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co18
Starting Member
Singapore
9 Posts |
 Posted - Apr 10 2007 : 12:42:04 PM
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Hi,
I previously ran the mri data through an FSL analysis, but discovered something was wrong, so I am trying to re-run through the data, using the "filtered_func_data.nii.gz" as the input file instead, and the same anat file.
However, when running the batch script, I got the following error message:
./batchp2_short: /home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/FEAT_1.fsf: A file or directory in the path name does not exist.
grep: 0652-033 Cannot open /home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/FEAT_1.fsf.
while executing
"exec sh -c "grep 'fmri(version)' $filename | awk '{ print \$3 }'" "
(procedure "feat5:load" line 6)
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)
/home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/run010
./batchp2_short: /home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/FEAT_10.fsf: A file or directory in the path name does not exist.
grep: 0652-033 Cannot open /home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/FEAT_10.fsf.
while executing
"exec sh -c "grep 'fmri(version)' $filename | awk '{ print \$3 }'" "
(procedure "feat5:load" line 6)
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)
Can someone enlighten me as to a couple of things I can try to correct the script?
Thanks,
Ooi |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 10 2007 : 1:03:50 PM
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| I don't know exactly why this particular error is happening, but filtered_func_data.nii.gz is pre-processed data -- so you would not want to re-run pre-processing on that data as an input. If you are re-running pre-processing, you should start with the raw data. |
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co18
Starting Member
Singapore
9 Posts |
Posted - Apr 10 2007 : 1:06:25 PM
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Hi,
I changed the template fsf file so that it only does the stats and post-stats as well. Any other ideas perhaps?
Thanks,
Ooi |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 10 2007 : 1:13:39 PM
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The errors you are getting are unrelated to what decisions you are making in FSL.
One error is that your script is looking for the following file:
/home/ooi/net/Nernst/Data1/ExecInfo.04/Data/FSL/44492/FEAT_1.fsf
and not finding it. If the script is supposed to generate that file, you may want to find out why it isn't doing so. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 10 2007 : 1:30:25 PM
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my guess is this:
"Nernst/Data1/ExecInfo.04" should actually be "nernst/data1/ExecInfo.04"
the mapping should be in lowecase |
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co18
Starting Member
Singapore
9 Posts |
Posted - Apr 10 2007 : 1:38:17 PM
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Hi,
I tried changing the case to lowercase, but the error message is the same. The file is right there, with the exact same case, when I check it, so might anyone know a possible reason why it's not detecting the file, even though it's there?
Thanks for the suggestions so far.
Yours,
Ooi |
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Topic |
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Running Analysis
