(Sorry, I meant "[NaN NaN NaN NaN NaN NaN]")
----- Original Message -----
From: jnechvat <[log in to unmask]>
To: Elisabeth Rounis <[log in to unmask]>, [log in to unmask]
Sent: Mon, 12 May 2014 08:39:24 -0700 (PDT)
Subject: Re: [SPM] FW: Preprocessing failing at normalisation step
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<span style="font-size:10pt;"><p style="margin-top:0;margin-bottom:0;">Dear Elisabeth,</p><p style="margin-top:0;margin-bottom:0;"> </p><p style="margin-top:0;margin-bottom:0;">You may want to try a larger bounding box or go with your native bounding space by using "[Na Na Na Na Na Na]" for the bounding box and see how that turns out.</p><p style="margin-top:0;margin-bottom:0;"> </p><p style="margin-top:0;margin-bottom:0;">Cheers,</p><p style="margin-top:0;margin-bottom:0;"> </p><p style="margin-top:0;margin-bottom:0;">- Jordan Nechvatal </p><br><br>------ Original message ------<br><b>From: </b>Elisabeth Rounis<br><b>Date: </b>5/12/2014 8:14 AM<br><b>To: </b>[log in to unmask];<br><b>Subject:</b>[SPM] FW: Preprocessing failing at normalisation step<br><br>
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<div style="font-family: Times New Roman; color: #000000; font-size: 16px">Dear All,<br>
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I'm analysing a very old dataset and am unable to get past the normalisation step for the following reason (see image below).
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I have converted my functional dataset into 4D.nii images and using these. Everything runs smoothly using batch scripts from spm8. At the normalisation step I am using the spm EPI template (have also tried T1, and EPI resliced) as I do not have all of my original dataset's structural images. The problem is that I am getting this odd appearance in some of the participants' scans (attached - with the dorsal part of the brain missing from the image, despite being there in the raw data).
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<img src="cid:NormaliseFailedrsmall.jpg@M1647543075U69186937"><br>
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<p>I'm inserting my batch script below in which I have tried changing some of the writing options (interpolation /size of voxels included etc) with no success.</p>
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<p>I'd be most grateful for your advice on how to solve this.</p>
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<p>Best wishes,</p>
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Elisabeth</p>
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<p>Dr Elisabeth Rounis</p>
<p>Clinical Lecturer in Neurology</p>
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<p>BATCH:</p>
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<p>%Normalisation<br>
clear matlabbatch;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.source = {[d filesep f '_prepro' ext ',1']};<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.wtsrc = '';<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.resample = {<br>
[d filesep f '_prepro' ext]<br>
};<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.template = {[spm_dir filesep 'templates' filesep 'rEPI.nii,1']};<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.weight = '';<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 8;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smoref = 0;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.regtype = 'mni';<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.cutoff = 25;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.nits = 16;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = 1;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.preserve = 0;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.bb = [-88 -122 -80<br>
88 86 95];<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.vox = [3 3 3];<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.interp = 4;<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.wrap = [0 0 0];<br>
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';<br>
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spm_jobman('run',matlabbatch);<br>
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Jordan M. Nechvatal, Ph.D.
Postdoctoral Fellow
VA Palo Alto Health Care System and
Stanford Psychiatry and Behavioral Sciences
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War Related Illness and Injury Study Center (WRIISC)
VA Palo Alto Health Care System
3801 Miranda Ave
Mail Code 151Y
Palo Alto, CA 94304-1290
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