<DIV>Dear Lilla </DIV><DIV> </DIV><DIV>thank you very much for your response. Swapping lpa and rpa does the trick.
<DIV>Now my brain looks much better. ;-)</DIV></DIV><DIV>The extra zpoint does not really help and I had it already implemented in my initial code.</DIV><DIV> </DIV><DIV>All the best </DIV><DIV>Markus </DIV><DIV> </DIV><DIV> </DIV><DIV> </DIV><SPAN>Am 09.10.12, schrieb Lilla.Magyari@mpi.nl:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:1173.80.101.124.103.1349804384.squirrel@80.101.124.103 type="cite">
<DIV class="mimepart text plain">hi Markus,<br /><br />When you use the ft_volumerealign function it doesn't necessarily will<br />show the right side of the brain on the right side of the image.<br />Orientation of the image depends on the coordinate system of the mri you<br />read in.<br /><br /> I tried also align the template mri to the fiducials, and I got the same<br />problem as you (z+ going to inferior in the aligned volume), but when I<br />switched the lpa with the rpa the orientation was fine. So, my conclusion<br />is that the right side shows up on the left of the image when you use<br />ft_volumerealign. Therefore, you have to mark the lpa on the right side<br />of the image and the rpa on the left side of the image. But there is also<br />another option implemented exactly because of this left/right flipping:<br />You can determine also a "z-point" (by pressing z in the image) that can<br />be anywhere at the top of the head. Then, the function will give you the<br />right alignment even if you did not determine the lpa and rpa on the<br />right side of the brain.<br />For this, you just have to do this:<br />cfg.fiducial.zpoint = [i j k], position of zpoint<br />when you also determine the positions for the nasion, lpa and rpa.<br /><br />And one more remark: I do not know if you have realized this yourself, and<br />I have just misunderstood your email: When you call ft_volumerealign in<br />interactive mode like this:<br /><br />cfg=[];<br />cfg.method='interactive';<br />mri_realigned=ft_volumerealign(cfg,mri);<br /><br />And you press the keys r/l/n/z at the right places in the volume (and quit<br />with q), the output (mri_realigned) will be the already aligned volume,<br />you do not need to call ft_volumerealign again with method 'fiducials'.<br /><br />Best,<br />Lilla<br /><br />> Dear list<br />><br />> when running ft_volumerealign with the spm template MRI in the interactive<br />> mode, I get something like: <br />><br />><br />> ===========================================================================voxel<br />> 838065, indices [46 54 85], location [0.0 -20.0 96.0] mm<br />> nas_voxel = [46.000000 104.000000 11.000000], nas_head = [0.000000<br />> 80.000000 -52.000000]<br />> lpa_voxel = [5.000000 54.000000 11.000000], lpa_head = [82.000000<br />> -20.000000 -52.000000]<br />> rpa_voxel = [85.000000 54.000000 11.000000], rpa_head = [-78.000000<br />> -20.000000 -52.000000]<br />> xzpoint_voxel = [46.000000 54.000000 85.000000], xzpoint_head = [0.000000<br />> -20.000000 96.000000]<br />> the call to "ft_volumerealign" took 136 seconds and an estimated 39 MB<br />><br />><br />> Now I would like to rerun it in the fiducial mode, using the above<br />> information.<br />> According to help, I need to do this:<br />><br />><br />> For realigning to the fiducials, you should specify the position of<br />> the fiducials in voxel indices.<br />> cfg.fiducial.nas = [i j k], position of nasion<br />> cfg.fiducial.lpa = [i j k], position of LPA<br />> cfg.fiducial.rpa = [i j k], position of RPA<br />><br />><br />><br />> I used the voxel indices (code below), but ended up with the MRI<br />> upside-down (see attached picture).<br />> Trying the landmark mode was also without success.<br />><br />><br />> Am I doing something silly here?<br />><br />><br />><br />> Thanks in advance<br />> Markus<br />><br />><br />><br />><br />> % Load SPM8 T1 template <br />><br />><br />> template = '/Documents/MATLAB/spm8/templates/T1.nii';<br />><br />><br />> template_mri = ft_read_mri(template);<br />><br />><br />> disp(template_mri)<br />><br />><br />> <br />><br />><br />> % 2. Realign the coordinate system<br />><br />><br />> cfg = []; <br />><br />><br />> cfg.method = 'fiducial'; % 'interactive';<br />><br />><br />> cfg.fiducial.nas = [46 104 11];<br />><br />><br />> cfg.fiducial.lpa = [5 54 11];<br />><br />><br />> cfg.fiducial.rpa = [85 54 12];<br />><br />><br />> cfg.fiducial.zpoint= [46 54 85];<br />><br />><br />> cfg.coordsys = 'ctf';<br />><br />><br />> template_mri_realigned = ft_volumerealign(cfg, template_mri);<br />><br />><br />><br />><br />><br />><br />> <br />><br />><br />> % 3. Check the coordinate system<br />><br />><br />> cfg = [];<br />><br />><br />> cfg.interactive = 'yes';<br />><br />><br />> template_mri_checked = ft_determine_coordsys(template_mri_realigned);<br />><br />><br />> _______________________________________________<br />> fieldtrip mailing list<br />> fieldtrip@donders.ru.nl<br />> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target=l >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</A><br /><br /><br />_______________________________________________<br />fieldtrip mailing list<br />fieldtrip@donders.ru.nl<br /><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target=l >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</A><br /></DIV></BLOCKQUOTE>
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