Dear Björn,
is the error consistent? I.e., if you were to run your script multiple times would the same subjects cause problems each time? If so, can you please upload an example where you have this problem? Please make a tar-ball containing all files alluded to be the eddy command line and upload it to
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F
Jesper
On 19 Apr 2016, at 09:54, Björn Åström <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi FSL experts
I'm currently running eddy and getting this error message (see below) on some of my subjects (roughly 1/10, meaning that 9/10 are processed properly), all files are formatted and named in exactly the same fashion among all subjects. I've seen that other people have had similar error messages in previous FSL-posts, possibly related to bval and/or bvec files? I have not noticed any discernible discrepancies between the bvecs of those analysis that work and those who don't.
$ ./eddy_prog_final160417.txt
0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
16
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1Segmentation violation, Unknown reason, Offending address = (nil)
eddy ) [0x5e0826] [
eddy ) [0x5db62b] [
eddy ) [0x43401b] [
./eddy_prog_final160417.txt: line 2: 5846 Segmentation fault (core dumped) eddy --imain="${katalog}_DTI.nii" --mask="${katalog}_DTI_bet_015_mask.nii" --acqp="${katalog}_acq.txt" --index="${katalog}_index.txt" --bvecs="${katalog}_DTI.bvec" --bvals="${katalog}_DTI.bval" --out="${katalog}_eddy" --slm=linear
This is my script:
#!/bin/bash
for kat_slash in */ # /home/lenf/test_fslpreproc/glm_160415/NYPUM_083_005_30T_V01
do
katalog=$(basename $kat_slash)
cd $katalog
fslroi "${katalog}_DTI.nii" "${katalog}_DTI_B0" 0 1 # B0-volymen
bet "${katalog}_DTI_B0" "${katalog}_DTI_bet_015" -m -f 0.15 # bet pa B0-volymen
printf "1 0 0 0.05" > "${katalog}_acq.txt" # skriv acq-filen
grad_vol=($(cat ${katalog}_DTI.bval)) # las in bvec i array grad_vol
echo ${grad_vol[*]}
echo ${#grad_vol[*]}
var_index="${grad_vol[@]//*0/1}" # ersatt varje b-value i grad_vol med 1 > lika manga 1:or som volymer
printf "${var_index}" > ${katalog}_index.txt # skriv ut var_index med ettor till indexfilen
echo $var_index
cat "${katalog}_index.txt"
eddy --imain="${katalog}_DTI.nii" --mask="${katalog}_DTI_bet_015_mask.nii" --acqp="${katalog}_acq.txt" --index="${katalog}_index.txt" --bvecs="${katalog}_DTI.bvec" --bvals="${katalog}_DTI.bval" --out="${katalog}_eddy" --slm=linear
cd ..
done
Any help on this would be greatly appreciated
Kind regards
Björn Åström
Department of clinical neuroscience
Umea University
