Can you upgrade to 6 or higher?
On 11/13/2020 1:32 PM, Wei Shao wrote:
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/MailScanner has detected a possible fraud attempt from
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[weishao@gra-login2 ~]$
Best,
Wei
On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto: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
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line 95: /cvmfs/MailScanner has detected a possible fraud attempt from
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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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