What version of FSL are you using?
On 11/10/2020 12:19 AM, Wei Shao wrote:
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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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