On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve <dgreve@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
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: 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: 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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