External Email - Use Caution
Hi, Wei,
I would recommend to use dwifslpreproc script from mrtrix3 suite instead.
https://mrtrix.readthedocs.io/en/latest/reference/commands/dwifslpreproc.html
https://www.mrtrix.org/
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide
The eddy_correct tool used in dt_recon is very old and suboptimal method for DWI preprocessing.
Antonin
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.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://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 > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer