hello,
i am testing out FSL 4.0.1 on ubuntu feisty (installed via apt-get
from the binary distribution), and ran FEEDS. it seem to ran fine,
and with acceptable errors (less than 1% in every test) but seemed to
break at the bedpost section.
it seems like the FSLMACHINELIST variable isn't set, but this is a
single processor machine and we didn't have to set this variable before.
any suggestions would be very much appreciated.
here's the benchmark log:
Create temporary working directory
Using /tmp/fsl-selftest.Ec5262 as working directory
FSL Evaluation and Example Data Suite v4.0
start time = Mon Sep 10 16:24:39 EDT 2007
hostname = frontend
os = Linux frontend 2.6.20-16-generic #2 SMP Fri Aug 31 00:55:27 UTC
2007 i686 GNU/Linux
/bin/rm -rf /tmp/fsl-selftest.Ec5262/results ; mkdir /tmp/fsl-
selftest.Ec5262/results
Starting PRELUDE & FUGUE at Mon Sep 10 16:24:39 EDT 2007
% error = 0.0
% error = 0.0
Starting SUSAN at Mon Sep 10 16:24:43 EDT 2007
% error = 0.0
Starting SIENAX (including testing BET and FLIRT and FAST) at Mon Sep
10 16:51:08 EDT 2007
checking error on BET:
% error = 0.0
checking error on FLIRT:
% error = 0.08
checking error on FAST:
checking error on single-image binary segmentation:
% error = 0.05
checking error on partial volume images:
% error = 0.22
% error = 0.25
% error = 0.24
checking error on SIENAX volume outputs:
% error = 0.17
% error = 0.0
% error = 0.23
% error = 0.17
% error = 0.41
Starting BET2 at Mon Sep 10 17:06:42 EDT 2007
checking error on T1 brain extraction:
% error = 0.0
checking error on skull and scalp surfaces:
% error = 0.07
% error = 0.21
% error = 0.29
Starting FEAT at Mon Sep 10 17:40:33 EDT 2007
checking error on filtered functional data:
% error = 0.12
checking error on raw Z stat images:
% error = 0.1
% error = 0.09
% error = 0.1
checking error on thresholded Z stat images:
% error = 0.26
% error = 0.15
% error = 0.19
checking error on position of largest cluster of Talairached zfstat1:
% error = 0.0
% error = 0.02
% error = 0.0
% error = 0.02
% error = 0.0
% error = 0.0
Starting MELODIC at Mon Sep 10 18:10:28 EDT 2007
% error = 0.1
Starting FIRST at Mon Sep 10 18:33:58 EDT 2007
% error = 0.2
Starting FDT (bedpost) at Mon Sep 10 19:01:24 EDT 2007
checking error on bedpost output:
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
Warning - not all tests passed
end time = Mon Sep 10 19:01:27 EDT 2007
[: 98: ==: unexpected operator
Done. Leaving results in /tmp/fsl-selftest.Ec5262
real 9408.43
user 6651.96
sys 87.74
here's the part of the LOG file from /tmp/fsl-selftest.Ec5262/results/
LOG that seems to relate to the bedpost error:
cp -r /tmp/fsl-selftest.Ec5262/data/fdt_subj1 /tmp/fsl-
selftest.Ec5262/results
unset FSLMACHINELIST; /usr/share/fsl/bin/bedpostx /tmp/fsl-
selftest.Ec5262/results/fdt_subj1 -n 1
subjectdir is /tmp/fsl-selftest.Ec5262/results/fdt_subj1
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
/usr/share/fsl/bin/bedpostx: 166: Syntax error: Bad for loop variable
thanks for any help with this
Lokke Highstein
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