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 Topic  |
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tankersley
BIAC Alum
USA
143 Posts |
 Posted - Nov 06 2006 : 2:30:14 PM
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We're trying to get an old data set to run with batchFSL scripts on Golgi and are getting the following error:
[tankersl@golgi: ~/net/nernst/data1/ExecInfo.04/Data/FSL] $ ./batchFSL 43044
bash: ./batchFSL: /bin/bash: bad interpreter: The file access permissions do not allow the specified action.
Any ideas on what we're doing wrong?
Thanks,
Dharol
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petty
BIAC Staff
USA
453 Posts |
Posted - Nov 06 2006 : 3:04:12 PM
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did you copy this batchFSL script to that directory? your may need to make the file executable first:
chmod +x batchFSL |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 06 2006 : 4:25:50 PM
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Also, did you edit the script on Windows? If so, you can't do that. You have to do it using nedit or some other golgi-based editor. To fix a script that was edited on Windows, you can try:
dos2unix myscript.txt
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Nov 07 2006 : 10:35:54 AM
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Thanks.
The chmod +x batchFSL thing got it.
-d |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Dec 13 2006 : 1:21:49 PM
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I'm trying to run third level FSL analyses (across subjects) and my script is stoping:
/usr/local/packages/fsl/bin/avwmaths mask -Tmin mask
/usr/local/packages/fsl/bin/avwmerge -t mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/30876/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/30972/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31049/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31051/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31058/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31111/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31130/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31135/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31180/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31181/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31195/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31234/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31238/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31252/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31271/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31318/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31349/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31360/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31366/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31378/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31385/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31387/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31396/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31403/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31413/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31414/Mixed.gfeat/cope1.feat/mean_func /mnt/katz/data/ExecInfo.09/Data/FSL/31489/Mixed.gfeat/cope1.feat/mean_func
/usr/local/packages/fsl/bin/avwmaths mean_func -Tmean mean_func
syntax error in expression "1.000000e+00 * -n
-n
-n
-n
-n
-n
-n
Any idea what this error means?
Thanks,
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
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rkozink
Junior Member
31 Posts |
Posted - Jan 10 2007 : 2:32:28 PM
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I am having problems with FSL exiting early. Here is the error message that I'm getting on golgi:
[kozink@golgi: ~] $ NFS write error on host localhost: 5.
/usr/local/sharity/var/mount/Goldman.Data/CNSCR/NicFree.01a/Data/Func/4301/4301_v1/run002_06/run06.feat/report.log: A file or directory in the path name does not exist.
while executing
"exec sh -c "tail -1 $logout" "
(procedure "fsl:exec" line 45)
invoked from within
"fsl:exec "${FSLDIR}/bin/slicetimer -i $funcdata --out=prefiltered_func_data_st -r $fmri(tr) $st_opts""
(procedure "feat5:proc" line 968)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
And the error message that I get on FEAT Watcher:
cat: 0652-050 Cannot open report.log.
When I look at the folders, the report is there, so I don't undertstand why it can't find it. I'm not using any batch scripts, and I have used this same template .fsf for previous runs and they have worked fine.
Thanks for the help,
Rachel |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 10 2007 : 3:25:07 PM
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Rachel,
This is the "filesystem disappears from under you" issue. Every once in a while, programs using filesystems that are mounted using CIFS with sharity on golgi lose connection to their current directory, and can't access anything from the current directory unless they navigate back to it. There is no known solution to this, most people are just re-running and hoping it doesn't happen again. This problem is much more likely to strike long-running jobs, and as such is pretty annoying. If you hit this a lot, you can consider running your FSL jobs in /data/users/kozink and then move the results back to your data directories. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 22 2007 : 3:02:57 PM
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Hope this is the right forum ? . . .
I'm getting the following error when I run this script:
[tankersl@golgi: ~/net/nernst/data1/ExecInfo.04/Data/FSL] $ ./batch_43044 43044
FSLOUTPUTTYPE NIFTI_GZ
Input Vox2RAS-----------------
-3.75 0 0 118.125
0 -3.75 0 118.125
0 0 -3.79999981504498 53.7000007629395
0 0 0 1
Input FSL Vox2RAS-----------------
3.75 0 0 0
0 3.75 0 0
0 0 3.79999981504498 0
0 0 0 1
Ref Vox2RAS -----------------
-2 0 0 91
0 2 0 -109
0 0 2 -91
0 0 0 1
Ref FSL Vox2RAS -----------------
2 0 0 0
0 2 0 0
0 0 2 0
0 0 0 1
-----------------
1 0 0 -27.125
0 -1 0 227.125
0 0 -1 144.70000076294
0 0 0 1
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_01.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_02.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_03.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_04.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_05.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_06.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_07.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_08.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_09.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
invalid command name "(mc)"
while executing
"(mc) 1"
(file "/home/tankersl/net/nernst/data1/ExecInfo.04/Data/FSL/43044/Nifti_Files/FEAT_10.fsf" line 81)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(procedure "feat5:proc" line 12)
invoked from within
"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
(file "/usr/local/packages/fsl/bin/feat" line 16)
I can't tell what's going on here. I've initialized the script with chmod +x but don't understand the message.
Any help would be appreciated.
