External Email - Use Caution
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
>
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