External Email - Use Caution
Hi, Wei,
I would recommend to use dwifslpreproc script from mrtrix3 suite instead.
https://secure-web.cisco.com/1EpWqxf1LAo_9zZza7TvgPO7braRXyCjrY1yjVepX0Quqt-... https://secure-web.cisco.com/1x4J2O9fRBQ-_W3GZxA80BfHGRWeAweDMEk3J-4c05mkYqy... https://secure-web.cisco.com/1FCDgvyDpzpGDaCElxPoPOlaMat5sHcKsF-7uMfRSQe8dp5...
The eddy_correct tool used in dt_recon is very old and suboptimal method for DWI preprocessing.
Antonin
Hi, DouglasSorry 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 CautionHi, 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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