<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:14px"><div id="yui_3_16_0_1_1439998086989_51359">Hi, Camino users</div><div id="yui_3_16_0_1_1439998086989_51359"><br></div><div id="yui_3_16_0_1_1439998086989_51359">I have encountered an issue using camino command 'conmat' and would appreciate your help on it:</div><div id="yui_3_16_0_1_1439998086989_51359"><br></div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr">I generated a brain atlas covering cortical and subcortical regions with values ranging from 33 to 122. The intensity values in the atlas are not continuos. When I tried to get the connectivity matrix, I got the follow error:</div><div id="yui_3_16_0_1_1439998086989_51359"><br></div><div id="yui_3_16_0_1_1439998086989_51359" class="" dir="ltr">my command: cat BedpostxTracksV2i5ct60ci4.Bfloat | conmat -targetfile brain_atlas.nii.gz -outputroot ./conmat_</div><div id="yui_3_16_0_1_1439998086989_51359" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" class="">Error:</div><div id="yui_3_16_0_1_1439998086989_51359" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" class="">Aug 19, 2015 12:12:48 PM tractography.TractSource <init></div><div id="yui_3_16_0_1_1439998086989_51359" class="">INFO: reading data from standard input</div><div id="yui_3_16_0_1_1439998086989_51359" class="">Exception in thread "main" java.lang.IllegalArgumentException: Illegal index -1 is < 0 or exceeds index of last point</div><div id="yui_3_16_0_1_1439998086989_51359" class=""> at tractography.Tract.pathLengthFromSeed(Tract.java:277)</div><div id="yui_3_16_0_1_1439998086989_51359" class=""> at tractography.StreamlineConnectivityGraph.processTract(StreamlineConnectivityGraph.java:281)</div><div id="yui_3_16_0_1_1439998086989_51359" class=""> at tractography.StreamlineConnectivityGraph.processTracts(StreamlineConnectivityGraph.java:201)</div><div id="yui_3_16_0_1_1439998086989_51359" class=""> at apps.ConnectivityMatrix.writeConnectivityGraph(ConnectivityMatrix.java:367)</div><div id="yui_3_16_0_1_1439998086989_51359" class=""> at apps.ConnectivityMatrix.execute(ConnectivityMatrix.java:138)</div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class=""> at apps.EntryPoint.main(EntryPoint.java:287)</div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class="">However, when I manually drew a few cortical ROIs in a brain mask and used 'conmat', I got sensible results. So, the problem is definitely somewhere in the brain atlas I used. So far, I have tried the following:</div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class="">(1) I loaded the brain atlas to matlab and saved it to nifti again using "save_avw", I got the program run, but all values are zero. The main difference in the matalab-saved brain atlas is that matlab "save_avw" will not save coordinate information in the brain atlas (will give a eye mat). So I assume the issue is related to the coordinates. Because there is no coordinate information in matlab-written brain atlas, there might be a mismatch in space between tracts and mask and therefore generated all zero results. </div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class="">(2): discontinued intensity values in the brain atlas is not an issue. </div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class=""><br></div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class="">Many thanks!</div><div id="yui_3_16_0_1_1439998086989_51359" dir="ltr" class="">Longchuan</div></div></body></html>