<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Beth,<div><br></div><div>Sorry for the bug. This is indeed a known problem which has found its way into recent versions. We are working on a permanent fix. I just checked in a temporary patch which should be available for download as of tonight (CET), or can be checked out from google-code soon. Alternatively, you could replace the recent version of ft_prepare_singleshell with and old version which works for you. This should affect anything else.</div><div><br></div><div>Thanks for reporting this and sorry for the inconvenience.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Jan-Mathijs</div><div><br></div><div><br><div><div>On Sep 16, 2011, at 11:31 PM, Belluscio, Beth (NIH/NINDS) [E] wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi fellow fieldtrip users-<br> I am currently using fieldtrip version 20110913 and have encountered a problem that wasn't there before. After reslicing and segmenting my mri data (which was realigned to CTF format), I segmented the data using cfg.output = {'skullstrip' 'brain'} and seg = ft_volumesegment(cfg, mri). I saved the resulting seg matrix. <br> Then, when I run ft_prepare_singleshell to generate my volumetric model (vol):<br><br>cfg = [];<br>vol = ft_prepare_singleshell(cfg, seg)<br><br>I get the following messages and error.<br><br><br><br>not downsampling anatomy<br>not downsampling brain<br>the call to "ft_volumedownsample" took 0 seconds and an estimated 0 MB<br>using the segmentation approach<br>Warning: adding /home/belluscb/nindsip/matlab/fieldtrip-20110913/external/spm8 toolbox to your<br>Matlab path <br>using the segmented MRI<br>??? Reference to non-existent field 'seg'.<br><br>Error in ==> prepare_mesh_segmentation at 63<br>[mrix, mriy, mriz] = ndgrid(1:size(mri.seg,1), 1:size(mri.seg,2), 1:size(mri.seg,3));<br><br>Error in ==> ft_prepare_mesh at 124<br> bnd = prepare_mesh_segmentation(cfg, mri);<br><br>Error in ==> ft_prepare_singleshell at 89<br> vol.bnd = ft_prepare_mesh(cfg, mri);<br><br><br><br><br>If I use an old version of fieldtrip (20100505) that I had, and run the same command cfg = [];<br>vol = ft_prepare_singleshell(cfg, seg) on the same seg matrix, it runs without a problem. <br><br>I am not skilled enough (yet) at reading code to figure out what is not working with the recent version of fieldtrip. <br>Can someone please assist me?<br><br>Thanks!<br>Beth.<br><br><br>Beth Belluscio MD-PhD<br>Clinical Fellow<br>Human Motor Control Section<br>NINDS, NIH<br>301-402-3495<br><br><br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div></div></span></div></span></div></span></span>
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