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</div><div id="yui_3_16_0_1_1444814207981_5362" class="">Dear community,</div><div id="yui_3_16_0_1_1444814207981_5409" class=""><br></div>
<div id="yui_3_16_0_1_1444814207981_5364" class="">I performed nonlinear normalizations and plotted the
resulting MRIs. I noticed the normalized MRIs had unwanted distortions, and were
clearly different from the normalized MRIs obtained directly in SPM. <br></div><div id="yui_3_16_0_1_1444814207981_5410" class=""><br></div>
<div id="yui_3_16_0_1_1444814207981_5366" class="">I noticed the default parameters (flags) in Fieldtrip’s spm_normalise()
are different from SPM’s spm_normalise(). In Fieldtrip, the amount of regularization
is too low (= 0.1, line 144 in spm_normalise) compared with SPM’s
default (=1). <br></div><div id="yui_3_16_0_1_1444814207981_5411" class=""><br></div>
<div id="yui_3_16_0_1_1444814207981_5368" class="">This may be a problem not only for normalization but when
computing MNI-aligned individual grids following the tutorial (“Create
MNI-aligned grids in individual”) because there is an implicit normalization
step.</div><div id="yui_3_16_0_1_1444814207981_5412" class=""><br></div>
<div id="yui_3_16_0_1_1444814207981_5370" class="">Possible solutions: <br></div><div id="yui_3_16_0_1_1444814207981_5423" class=""><br></div>
<div id="yui_3_16_0_1_1444814207981_5372" class="" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><span class="" id="yui_3_16_0_1_1444814207981_5374" style="mso-ascii-font-family:Calibri;mso-fareast-font-family:Calibri;mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri"><span class="" id="yui_3_16_0_1_1444814207981_5376" style="mso-list:Ignore">-<span class="" id="yui_3_16_0_1_1444814207981_5378" style="font:7.0pt "Times New Roman"">
</span></span></span>Call/substitute Fieldtrip’s spm_normalise() by
SPM’s function or change Fieldtrip’s default flags values.</div>
<div id="yui_3_16_0_1_1444814207981_5380" class="" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><span class="" id="yui_3_16_0_1_1444814207981_5382" style="mso-ascii-font-family:Calibri;mso-fareast-font-family:Calibri;mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri"><span class="" id="yui_3_16_0_1_1444814207981_5384" style="mso-list:Ignore">-<span class="" id="yui_3_16_0_1_1444814207981_5386" style="font:7.0pt "Times New Roman"">
</span></span></span>Perform the normalization outside in SPM and
provide the cfg.spmparams.flags. However, there is a bug in ft_volumenormalise()
using that option. I think it may be because the flags are not passed to spm_normalise
(line 239). As a fix, I have modified the function with the lines below. But
surely there is a more direct way to avoid the problem.</div>
<div id="yui_3_16_0_1_1444814207981_5388" class="" style="margin-top:0in;margin-right:0in;margin-bottom:0in;margin-left:.75in;margin-bottom:.0001pt;line-height:normal">VF<span class="" id="yui_3_16_0_1_1444814207981_5390" style="mso-spacerun:yes"> </span>=
spm_vol([cfg.intermediatename,'_anatomy.img']);</div>
<div id="yui_3_16_0_1_1444814207981_5392" class="" style="margin-top:0in;margin-right:0in;margin-bottom:0in;margin-left:.75in;margin-bottom:.0001pt;line-height:normal">params<span class="" id="yui_3_16_0_1_1444814207981_5394" style="mso-spacerun:yes"> </span>=
spm_normalise(VG,VF,[],[],[],cfg.spmparams.flags);</div>
<div id="yui_3_16_0_1_1444814207981_5396" class="" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"> </div><div id="yui_3_16_0_1_1444814207981_5400" class="" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal">I wish this report helps. </div>
<div id="yui_3_16_0_1_1444814207981_5402" class="" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"> </div>
<div id="yui_3_16_0_1_1444814207981_5404" class="" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal">Best regards,</div>
<div id="yui_3_16_0_1_1444814207981_5406" class="" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal">Mait<span class="" id="yui_3_16_0_1_1444814207981_5408" style="mso-ansi-language:ES" lang="ES">é</span></div><div dir="ltr">
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