Hello Irvin,<br><br>Your ROI <i>intensity </i>values should not be more than 178 if you have 178 ROIs. That said I think there are some things in conmap that I don't fully understand.<br><br><div class="gmail_quote">On Tue, Oct 11, 2011 at 5:20 AM, Irvin Teh <span dir="ltr"><<a href="mailto:medv820@nus.edu.sg">medv820@nus.edu.sg</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Forgot to mention, we're on Camino R1010 running on 64-bit Linux with Sun Java ver 1.6.0_27.<br>
<br>
Thanks.<br>
<br>
________________________________________<br>
From: Irvin Teh<br>
Sent: Tuesday, October 11, 2011 5:28 PM<br>
To: <a href="mailto:camino-users@www.nitrc.org">camino-users@www.nitrc.org</a><br>
Subject: Trouble getting conmap to work<br>
<div><div></div><div class="h5"><br>
Hello all,<br>
<br>
I'm trying to setup a pipeline for connectivity mapping using Camino & Freesurfer and followed the instructions here.<br>
<a href="http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Tutorials.ConnectivityMapping" target="_blank">http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Tutorials.ConnectivityMapping</a><br>
<br>
There seems to be no problem (eg. the wm_undersampled.nii.gz looks correctly segmented and downsampled to the resolution of the diffusion images) till I get to the final conmap step whereby I get the error message below.<br>
I've tried with to troubleshoot by using slightly different ROIs of the whole brain (created using different intensity filters in Mricron), and also tried using running conmap with a track file created using PICo, but repeatedly faced the same error.<br>
<br>
<br>
[irvin@server dti68]$ conmap -inputfile brain_track.Bdouble -roifile wm_undersampled.nii.gz<br>
Exception in thread "main" java.lang.IllegalArgumentException: ROI index out of bounds. This ROI contains 178 regions<br>
at tractography.FreeFormROI.getRegion(FreeFormROI.java:345)<br>
at apps.ConnectivityMapping.main(ConnectivityMapping.java:238)<br>
[irvin@server dti68]$<br>
<br>
<br>
Could it be due to imperfect anatomical segmentation, or incorrect ROI selection?<br>
Would be very grateful for any suggestions and fixes, thanks!<br>
<br>
Irvin<br>
Singapore<br>
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</div></div></blockquote></div><br>