_cor_set with –talairach SomeOtherTransformation but Mrilab doesn’t appear to care.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">In addition, it’s not clear to me what transform to use even if it does work; maybe tkr2scanner .<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Any thoughts would be welcome and thanks.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best - Don<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; 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---------<br class=""><br class="">Matti Hamalainen, Ph.D.<br class="">Athinoula A. Martinos Center for Biomedical Imaging<br class="">Massachusetts General Hospital<br class=""><br class=""><a href="mailto:msh@nmr.mgh.harvard.edu" class="">msh@nmr.mgh.harvard.edu</a><br class="">mhamalainen@partners.org<br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class="">
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