External Email - Use Caution Hi, Douglas
Sorry to bother you again, do you think the problem is the old version of FSL? Best, Wei On Fri, Nov 13, 2020 at 1:32 PM Wei Shao <ws...@research.baycrest.org> wrote: > Hi Douglas > > I think it's 5.0.11 > > [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0 > To initialize FreeSurfer, > do (sh, ash, ksh, and bash) > source $EBROOTFREESURFER/FreeSurferEnv.sh > or (csh, tcsh) > $EBROOTFREESURFER/FreeSurferEnv.csh > > [weishao@gra-login2 ~]$ module load fsl > [weishao@gra-login2 ~]$ which fsl > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl > [weishao@gra-login2 ~]$ > > Best, > Wei > > On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> What version of FSL are you using? >> >> On 11/10/2020 12:19 AM, Wei Shao wrote: >> >> External Email - Use Caution >> Hi, Freesurfer team, >> >> My name is Weishao, Here is a problem that bothers me a lot I try to run >> DTI. I have loaded the FSL module and use the most recent version of >> Freesurfer. it's appreciated if someone can help. Thanks. >> >> Here is the script. >> >> dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec >> --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> --s /home/weishao/scratch/rawdata/sub-AVP6176/ >> --o /home/weishao/scratch/rawdata/sub-AVP6176/ >> >> Here is feedback >> >> -rw-r----- 1 weishao weishao 49041968 Sep 9 11:41 >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> INFO: SUBJECTS_DIR is >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> dt_recon logfile >> Tue Oct 27 16:19:28 EDT 2020 >> VERSION dt_recon 7.1.0 >> setenv SUBJECTS_DIR >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon >> --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s >> /home/weishao/scratch/rawdata/sub-AVP6176/ --o >> /home/weishao/scratch/rawdata/sub-AVP6176/ >> gra95 >> weishao >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1_VxhPa3XI-Yzkt8JU2cwsw/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Feddy_correct> >> ECRefTP 0 >> #@#------------------------------- >> Converting input >> Tue Oct 27 16:19:28 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> reading from >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... >> TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.999608, 0.017447, -0.021891) >> j_ras = (0.0104682, 0.958258, 0.285714) >> k_ras = (-0.0259621, -0.285373, 0.958065) >> writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... >> >> >> #@#------------------------------- >> Eddy/Motion Correct >> Tue Oct 27 16:19:44 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/ectmp >> eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1_VxhPa3XI-Yzkt8JU2cwsw/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Feddy_correct>: >> line 95: /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob >> <http://secure-web.cisco.com/14GGFn_nc9xX-9O7KFUQlMhTcuKP2UzYHSyRZ1KY8WmZVDHlU9CvRqNtyi2-o9brT81R93N0ywcGuNRVh631lH6E_b01B9YCYcb1m95SVUKoP7sHDhles5fDfP-RqeSO5lJL1PRxEKZhWppXivZAkjzY2HbqTD33w2i7lP84LQKEu9fSk0Twg01KT3DfLHHhQE9qfBWwuetCA_ZrRfGWWHQ/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Fimglob> >> : *No such file or directory* >> >> Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value >> in seconds] >> -t : concatenate images in time >> -x : concatenate images in the x direction >> -y : concatenate images in the y direction >> -z : concatenate images in the z direction >> -a : auto-choose: single slices -> volume, volumes -> 4D (time >> series) >> -tr : concatenate images in time and set the output image tr to the >> final option value >> >> *ERROR: when running eddy_correct * >> >> >> Best, >> Wei >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1UPFJbsNdF96Nz5jI3AlTvvxeJFJTSTC6MLT1osyRwjDOD4uprCXnY4B4FNQ2UobqhXAcWOpEpLeF6qS5XvulI6OP3ytmiiYgjsfurM8tHhvar28f0Mre1MQAwNR3eu_OjC4o-iEqlDk6dKGx1hKoGRApZDoVUpf9-M32CFUYEz4MGRpKcnjA_4byahxpc58li0y5Msm7U-s3GriWeDSZ3-uej_yqSwHBuIiQGZXPruvsiEEQboQrGyuSVEsKqKAOP7Rk6DDg6Zqzcpsje_-GvQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > >
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