[Neurodebian-users] fslview atlases problem

[Yaroslav Halchenko]

On Wed, 01 Aug 2012, Hidayath Ansari wrote:
>      � grep atlas /tmp/strace-output.txt
>    $ grep atlas /tmp/strace-output.txt
>    30625 getcwd("/usr/share/data/jhu-dti-whitematter-atlas/JHU", 2048) = 46
>    30625 open("/usr/share/fsl/4.1/data/atlases", O_RDONLY) = -1 ENOENT (No
>    such file or directory)
>    So it's opening correctly?

awesome!  Now I got it ;)  the reason is the environment variable FSLDIR
which you have  /usr/share/fsl/4.1/data --- inside the chroot we do not
have fsl installed, thus no this directory (we installed only
fslview)... that is why with this explicit, wrong for the chroot
setup, FSLDIR it fails.  I recommend adding in your
/usr/local/bin/fslview explicit correct FSLDIR for the chroot:

#!/bin/sh
export FSLDIR=/usr/share/fsl
schroot -p -c squeeze /usr/bin/fslview "$@"


please try and report back if that helps

> But when I click on Toolbars -> Atlas Tools,
>    nothing shows up ...
-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik