My peak_nii tool can be scripted. It saves out the thresholded images. It also saves out the clusters and peaks and subsequently labels all the peaks as well. In the next release, it will also provide the corrected statistics (FWE/FDR) at both the voxel and cluster level.<br>
<br><a href="http://www.martinos.org/~mclaren/Utilities_DGM">http://www.martinos.org/~mclaren/Utilities_DGM</a><br><br clear="all">Best Regards, Donald McLaren<br>=================<br>D.G. McLaren, Ph.D.<br>Postdoctoral Research Fellow, GRECC, Bedford VA<br>
Research Fellow, Department of Neurology, Massachusetts General Hospital and <br>Harvard Medical School<br>Website: <a href="http://www.martinos.org/%7Emclaren" target="_blank">http://www.martinos.org/~mclaren</a><br>Office: (773) 406-2464<br>
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<br><br><div class="gmail_quote">On Tue, Mar 13, 2012 at 11:24 AM, Aaron Oliver-Taylor <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1203%26L%3DSPM%26E%3Dquoted-printable%26P%3D1560464%26B%3D--f46d044268e6e7d99a04bb21d238%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hello,<div><br></div><div>I was wondering if anyone could tell me how to batch/automatically/programatically save the activation maps for each contrast during standard fMRI analysis.  This would manually be achieved by going to the results window, selecting spm.mat, selecting the contrast, clicking save and entering a filename.  I have a batch job which handles all of the other aspects of processing, and is similar to the batch job example in the spm 8 manual.</div>


<div><br></div><div>Many thanks,</div><div><br></div><div>Aaron<br clear="all">__________________________________________<span class="HOEnZb"><font color="#888888"><br>Aaron Oliver-Taylor<br>Ph.D Student<br>The Advanced Magnetic Resonance Imaging Group<br>
Department of Medical Physics and Bioengineering<br>

University College London<br><a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1203%26L%3DSPM%26E%3Dquoted-printable%26P%3D1560464%26B%3D--f46d044268e6e7d99a04bb21d238%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a><br><br>
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