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syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Sep 25 2006 : 12:05:32 PM
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Moved this to a new topic with appropriate subject line.
quote:
Originally posted by tankersley
I'm trying to run batch scripts for first level FEAT analysis in fsl. I enter the command in Golgi and the following happens:
[tankersl@golgi: ~/net/katz/data/ExecInfo.09/Data/FSL] $ ./batchFSL 31238
Input Vox2RAS-----------------
-3.99903988838196 0.0402844697237016 0.0779120706219313 121.95130161196
-0.0433365702629088 -3.99645566940308 -0.162675802157025 152.620057493448
0.0761745125055312 -0.163456976413727 3.9959329546664 -63.1834804043174
0 0 0 1
Input FSL Vox2RAS-----------------
4 0 0 0
0 4 0 0
0 0 4.000001569315 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
-----------------
0.99975997209549 -0.0100711174309254 -0.0194780100136995 -30.95130161196
-0.0108341425657272 -0.999113917350769 -0.0406689345836639 261.620057493448
0.0190436281263828 -0.0408642441034317 0.998982846736908 27.8165195956826
0 0 0 1
/mnt/katz/data/ExecInfo.09/Data/FSL/31238/run1_output
And then it just sits there for a couple of hours, producing no files or error messages.
Any one know what this means?
Thanks,
Dharol
Your script seems to be hanging on the following command:sed -e s@OUTPUT@/mnt/katz/data/ExecInfo.09/Data/FSL/31366/run1_output@g -e s@ANAT@/mnt/katz/data/ExecInfo.09/Data/FSL/31366/anat_BET.nii@g -e s@ORIENT@/mnt/katz/data/ExecInfo.09/Data/FSL/31366/ORIENT.mat@g -e s@DELAY@0@g The "sed" command requires an input file; otherwise it tries to read from standard input. There doesn't seem to be an input file on that command line. Perhaps your script is missing that?
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 25 2006 : 12:08:54 PM
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there actually is a file pointer in the script:
for i in 'template.fsf'; do
sed -e 's@OUTPUT@'$OUTPUT'@g' \
-e 's@ANAT@'$ANATFILE'@g' \
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Sep 25 2006 : 12:16:50 PM
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It turned out that Dharol's script had some extra newlines that ended the command prematurely. i.e. the script originally had something like:command arg1 arg2 \
arg3 arg4 arg5 \
arg6 arg7 arg8with the backslashes at the very end of the line indicating that the command continues on the next line. Her version had something like:command arg1 arg2 \
arg3 arg4 arg5 \
arg6 arg7 arg8The extra blank line without a backslash meant that the command ended at arg5, ignoring arguments 6-8.
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Sep 29 2006 : 11:01:32 AM
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I'm getting this obscenely long error message now when I try to run my batchFSL script:
[tankersl@golgi: ~/net/katz/data/ExecInfo.09/Data/FSL] $ ./batchFSL 31238
Input Vox2RAS-----------------
-3.99903988838196 0.0402844697237016 0.0779120706219313 121.95130161196
-0.0433365702629088 -3.99645566940308 -0.162675802157025 152.620057493448
0.0761745125055312 -0.163456976413727 3.9959329546664 -63.1834804043174
0 0 0 1
Input FSL Vox2RAS-----------------
4 0 0 0
0 4 0 0
0 0 4.000001569315 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
-----------------
0.99975997209549 -0.0100711174309254 -0.0194780100136995 -30.95130161196
-0.0108341425657272 -0.999113917350769 -0.0406689345836639 261.620057493448
0.0190436281263828 -0.0408642441034317 0.998982846736908 27.8165195956826
0 0 0 1
/mnt/katz/data/ExecInfo.09/Data/FSL/31238/run1
sed: 0602-419 Cannot find or open file .
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
invalid command name "toplevel"
while executing
"toplevel .prompt -borderwidth 5"
(procedure "MxPause" line 4)
invoked from within
"MxPause "FEAT setup file is too old to load - sorry!""
(procedure "feat5:load" line 51)
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)
/mnt/katz/data/ExecInfo.09/Data/FSL/31238/run2
sed: 0602-419 Cannot find or open file .
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
invalid command name "toplevel"
while executing
"toplevel .prompt -borderwidth 5"
(procedure "MxPause" line 4)
invoked from within
"MxPause "FEAT setup file is too old to load - sorry!""
(procedure "feat5:load" line 51)
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)
/mnt/katz/data/ExecInfo.09/Data/FSL/31238/run3
sed: 0602-419 Cannot find or open file .
