External Email - Use Caution Hi Ela,
I ran into the exact same problem. Here is how I fix it. 1) edit pre.Parallel.docx bedpostx_preproc.sh takes 2 arguments. Add a 2nd argument 0 at the end bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri 0 bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/58/dmri 0 2) create nodif_brain_mask.nii.gz link in dmri cd /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri ln -s ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz nodif_brain_mask.nii.gz 3) create dirs dmri.bedpostX/diff_slices dmri.bedpostX/logs/monitor dmri.bedpostX/xfms in /home2/am2359/fs6_data/TRACULA/subjects_dir/57 same for 58 now you can run Parallel.docx Hope I didn't miss anything. Best, King-Wai Chu On Tue, Jun 14, 2022 at 8:55 PM Salar Dini, Elaheh < elaheh.salard...@yale.edu> wrote: > External Email - Use Caution > > I tried to troubleshoot this, but I couldn't. I just want to follow-up and > make sure no other solutions come to your mind. If not, we will run it out > of cluster which seems to work just fine. > > Thanks and all the best, > Ela > ------------------------------ > *From:* Salar Dini, Elaheh <elaheh.salard...@yale.edu> > *Sent:* Wednesday, June 8, 2022 3:32 PM > *To:* Yendiki, Anastasia <ayend...@mgh.harvard.edu>; Freesurfer support > list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: TRACULA -bedp parallel processing > > > Thanks Paul. > > bedpostx_preproc.sh is the first job that is I submit to my cluster. My input > file is attached to this email. > > > Thanks, > > Ela > > > > *From: *Wighton, Paul > <https://secure-web.cisco.com/1NvethJ2okwtBXYYV_EyxsXJx5qGOow2E5QtYJaKI1BCp3t8jVc7IQ9rNW9tMpRV7L5vP3mrgesq1jcnJKE5f_4HVbjGFYV70G8S40lFftxXK7lxGCnq56Ox0Mu9_i7WwuRnk-7bEGf-7R5dadwyxjWvyMgzXEvQhgfKan92fgm9AL_h7CtjK-_N5jWdO_f-cmdqFGeCspKHVODcFE4-d20kekjIkZbYia8GoJDcu27_d-Srd8pTig-g2Hi5NunkLAfpIgE4Io3ruNC0zu8Zvn6VCWVq-hy4a2HZ9ZIw7dodjmDWPVKcHcEqYkVV6sxGCB2gOlbzBrL_eeK8QHBJI7gRy-z5aUx-9dp2Io1Ww55g/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Wighton%252C%2BPaul%2522> > *Sent: *Wed, 08 Jun 2022 10:06:21 -0700 > <https://secure-web.cisco.com/15JpdRjHpUwrjYyCfG0RWTJDoX413v5LN2Sed5H1OslWtt5j0CeOmss-WcOppPt0oWLSB3h1PXVS_mcB3lalLOjHb6zPQlqIN5vKRfohF0Mj1EXgkfg0eUNX1yvy0h7osnt39YaN4kHZT7dfh8b7lz5n4RFrfT49bz3uqGnbqEs88Gh1DFJfa0LBN6nlNlEKYcoVvEErAAZFcteu_-Fs__cSYKIWeATxNwCnCosyRS6peTz-ZPAzsA-i_ouJNkB4PDeJ7ZZm-i4vAbOAQGsBIU2404dp98DCAambIEO3SOkLgFcCG2V6DbgqudzsWc-oSIdI2OS0Pz_xJc4IFm7JoPovTTYe4NOyIusf9MhmMMAY/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220608> > > *Subject:*Re: TRACULA -bedp parallel processing > > > Hi Ela, > > It looks to me like line 79 of bedpostx_preproc.sh is: > > if [ ${gflag} -eq 1 ]; then > > Which is consistent with the error: > > -eq: unary operator expected > > What this error is saying is that the variable `gflag` has not been set, so > the > script does not know how to perform the comparison. > > `gflag` is set a few lines above to the second parameter passed when executing > `bedpostx_preproc.sh`. I would investigate how `bedpostx_preproc.sh` is being > invoked to chase down the cause of this error. > > -Paul > > > ------------------------------ > *From:* Salar Dini, Elaheh <elaheh.salard...@yale.edu> > *Sent:* Wednesday, June 8, 2022 12:32 PM > *To:* Yendiki, Anastasia <ayend...