Thanks,
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 22 2007 : 3:09:26 PM
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Do you have a line:
(mc) 1
in your .fsf files? It should probably be:
set fmri(mc) 1 |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 22 2007 : 3:18:43 PM
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Thanks! I must have unwittingly cut it off when editing.
Dharol |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Mar 28 2007 : 2:27:10 PM
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I'm getting the following error message when I try to run a batch script:
line 69: syntax error: unexpected end of file
I've checked for extra spaces at ends of lines and there are none. Script listed below. Any idea what my syntax error could be? Line 69 is the last line of the script.
Thanks,
Dharol
############
#!/bin/bash
#for each subject you will have to modify this script for the number of runs and
#the subject number
#loads the fsl program
export FSLDIR=/usr/local/packages/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
#change this part
SUBJ=$1
FSLDATADIR=/mnt/katz/data/Reward.01/Data/FSL/$SUBJ
ANATFILE=${FSLDATADIR}/anat_BET.nii.gz
#########
#to convert from bxhheader to nifti look in the fileconverter file in this
#directory
MkFlirtInitMtx.pl --in $FSLDATADIR/run2.bxh --stdref --o $FSLDATADIR/ORIENT.mat
ORIENT=$FSLDATADIR/ORIENT.mat
for run in 1 2; do
DELAY=0
OUTPUT=${FSLDATADIR}run${run}
DATA=${FSLDATADIR}/run0${run}.hdr
VARS1=${FSLDATADIR_2}/${run}_s1.txt
VARS2=${FSLDATADIR_2}/${run}_s2.txt
VARS3=${FSLDATADIR_2}/${run}_s3.txt
VARS4=${FSLDATADIR_2}/${run}_s4.txt
VARS5=${FSLDATADIR_2}/${run}_s5.txt
VARS6=${FSLDATADIR_2}/${run}_s6.txt
VARS7=${FSLDATADIR_2}/${run}_s7.txt
VARS8=${FSLDATADIR_2}/${run}_s8.txt
VARP1=${FSLDATADIR_2}/${run}_p1.txt
VARP2=${FSLDATADIR_2}/${run}_p2.txt
VARP3=${FSLDATADIR_2}/${run}_p3.txt
VARP4=${FSLDATADIR_2}/${run}_p4.txt
VARP5=${FSLDATADIR_2}/${run}_p5.txt
VARP6=${FSLDATADIR_2}/${run}_p6.txt
VARP7=${FSLDATADIR_2}/${run}_p7.txt
VARP8=${FSLDATADIR_2}/${run}_p8.txt
VARF=${FSLDATADIR_2}/${run}_Fixation.txt
echo $OUTPUT
#makes the fsf files from the template fsf file
for i in 'template_p2.fsf'; do
sed -e 's@OUTPUT@'$OUTPUT'@g' \
-e 's@ANAT@'$ANATFILE'@g' \
-e 's@ORIENT@'$ORIENT'@g' \
-e 's@DELAY@'$DELAY'@g' \
-e 's@DATA@'$DATA'@g' <$i> ${FSLDATADIR}/FEAT_${run}.fsf \
-e 's@VARS1@'$VARS1'@g' \
-e 's@VARS2@'$VARS2'@g' \
-e 's@VARS3@'$VARS3'@g' \
-e 's@VARS4@'$VARS4'@g' \
-e 's@VARS5@'$VARS5'@g' \
-e 's@VARS6@'$VARS6'@g' \
-e 's@VARS7@'$VARS7'@g' \
-e 's@VARS8@'$VARS8'@g' \
-e 's@VARP1@'$VARP1'@g' \
-e 's@VARP2@'$VARP2'@g' \
-e 's@VARP3@'$VARP3'@g' \
-e 's@VARP4@'$VARP4'@g' \
-e 's@VARP5@'$VARP5'@g' \
-e 's@VARP6@'$VARP6'@g' \
-e 's@VARP7@'$VARP7'@g' \
-e 's@VARP8@'$VARP8'@g' \
-e 's@VARF@'$VARF'@g' \
done
#runs the analysis using the newly created fsf file
feat ${FSLDATADIR}/FEAT_${run}.fsf
done
########### |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 28 2007 : 3:03:15 PM
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| There is a backslash (\) at the end of the last -e line of your sed command -- that says to make the next line a continuation of the current line. The next line is "done" which ends the for loop and needs to be on its own line. So get rid of the last backslash and I think that might fix it. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Mar 29 2007 : 1:18:49 PM
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Thanks Syam.
Can anyone explain what the following line means:
MkFlirtInitMtx.pl --in $FSLDATADIR/run02.bxh --stdref --o $FSLDATADIR/ORIENT.mat
It's causing the script listed in the previous post to crash and giving the following error:
ERROR: Input volume /mnt/katz/data/Reward.01/Data/FSL/32865/run2.bxh does not exist
I'm confused, since this line is in all the other batch scripts i've run and never caused a problem before.
Thanks :)
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 29 2007 : 1:23:33 PM
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| That line is creating an initial matrix to start the registration. It is apparently complaining that run2.bxh does not exist. You may need to go back to whatever script is creating (or trying to create) the run2.bxh file and see what errors it might have generated. |
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Topic |
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FSL script hanging
