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

[Ian Malone]

Hi,

This is the issue I was talking about in my reply to Gavin Winston (Re: 
Connectivity Mapping with Camino). You're right: the FreeFormROI class 
assumes that ROI are sequential (they can actually start at a whole 
number other than 1, so can range [m, m+N-1] for N ROI). The problem is 
that if trying to use FreeSurfer as described for region labels you do 
not have sequential ROI indices, for example 1xxx is used for one side 
of the cortex and 2xxx for the other hemisphere. The patch in my other 
email fixes (I think) the mapping that FreeFormROI uses between indices 
and its internal ROI list (so far as conmap is concerned) to remove this 
requirement. However I should warn I haven't tested extensively against 
the other utilities that use ROIs (e.g. seeds and waypoints for 
tractography).

Ian

On 11/10/11 20:32, Nagesh Adluru wrote:
> 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 
> <mailto: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 <mailto: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
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