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

[Nagesh Adluru]

Hello Irvin,

Your ROI *intensity *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.

On Tue, Oct 11, 2011 at 5:20 AM, Irvin Teh <medv820 at nus.edu.sg> wrote:

> 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
> _______________________________________________
> Camino-users mailing list
> Camino-users at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/camino-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/camino-users/attachments/20111011/7d8802f1/attachment.html