Hello All,
I am trying to run siena for many datasets. To make the processing of these datasets easier, I
wrote a perl script that, in turn, creates a bourne sh script that runs siena. The call to siena_flirt
gives me this error message (as found in report.siena):
/usr/local/fsl4.0.2/bin/siena_flirt: /dev/null: bad number
I think this error occurs is caused by (double?) redirection. When I issue the siena_flirt command
at the command line, I do not get this error. How might I correct or work around this problem
when running siena/siena_flirt from a script?
In the hope of being clearer, my perl script creates bourne sh script 'driver_siena_398.sh' (shown
below). I run driver_siena_398.sh in the background by issuing this command (in tcsh):
% driver_siena_398.sh >& driver_siena_398.88.log &
creating redo_888/report.siena (shown below). I also list, below, the files that exist when
siena_flirt bombs out.
Any help with this unix (redirection?) problem is much appreciated.
Thank you,
- BettyAnn
#==== driver_siena_398.sh ============
#!/bin/sh
# Created Mon Jul 7 18:56:18 2008 by 00_setup.pl
# be sure to use fsl v4.0.2
. $HOME/Development/fsl/siena/fsl4.0.2.sh
# save current working directory
cwd=`pwd`
# cd to dstDir
cd /kki/g1/ba/data/sienaAll
echo
echo "Begin siena dataset_01 at `date`"
siena reference dataset_01 -o redo_888 -B "-f 0.18" >> siena_000.88.log 2>&1
echo "End siena dataset_01 at `date`"
exit
#==== redo_8888/report.siena ============
-----------------------------------------------------------------------
SIENA - Structural Image Evaluation, using Normalisation, of Atrophy
part of FSL www.fmrib.ox.ac.uk/fsl
running longitudinal atrophy measurement: siena version 2.5
siena
---------- extract brain --------------------------------------------
---------- register brains and skulls -------------------------------
(do not worry about histogram warnings)
/usr/local/fsl4.0.2/bin/siena_flirt: /dev/null: bad number
#=============================
% pwd
/kki/g1/ba/data/sienaAll/redo_888
% ls -l
total 192636
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:00 A.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:00 A.img
-rw-rw-r-- 1 bettyann fmri 150006 Jul 7 19:03 A_bet.png
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:03 A_brain.hdr
-rw-rw-r-- 1 bettyann fmri 39321600 Jul 7 19:03 A_brain.img
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:01 A_brain_mask.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:01 A_brain_mask.img
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:01 A_brain_skull.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:01 A_brain_skull.img
-rw-rw-r-- 1 bettyann fmri 150 Jul 7 19:39 A_halfwayto_B.mat
-rw-rw-r-- 1 bettyann fmri 103 Jul 7 19:39 A_to_B.mat
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:00 B.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:00 B.img
-rw-rw-r-- 1 bettyann fmri 150006 Jul 7 19:04 B_bet.png
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:03 B_brain.hdr
-rw-rw-r-- 1 bettyann fmri 39321600 Jul 7 19:03 B_brain.img
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:02 B_brain_mask.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:02 B_brain_mask.img
-rw-rw-r-- 1 bettyann fmri 348 Jul 7 19:02 B_brain_skull.hdr
-rw-rw-r-- 1 bettyann fmri 19660800 Jul 7 19:02 B_brain_skull.img
-rw-rw-r-- 1 bettyann fmri 151 Jul 7 19:39 B_halfwayto_A.mat
-rw-rw-r-- 1 bettyann fmri 104 Jul 7 19:39 B_to_A.mat
-rw-rw-r-- 1 bettyann fmri 704 Jul 7 19:39 B_to_A.mat_avscale
-rw-rw-r-- 1 bettyann fmri 621 Jul 7 19:40 report.html
-rw-rw-r-- 1 bettyann fmri 493 Jul 7 19:40 report.siena
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