@mgh.harvard.edu>; Freesurfer support > list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: TRACULA -bedp parallel processing > > That actually helps but not solving all the problems. So, what happens is > that if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: > target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is > not a directory). However, the second error still exists: a.k.a. > (home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator > expected". line 79 is "${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/1gMhd-NtfGQoo4sxXlV5w2SPV4n_Xtg7gFkKUX8CyfIQwAn4-G1nOI0ITlaiQWxefvTnqTHnA-6vk79vZCjSWSy1KCMT_-MwPWEFuwhkyc2dz-PgJLgbqp3JaH-7jrpNxtc1HR0CeUVCEsSUa66xNn5ZECBZQIDcLNngonv7k259pMbYb5noKJsvD0-IkWR6z1vft9vCm_kjpLgCcF6CHsMOW5crdjpKmYHEDqm_GyYpNJq2IBXxv8nB26Y6mK738_pdUMiFBZSv6cikz3yPkmKchzvveAndce4soVa9DIu0hL6T15aJRA9KY_FXOu7yWwjIKRuXxGqprVQLUEFm7nPtvw5szvaKBFgTQSegCrj0/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 -0700 > <https://secure-web.cisco.com/1hIh3BL11gmgVBTk8xY-63vXTjASmE7KTXnal24JHbAwq-CzcQ5-4e_ro2Jjwt-v5v3MYMO2xmdcbeTpZlE2Q8dy92smW7NwHdkbEsgZ7YFmPOzANViTjOjwWHy_6Xc7C6nMq_tl_LODu8pRKCpGwb3gJ6443qZ6gBG38_lsXsl3M98zzTsyEamnKgQJK-07yiLoi-1_5i4-6UYufuku3iFS8KpGGpo_9oOeK6xRcETIIVTcAy6Fsajz5F9_G7R1qd3Zd3d9r8AudiFrk_eSvxL1_vavtgklbDlfQrNoJGbTmqmn8Bsg04OBMnO1Hye4I-a9qAzdxLdLCol_eou6EPACjSPUmd_sCrnPiGs0_O4I/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11YTHE-9SnX_d-1PQ1yyK7EQYy82okQBAj3-aNpNvl-kJp3dN1G0QO8yztwo24IehLoqbE2gQ5JGCUFPjW6OE2T4RUxK5mY_WuSdC8Ue2dm5d1AI14zEzhbEnoH2wGcaNwmtL3nenG_qHdKlN8qkHjRZ4nU3njkcFajT4valovVZnht7U-peLk4QVCqIzRR3RvYd6vodHNFqPwl3ATlbX3K3dbofDxEC-a4Sn2dutAOC3g_eaOsE2xGmuaALZsSorg81MF_6V-T87knaRRfrG7iiWb-SF0r5wvo_-8AzTyg6VpgSudF4_rFltDEUU3VtoK1OfkbMTczhhRKQvIGphpw%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Ddate%25253A20220606%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DzMpmkQAaTcNySHOkozbk0Y6iqtZuuMKsFmFZ7c%252FKgmE%253D%26reserved%3D0> > > *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/1-yWhuVTBvU0ipygFGOqpnutc2Jb8xnuJeVfcsaMDUedHZvLxF46H7ez8w803E1qWE9-PQ9O7_xUtKR19mN5EMsYNi58wrPEj_DrNr9-KAmJUNqev7dphL8BKZQmPc8B1BCQj_3Akuqa5giyC-7XeUUBmAiOy_RuUOmeEcHOyA9RuGIvBA-sucP0uCV-2evtSkaEBSLRCq2JsuE2B1iWhEuo1AfOKk0Trw8Wk2005XBNZwjDjhwyoF6h9r1_bO18M0fAD6Q5eEIWwRV65YPhbKXkUC482BlAImfEtB-4fpoA/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 -0700 > <https://secure-web.cisco.com/1AfYq8jnFCxHkcZ_2llYEPV8Uf58K004nQSATYB-J3aE17rdIzD3-DVdiF46UvUISjxTF5yDQuzcNYUq9MbPSu0VxokgXRl9w7W-RHfbPxGfXPIFNyW92A1KNu-jRrE8QkXFLhETHCZF8kaOBI9vDF7HhU_KcjNw8ffKBwVKZI1hgXcRviub1XxnwlNT31Nr-5LG1Jxk_n32r7EPytgNC_X7-PaWjOCUcvsR42LBQof29hRkJO3E6GnJd83x3sMI5bsh761_O-O8A7VQckROHSeFDpVi-gXhJOHUPbHd6Vw8/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1gKvv3tr9pzmhMB4kDdL5aXTm3s6QSf66X1_53XzzwzQ-qr-kLvP4NofuafqyR8j0uDE4BHSmlntlNLh87PHKp1_8PjIfaiIuw4S-_QaS_f3fDEWSXc-kcf9gtauza-oYDksMLtZnQMJp5lqXchcsNqfhW5LDYySy5LSCJX4RlNqrpmbZ8rInBttnCuMte6l7kfChFYFAjuY45FD8hJsh6TNKrmK22nFGT13ZUi1kLFPDKqvxAjUwzfhd8La3LIj9KrX0srPmLRmOf7LtM3m4DeWISOs14TiEcMTMfZYwP_SuqvMl3KqUCiSzGjJWm_Ze9KbXqyJ2vB-l8VuTAEOQUQ%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1iYzYcIZ2Tv5TyWUw9JGlBd7DX9rmkvS3srfzOnjM7W5wDlS5mF-XUghEX0MBAJukuwvtixbFdMX-6eBxEISsPVlQe10qbKLqXqT8Tv1g39yAMs4c3K9Nfqkd58NaNrxti_-RKIDjVsEBpMelHDNmBQlsWXArIO0tdqC9SoXYo_E2vpftbYM2zy5FOy7wbHPB2gmrO2gS_majAlXWb0hBmDKLkKQMkeCyYDcjU9CyVOOmz9sxx6hYYzkg2HQNj1-bzqnxoI-yRJN9TwIZm1gVP0qxGRkfIC6NfDCgptJfFkTRATxYIBwSIF6SuUOIZOW-1TQ7cZSHzp-Wc-P9rfXP2w%2525252Fhttps%252525253A%252525252F%252525252Fwww.mail-archive.com%252525252Fsearch%252525253Fl%252525253Dfreesurfer%2525252540nmr.mgh.harvard.edu%2525252526q%252525253Ddate%252525253A20220603%252526data%25253D05%2525257C01%2525257Celaheh.salardini%25252540yale.edu%2525257C4f2704fc4f23487cf9c408da45e7d678%2525257Cdd8cbebb21394df8b4114e3e87abeb5c%2525257C0%2525257C0%2525257C637899159291945719%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DVSpBZUHD%2525252FOjwWfwL44ATvZZyAh2cjBZWMgP6JxFedto%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsOYwmPDwJDFqqbj8ZU6HiKdKqb29nPUV8jn7SgeFvNA%253D%26reserved%3D0> > > > > > 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 > > The information in this e-mail is intended only for the person to whom it > is addressed. 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
