<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
{mso-style-priority:1;
margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNoSpacing"><span style="font-size:10.0pt">Dear FieldTrippers:<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">Wanted to follow-up on a discussion regarding poor normalization, and specifically, an inward bias, when warping template (MNI space) source positions to individual subject space. This is a useful approach
to normalization, facilitating group-level analyses and anatomical referencing, though meaningful inference is predicated on having accurate normalization/warps. At least one relevant discussion thread, here:
<a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009111.html">
https://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009111.html</a>, though I don’t see resolution.<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">In my lab, we’re consistently observing an ‘inward bias’ when warping template source positions to individual space (see attached). Superficial sources seem to shift excessively deep, particularly at the
dorsum. Has anyone adjusted the normalization parameters or implemented alternate warping procedures to generate accurate transformations? I will note that default normalization of individual MRI to template works well in both SPM8 and SPM12 (confirmed with
checkreg).<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">I believe ft_preparesourcemodel calls upon ft_volumenormalize and spm routines to generate the deformation field. We’ve tried adjusted the warping regularization parameters in ft_volumenormalise both up
and down by an order of magnitude, but did not see any real improvement. Suggestions?<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">Below, I’m sharing a short script used to visualize the relative performance of normalization with SPM8, SPM12 linear-only, and SPM12 nonlinear approaches, as implemented in FieldTrip. I used 346 source
positions, located approximately 3.6mm deep to the template brain surface (roughly corresponding to mid-sulcal depth across the cerebral mantle; attached).<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">%% start<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">clear all; close all;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">restoredefaultpath; addpath('PATH TO CURRENT FIELDTRIP DISTRO');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">ft_defaults;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">vs_pos = []; % n×3, coords of interest, MNI space; see attached text, if interested in replicating<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">template_mri = ft_read_mri('PATH TO SPM12\spm12\canonical\avg152T1.nii');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">template_mri.coordsys = 'spm'; % ft_volumesegment needs coordsys of the template volume<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.output = {'brain', 'skull', 'scalp'};<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm12';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmmethod = 'new';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">template_seg = ft_volumesegment(cfg, template_mri);
<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.method = 'singleshell';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">template_headmodel = ft_prepare_headmodel(cfg, template_seg);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.pos = vs_pos;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm12';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmmethod = 'new';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.headmodel = template_headmodel;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">template_grid = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">% evaluate dipole positions relative to modeled brain<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">figure; ft_plot_vol(template_headmodel, 'facecolor', 'cortex', 'edgecolor', 'none'); alpha 0.5; camlight; hold on; ft_plot_mesh(template_grid.pos);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">% generate the individual headmodel; warp source positions from template to subject space<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">T1 = 'PATH TO SUBJECT T1'; % high-quality 3D-T1, 1mm isotropic, here<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_mri = ft_read_mri(T1, 'dataformat', 'nifti_spm');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_mri.coordsys = 'spm';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.output = {'brain', 'skull', 'scalp'};<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm12';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmmethod = 'new';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_segmented_mri = ft_volumesegment(cfg, individual_mri);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.method = 'singleshell';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_headmodel = ft_prepare_headmodel(cfg, individual_segmented_mri);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_headmodel = ft_convert_units(individual_headmodel, 'cm');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.warpmni = 'yes';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.template = template_grid;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.nonlinear = 'yes';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm8';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.mri = individual_mri;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_grid_spm8 = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.warpmni = 'yes';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.template = template_grid;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.nonlinear = 'no';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm12';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmmethod = 'new';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.mri = individual_mri;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_grid_spm12_linear = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg = [];<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.warpmni = 'yes';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.template = template_grid;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.grid.nonlinear = 'yes';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmversion = 'spm12';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.spmmethod = 'old';<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">cfg.mri = individual_mri;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">individual_grid_spm12_nonlinear = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">figure;<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">subplot(2, 2, 1); ft_plot_vol(template_headmodel, 'facecolor', 'cortex', 'edgecolor', 'none'); alpha 0.25; camlight; hold on; ft_plot_mesh(template_grid.pos, 'vertexcolor', 'red'); title('template');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">subplot(2, 2, 2); ft_plot_vol(individual_headmodel, 'facecolor', 'cortex', 'edgecolor', 'none'); alpha 0.25; camlight; hold on; ft_plot_mesh(individual_grid_spm8.pos); title('individual spm8 nonlinear');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">subplot(2, 2, 3); ft_plot_vol(individual_headmodel, 'facecolor', 'cortex', 'edgecolor', 'none'); alpha 0.25; camlight; hold on; ft_plot_mesh(individual_grid_spm12_linear.pos); title('individual spm12 linear
only');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">subplot(2, 2, 4); ft_plot_vol(individual_headmodel, 'facecolor', 'cortex', 'edgecolor', 'none'); alpha 0.25; camlight; hold on; ft_plot_mesh(individual_grid_spm12_nonlinear.pos); title('individual spm12
nonlinear');<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">%% end<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-size:10.0pt">In advance, thanks for your help.</span><span style="color:#0D0D0D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#0D0D0D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#404040">Darren S. Kadis, PhD<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Assistant Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Co-Director, MEG Core<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Division of Neurology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Pediatric Neuroimaging Research Consortium<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Cincinnati Children's Hospital Medical Center<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">MLC 15008, 3333 Burnet Avenue<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Cincinnati, OH 45229-3026<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">Neurology and Neuroscience Graduate Program<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">College of Medicine, Department of Pediatrics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#404040">University of Cincinnati<o:p></o:p></span></p>
</div>
</body>
</html>