[Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-09 Thread Wei Shao 
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/
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/
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct:
line 95: /cvmfs/
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>   [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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-13 Thread Douglas N. Greve 

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>   [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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.n

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-13 Thread Wei Shao 
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 
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>   [t

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-20 Thread Wei Shao 
External Email - Use Caution

Hi,  Douglas

Sorry 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 
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 
> 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
>>

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-21 Thread Antonín Škoch 
External Email - Use Caution

Hi, Wei,


I would recommend to use dwifslpreproc script from mrtrix3 suite instead.

https://secure-web.cisco.com/1EpWqxf1LAo_9zZza7TvgPO7braRXyCjrY1yjVepX0Quqt-Ac1b-Jn1Bh1FMt6xWVwHRFmBKER3JkEFvxatFejuIwONb_4DCvX9cyy6h5BZ1bkwko3O30atWjFN-IqfBXI0e7bQXosIN4lrDQ0lw08AZUxZqKtVgZ-Q7YvlGqpDZa8c-7oRILZnLvvCaWAEZUN_QbVyns2LK4u1ubZIh2_mmAJ2bNf_9DYJgvbBPm8itBEAp-ED3I4T7xxrMD5ySuakXnPoQVJIFy6pzkfkNAAA/https%3A%2F%2Fmrtrix.readthedocs.io%2Fen%2Flatest%2Freference%2Fcommands%2Fdwifslpreproc.html
https://secure-web.cisco.com/1x4J2O9fRBQ-_W3GZxA80BfHGRWeAweDMEk3J-4c05mkYqy4dUQ3Cct54nPatNih3zSWTJ1Db_2vqfNPpe-m6H_HaHvozi5-TBX6Uav8OxegqcnfLwXtp0GaLneyuC85uXK8Hsac-IHrCyLwzu-IW_KfvP46bmSR32OL5gfxgGSojUeBtYoZocz7f89yw7dZ5fym7qxh6DMGUoXOQKdGTtYwwmk1YrvuSavv7_0RFSRvc7BvxMa0qzNf-QUhepiBvCxZ-rBykf9ZmM0Ti-HxXPQ/https%3A%2F%2Fwww.mrtrix.org%2F
https://secure-web.cisco.com/1FCDgvyDpzpGDaCElxPoPOlaMat5sHcKsF-7uMfRSQe8dp51q8594fSetwAl8nGB4B1xjWJ-6e2VcEXb_drs8EdeTr7ZqXl87NS3x05c4M5hAmWcwzxwIlzeY8jLZ8uZoL9hNODjUT4mfNh8-kCNc2FESAgfwS8mcRyU3XyiwdybpZrYQo_DPAgJPRRDbempjAdm6R8x0dIyuuG8aaLHQPZZZ09qomAo7mUbc_LEdWOxljI15zVl4bwPYzexF5C28Capn4dBU21nufspN-YOa9A/https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FFDT%2FUserGuide

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 
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 
> 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

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

2020-11-29 Thread Greve, Douglas N.,Ph.D. 
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 
"secure-web.cisco.com" claiming to be 
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 
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
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/a