Hi Ela,
It looks to me like line 79 of bedpostx_preproc.sh is:
if [ ${gflag} -eq 1 ]; then
Which is consistent with the error:
-eq: unary operator expected
What this error is saying is that the variable `gflag` has not been set, so the
script does not know how to perform the comparison.
`gflag` is set a few lines above to the second parameter passed when executing
`bedpostx_preproc.sh`. I would investigate how `bedpostx_preproc.sh` is being
invoked to chase down the cause of this error.
-Paul
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh
<elaheh.salard...@yale.edu>
Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia <ayend...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
External Email - Use Caution
That actually helps but not solving all the problems. So, what happens is that
if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target
'/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a
directory). However, the second error still exists: a.k.a.
(home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator
expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And
when I try to run Parallel lines, I still get the error
(dmri.bedpostX/logs/log0000: No such file or directory). So, my guess is, it
still doesn't copy the whole needed package for some reason. So, what we end up
having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.
I can always manually copy all needed file from fsl folder to our subjects
folder, but I am curious why we get the error and why everything is not copied
automatically. I also don't know what files we need to manually copy.
Thanks again,
Ela
________________________________
From: Yendiki, Anastasia <ayend...@mgh.harvard.edu>
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh <elaheh.salard...@yale.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
What if you create the directory (that shows up in the "not a directory" error)?
________________________________
From: Salar Dini, Elaheh <elaheh.salard...@yale.edu>
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia <ayend...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
External Email - Use Caution
Hi Anastasia,
FSL version is 6.0.5.1
Thanks,
Ela
From: Yendiki,
Anastasia<https://secure-web.cisco.com/1d4mPX-FtzaeHTx-d4ry-NXg8fIMj3367595FfyrtHXa1igyStVPbWUsDT-UJ-WYeKP8cZIEADYrswQBEevf7QStdkCmOWKBDSnHRh7V2HfNtrl4PxuecqQQ-GKIEnqFRr2k9kRwy5P0I-QiGTuvS2OGoT9UPf7ouSig_CJyqx2yu_OLhg2FyuBIJ17ihKlQHYbpiMGfCra21Nx38E0wYOxumvPbHdQyQGKOlI1YcJMDfqzC1vowurylhIHa1MxuzJMgxcYQfMdvG15U3DqXn0dm_v86-o6WYBp7SDHxhp-zANewR9sflA1T8nHErz8Vrc5doxlN3oHm4iqtR9ipmhQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1hjYaRQ7IoVBQWPddYegWDBTN53vXlBeQHNhe3Bi5HppHR0gq6LIuV4XGy4IS5Tpq8kTOGEgh7qmRZCAonXnVmDmmMHuIq9hHRs8H1uARdoYBvhOmHwqr37Aq_1_pNjH11X0MOXTbh_qNah0f88oGiq4JqracaGbTOkCJrcQYtHrK5lG5VkResx7NDiAElWs23nqCHPOGUV1WlVs8vBKNig0vk1fqs4MPzqx6cb-TK3coYNutw718WC_BSCkCTnqM_4W9KJr3x8w-gN74tO2ekUXxDL9mhUTNJNcjOiAxAbGsMu-hMNHRqDAnV6JtJ1y5aey5xUu0j9jNW2CesCgo-g%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Dfrom%25253A%25252522Yendiki%2525252C%25252BAnastasia%25252522%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252BFlNdHFAkB2YqWdzEtpZNqMkw2J4plyDuHqB1gqyJJ8%253D%26reserved%3D0>
Sent: Mon, 06 Jun 2022 20:17:47
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To: Salar Dini, Elaheh <elaheh.salard...@yale.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processin
Hi Ela - Which version of FSL are you using?
Anastasia.
________________________________
From: Salar Dini, Elaheh <elaheh.salard...@yale.edu>
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia <ayend...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
Thanks for the reply. I'm not sure if you are looking for this: we use a small
cluster with 40 nodes, 512 CPU cores. We are still using PBS.
Thanks,
Ela
________________________________
From: Yendiki, Anastasia <ayend...@mgh.harvard.edu>
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh <elaheh.salard...@yale.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
What kind of cluster are you running the parallel processes on?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh
<elaheh.salard...@yale.edu>
Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
External Email - Use Caution
Thank you for the guidance.
When it tries to run pre.ParallelI , I'll get this:
Copying files to bedpost directory
cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator
expected
Done
This happens for all subjects.
After this, when I check the subject 57 folder in subjects_dir, there is a file
named "dmri.bedpostX.nii.gz".
