<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Erik,<div class=""><br class=""></div><div class="">It sounds like this is an ANTs-specific issue. If you have any further </div><div class="">questions, I would recommend asking at that forum.</div><div class=""><br class=""></div><div class=""><a href="https://github.com/stnava/ANTs/issues" class="">https://github.com/stnava/ANTs/issues</a></div><div class=""><br class=""></div><div class="">The command line interface that you reference is ANTs-specific and</div><div class="">should have brackets around it e.g.,</div><div class=""><br class=""></div><div class="">-c [50x50x50x50,0.0001]</div><div class=""><br class=""></div><div class="">I don’t know about the rescale problem. Does it happen on any image </div><div class="">or just that specific T2?</div><div class=""><br class=""></div><div class="">Anyway, meet me over on the ANTs forum if you have further questions/</div><div class="">issues.</div><div class=""><br class=""></div><div class="">Nick</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 20, 2015, at 12:04 PM, Erik Olsson <<a href="mailto:Erik.Olsson@neuro.gu.se" class="">Erik.Olsson@neuro.gu.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; direction: ltr; font-family: Tahoma; font-size: 10pt;" class=""><div style="font-family: 'Times New Roman'; font-size: 16px;" class=""><div id="divRpF486137" style="direction: ltr;" class=""><br class="Apple-interchange-newline"><br class=""></div><div class=""></div><div class=""><div style="direction: ltr; font-family: Tahoma; font-size: 10pt;" class="">Hi,<br class=""><br class="">I have recently started to use N4 as a command line installation and the bias field correction works great in general.<span class="Apple-converted-space"> </span><br class=""><br class="">I am trying to figure out how to configure the flags for best performance on our T2 MRI images and when trying the rescale intensities I get the error message "segmentation fault 11" for both options ( -r 1 as well as -r 0). I also have a problem with the convergence flag -c, all works fine when I leave this flag out but when trying for example -c 50x50x50x50,0.0001 it stops after 1 iteration (Current level = 1<br class=""> Iteration 1 (of 50). Current convergence value = 0.000816419 (threshold = 0.001). It does not seem like my specification of the threshold is read but the default value is used. Do you have an example of a typical setting for the -c flag other than the default values?<br class=""><br class="">best regards<br class="">Erik<br class=""><div class=""><br class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><font size="2" class=""><span style="font-size: 10pt;" class=""><font size="1" class="">Erik Olsson<br class="">PhD</font><span class="Apple-converted-space"> </span><font size="1" class=""><br class=""><br class="">Institute of Psychiatry and Neurochemistry</font><span class="Apple-converted-space"> </span><font size="1" class=""><br class="">Department of Neuroscience & physiology<br class="">The Sahlgrenska academy<br class="">Gothenburg University</font><br class=""><font size="1" class="">Sweden</font></span></font></div></div></div></div></div></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; 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