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
invalid command name "toplevel"
while executing
"toplevel .prompt -borderwidth 5"
(procedure "MxPause" line 4)
invoked from within
"MxPause "FEAT setup file is too old to load - sorry!""
(procedure "feat5:load" line 51)
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)
/mnt/katz/data/ExecInfo.09/Data/FSL/31238/run4
sed: 0602-419 Cannot find or open file .
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
./batchFSL: -e: command not found
invalid command name "toplevel"
while executing
"toplevel .prompt -borderwidth 5"
(procedure "MxPause" line 4)
invoked from within
"MxPause "FEAT setup file is too old to load - sorry!""
(procedure "feat5:load" line 51)
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 think there are 2 primary problems,
1.one dealing with:
sed: 0602-419 Cannot find or open file .
but I don't know what the 0602-419 refers to.
2.And the other having to do with some invalid "top level" command, which I also don't understand. Is there documentation somewhere that explains these error messages?
Thanks,
Dharol |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 29 2006 : 11:05:27 AM
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| looks like its not finding the template.fsf file that your sed command is trying to open and edit. |
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syam.gadde
BIAC Staff
USA
421 Posts |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Sep 29 2006 : 4:45:28 PM
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Does anyone know why I might be running out of memory? I'm not having this problem with Reward.01 but am having it with Execinfo.09, both of which are on Katz???
Error: FILM did not complete - it probably ran out of memory
Thanks,
Dharol
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Oct 04 2006 : 1:47:35 PM
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I'm running this commmand:
./batchFSL 46158
And getting this error:
Can't locate object method "new" via package "XML::LibXML::SAX" at /usr/opt/perl5/lib/site_perl/5.8.0/XML/SAX/ParserFactory.pm line 43.
I've looked at the script and have no idea what it's saying.
Has anyone else had this error?
Thanks,
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Oct 04 2006 : 1:52:02 PM
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| Can you try this again? I have just reinstalled the offending module. |
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deshmukh
BIAC Alum
40 Posts |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Oct 24 2006 : 1:39:56 PM
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I'm running FSL and getting the following error in the Golgi command window:
Log directory is: stats
Unable to open design.mat
Error: FILM did not complete - it probably ran out of memory
I get the exact same error at the end of my log.txt file.
When this happens, it looks like FSL has created a design.fsf and design.con, but never made a design.mat.
I'm confused, because this doesn't happen every time I run the script.
Any advice?
Thanks,
Dharol |
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petty
BIAC Staff
USA
453 Posts |
Posted - Oct 25 2006 : 09:22:12 AM
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"Error: FILM did not complete - it probably ran out of memory"
either the hard drive is full .. or the cpus are maxing out somewhere because of the amount of processes that are running
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Oct 25 2006 : 09:23:15 AM
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Does this mean I should just try again later?
Thanks,
Dharol |
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petty
BIAC Staff
USA
453 Posts |
Posted - Oct 25 2006 : 09:27:09 AM
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| you could remove some un-needed data, then try again and see what happens. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Oct 25 2006 : 1:25:19 PM
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I would like to define 10 variables in a batch script I'm running on Golgi for FSL, but
it(?) is interpreting variable 10 as variable 1 with an extra "0" at the end:
batch script:
VAR1=${FSLDATADIR}/Column_Data/ANT13_TT1_${run}00.txt
VAR10=${FSLDATADIR}/Column_Data/HF_${run}00.txt
How var1 is being interpreted:
# Custom EV file (EV 1)
set fmri(custom1) "/mnt/katz/data/ExecInfo.09/Data/FSL/31049/Column_Data/ANT13_TT1_100.txt"
How var10 is being interpreted:
# Custom EV file (EV 10)
set fmri(ortho10.0) "/mnt/katz/data/ExecInfo.09/Data/FSL/31049/Column_Data/ANT13_TT1_100.txt0"
Am I allowed to specify 10 variables, and is there a certain format I need to use?
Thanks,
Dharol |
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petty
BIAC Staff
USA
453 Posts |
Posted - Oct 25 2006 : 2:31:20 PM
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basically whats happening is when sed is doing a search and replace it is replacing VAR1 first ... then VAR10.
so all sed sees is the VAR1 (which really is VAR10) and does its replacement giving you whatever VAR1 is + and extra 0 .. and therefore VAR10 no longer exists.
"/mnt/katz/data/ExecInfo.09/Data/FSL/31049/Column_Data/ANT13_TT1_100.txt0"
the easy fix would be to move VAR10 infront of VAR1 in the sed replacement order.
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FSL script hanging
