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Unfortunately, I had already tried that and it doesn’t help. Still getting the same error.
Is it possible that there is an environment variable which is not set correctly for fsl_sub to run properly? If I try to simply putting the command into a
one line bash script, with the line being the call to run_first_all, I get the error that this command is not found. Thanks for any advice you can provide.
Best,
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
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From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
On Behalf Of paul mccarthy
Sent: Friday, January 19, 2018 4:31 AM
To: [log in to unmask]
Subject: Re: [FSL] Error with fsl_sub - No such file
Hi Mark,
It might work if you use absolute paths when specifying your input/output files.
Cheers,
Paul
On 18 January 2018 at 23:26, Mark Wagshul <[log in to unmask]> wrote:
Hi.
I am trying to run FIRST with the run_first_all command, and getting an error because it doesn't recognize the default queue, veryshort.q. So, I am running it with fsl_sub to specify the queue, as follows:
fsl_sub -q all.q run_first_name -i input_file.nii.gz -o output_file.nii.gz
I get an error which says it can't find the file (actually, the error says:
execvp(run_first_all, "run_first_name" "-i" "input_file.nii.gz" "-o" "output_file.nii.gz") failed: No such file or directory.
I am quite sure the input_file.nii.gz exists, I have even tried using the full path and making sure the file has complete read/write access for all. Also, this is not unique to FIRST, it happens with any fsl command I attempt to run in this way through fsl_sub.
Right now I'm stuck, so any advice as to what we are doing wrong would be much appreciated.
Thanks,
Mark W.