However, when it tries to run Parallel lines, these errors coming up:
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77:
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0000: No
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77:
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No
such file or directory
...
If I run trac-all -bedp -c <Cinfig File> , and not try to process parallelly,
it runs without any errors to the end.
Do you have any thoughts what goes wrong?
Thanks again,
Ela
From:Yendiki,
Anastasia<https://secure-web.cisco.com/1VSvVIiW_vnEGs2LzObbHY9QP0ZW-cZV5W696lIIR-D3jL_xrcyvpjVjDUZH3-fK6Z0r7w0TSWfZbSbt8Jgh9TMjek9iM2UgOzUj27-6K-iEZwx2szKM91dmntDUUuG73vbR6Jmt710rIjWhTs7Jm4NBm0QhOY0VSw3mahiy8tVbtvloLKWWLbDsxR1dR4J_fm7x5G3vr6QXuohdNnPo0mCHzfqZ3_XNsKDc4mxqwyR09AkDfYKYvf2IDVW3Wihgp-XAV7iDrPKtmiV7SyurhwHqgQy0FITwh8TeiwmeAgiY/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13C1JAwso_YuO5y9tMvPeX2Y5QGVzJPHKFw48WPzGirv3xqXaE8lnYxUF5YaNpJD-UZY_cUKxwHv4zjCqlZ5cs6OWOpVh0T7syTmN22KmXw5IFlmDxw09yZuYznZgJ9w_Qr41N29l88aKVQbiZXJt3zGjH4uAyG1B94DgOWjlOxY-SCFvNh6IlxUFomOwVJdhHZkpLY28J-SJFxxZZdMuG_L_iRpg7OHwOPOvLSvOzyG-bA0ieiRd9RGAzx14jp5Wv38KZu1zNLWoiuoh5UXPdAjxX18Y8uY-3oh8R_5LE2yd9QYXWY9buODXtppSgUn_3YHjQkypQzagyqDAzdVTcQ%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1G98lOaD7jG4iq2WjhE3v99As-QgUtMchD9KHZnXE856VPloJEJudQYJSktQvjbe3mj5zEABWY69ORy-E8CDVgclUx9YsdRIfflLP65rQJy59lQgsEF1hGeLoEMYYRqDTV67OUdihog0Nnh_Do2yaKbrGKJJLm2Eit2g-sAMRdrEICAyqi1PTydY_vN2riFdamFcpjYp9DA8Y2gWGC-Z3mBXh28v-uHYJZB1uK15w9cYUm9uutMsKCR9p7xJGcF9ZHyTO-Kzkk8ulOYkXE1RjXy6VxvEw-ZSGRItT-3jswRjK4lgWE_ZDvGIvLQzOmnSv7hTYvLO2lXCX2AKLsOGuww%2525252Fhttps%252525253A%252525252F%252525252Fwww.mail-archive.com%252525252Fsearch%252525253Fl%252525253Dfreesurfer%2525252540nmr.mgh.harvard.edu%2525252526q%252525253Dfrom%252525253A%252525252522Yendiki%25252525252C%252525252BAnastasia%252525252522%252526data%25253D05%2525257C01%2525257Celaheh.salardini%25252540yale.edu%2525257C4f2704fc4f23487cf9c408da45e7d678%2525257Cdd8cbebb21394df8b4114e3e87abeb5c%2525257C0%2525257C0%2525257C637899159291945719%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DlMsbgJ1yg5I8oDT95wdTG4cgXjIZikilz9jBBsmVrAo%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3Dw2IO6fj2hRMfvXX15oB77L1lfMbNK6kbXwKtPpMh1bw%253D%26reserved%3D0>
Fri, 03 Jun 2022 12:24:56
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You run them in that order. First the pre, then the parallel, then the post.
You can queue them that way, so that the parallel jobs wait for the pre to
finish, and the post waits for all the parallel jobs to finish.
________________________________
From: Salar Dini, Elaheh
Sent: Friday, June 3, 2022 3:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: TRACULA -bedp parallel processing
Hello,
I have tried to create a text file with command lines that can be run in
parallel by using trac-all -bedp -c <config file> -jobs Parallel.
When I use this command three text files are produced named: pre.Parallel,
post.Parallel, and Parallel. Should I just use Parallel as a source for command
lines? What are pre.Parallel and post.Parallel for? I am attaching my
Configuration file, pre.Parallel, post.Parallel, and Parallel to this message
as well.
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your help.
Kindly,
Ela
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