[Camino-users] RE: Trouble getting conmap to work

[Irvin Teh]

Forgot to mention, we're on Camino R1010 running on 64-bit Linux with Sun Java ver 1.6.0_27. 

Thanks.

________________________________________
From: Irvin Teh
Sent: Tuesday, October 11, 2011 5:28 PM
To: camino-users at www.nitrc.org
Subject: Trouble getting conmap to work

Hello all,

I'm trying to setup a pipeline for connectivity mapping using Camino & Freesurfer and followed the instructions here.
http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Tutorials.ConnectivityMapping

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.
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.


[irvin at server dti68]$ conmap -inputfile brain_track.Bdouble -roifile wm_undersampled.nii.gz
Exception in thread "main" java.lang.IllegalArgumentException: ROI index out of bounds. This ROI contains 178 regions
        at tractography.FreeFormROI.getRegion(FreeFormROI.java:345)
        at apps.ConnectivityMapping.main(ConnectivityMapping.java:238)
[irvin at server dti68]$


Could it be due to imperfect anatomical segmentation, or incorrect ROI selection?
Would be very grateful for any suggestions and fixes, thanks!

Irvin
Singapore