[Freesurfer] TRACULA error: lowb_brain_mask.bbr.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi FreeSurfers,

I am attempting to run tracula on longitudinal DTI data however during trac-all 
-prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz 
from mri_concat.


#-

/Applications/freesurfer/7.3.2/bin/trac-preproc

#-

#@# Intra-subject registration (base template) Mon Nov 13 14:13:56 PST 2023

mri_concat --i 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/aparc+aseg_mask.nii.gz
 --min --o 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz

ninputs = 1

Checking inputs

nframestot = 1

Allocing output

Done allocing

nframes = 1

Computing min across all frames

Writing to 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz

mri_concat --i 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz
 --min --o 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

ninputs = 1

Checking inputs

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

ERROR: reading 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed 
Oct  4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Nov 13 14:13:58 PST 2023


I am using FreeSurfer 7.3.2 on an iMac Pro running Ventura 13.6.1.


Any suggestions for how to clear this error would be greatly appreciated!


Thank you,


Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi Woo-Suk,

The change you suggested did work when i made a second attempt.  The files were 
getting mixed in with the trac-preproc copy I created in case of errors.

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Woo-Suk Tae 

Sent: Monday, October 30, 2023 8:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you 
corrected?

best regards

Woo-Suk, Tae

On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi Woo-Suk,

I was able to make the change however, I am still receiving the same error.


mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

reading from 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

Darwin 
PSYC-C02DP05D0833.stanford.edu<http://secure-web.cisco.com/1hfiYFGQhzjFVnZavl-fTMAJOa_JE9bzjVA8nrzYF3yRbWe4VzGqfDesdrYhWYxOR5nsphpAwt1gyWvjHUHQdWEiA9qbrEWmQFdrmnEbo5BDDYjQ6O-KnWv9c1QD7bhdcX5EzX6HzbBIFX0ir6HvpcK-2VMbNvy-cC26PgUPAXxjO_gI43uMjUhPyKeIEY1j_k9KKcxCGxdVYQrCLxLSs0xrHxxEIjtuNcmEEMkiviG30UZwoYYCAL2B9dYpccBFZ_PcMy-xXHxsefxUDMgA-ehOWri2bOrXsubbsWH6K3u6VLMCziEZcNfVMRF2yYF4_/http%3A%2F%2FPSYC-C02DP05D0833.stanford.edu>
 22.6.0 Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; 
root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023

Do you have any further suggestions to fix this issue?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Woo-Suk Tae mailto:woos...@gmail.com>>
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can 
get  an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic 
nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medic

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Woo-Suk Tae]

External Email - Use Caution

Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file,
you corrected?

best regards

Woo-Suk, Tae

On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens 
wrote:

> External Email - Use Caution
>
> Hi Woo-Suk,
>
> I was able to make the change however, I am still receiving the same
> error.
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
>
> reading from
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...
>
> error: niiRead(): error opening file
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
>
> Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version
> 22.6.0: Fri Sep 15 13:39:52 PDT 2023;
> root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023
>
> Do you have any further suggestions to fix this issue?
>
> Thank you,
>
> Lauren Stephens
>
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae <
> woos...@gmail.com>
> *Sent:* Saturday, October 28, 2023 10:34 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation
> aparc+aseg+thalnuc.nii.gz
>
>
> External Email - Use Caution
>
> Hi, Lauren Stephens.
> If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
> can get  an aparc+aseg+thalnuc.nii.gz file without error, and make
> subthalamic nuclei related tracks.
>
> #chage codes from
> set cmd = mri_binarize
> set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
> set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)
>
> #to
> set cmd = mri_convert
> set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
> set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)
>
> Woo-Suk, Tae Ph.D.
> Seoul, Korea
>
> On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
> wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfers,
>
> I am trying to troubleshoot an error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The
> subregion segmentation prior to trac-all -prep was successful and 
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated.  In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1jsysVCI-hdZBfcsIdJ0SdbSI3Nhmea9kE6wDEb2pNW-LnsK8yE4zpaUvfC4oDCLTEGRbuJm2HlBf5tlzb7YhGOU0zcWpl_PSsejlTzAk5toKxCJxgdSTt3sUkPwpuBeCL0-zm3O4ZTDfwDuh0aZ3AmbFRfZIexCVr9i7FjzBZq56MuM0XN0vbYAwcKe6tZzij4TW2XEjg0pLvvMpv756o_EIqBXgFyTqdIbBRAs0272gvcYebjMFHLcDF3khd_VKD8qm6K0A-hVZSJTqQH9met_fl77QEiQGBxj2fBsl42EtTLq8g0R7nPxlzTRikmiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> &

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi Woo-Suk,

I was able to make the change however, I am still receiving the same error.


mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

reading from 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Fri 
Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023

Do you have any further suggestions to fix this issue?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Woo-Suk Tae 

Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can 
get  an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic 
nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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https://secure-web.cisco.com/1gz6yn9QsgV_Hqri9jvSaBRiteK8cFRBmdURe3A_IGo7zDbORmSXD_VjdMoKGHx2-m3l-VdTI5FLGudgCKE-lnbq2azxQG7TkhnkngYMbn2N1mTs46_HjFjkgrs8WI4TwFkig58JvhBASXiAE-39pyVFor_W3_wRRni-0B5WayaDQ1q9WTiT02s8Q3CipEVBJ0PbbI0L9OGmunSHoSwznKK17rGUv85NsLFj0pNDs18ih8AFbvnaY8qsjAkcCTNlYtTL6VW2hCf0PazI2OXC-dkoaWXI4vfQMg_aVRggUUtB6G-tDwKHj0dSGUS7uhQGXPiSeDb9mRCl5J1hHf4fzhQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1mbZ6TiwAjZyXHWt0vWwUF4mmwAlMoO41mwD4m80I0xkM0yxR3a_Z7YeDCGNXtP3wyVlhdxN0ChbZDaAjEuhQoghPYxMAJSteUSqeB7MF4-L0Tf8FsDLFXiWNz-KnU-re_mqlz-AXa2mAnoH8hvKI6IJ23ANyNMGBis5RO1oMhTy5yDaI833kgeGvPVzrc3UXngF13YAI3utqkrkb0ssut4jifFVnS-uAlo1HkadPcWDYYEsre38v2YeJ7XQTOanc719223QJmCY28ugu02PGBxFplISpgGt8DWtq6RSKnosmxtFNVPUXPLSCWLjQ8b1R/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>


--


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr<mailto:ws...@korea.ac.kr>, 
woo

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Woo-Suk Tae]

External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get  an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
wrote:

> External Email - Use Caution
>
> Hi FreeSurfers,
>
> I am trying to troubleshoot an error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The
> subregion segmentation prior to trac-all -prep was successful and 
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated.  In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1mbZ6TiwAjZyXHWt0vWwUF4mmwAlMoO41mwD4m80I0xkM0yxR3a_Z7YeDCGNXtP3wyVlhdxN0ChbZDaAjEuhQoghPYxMAJSteUSqeB7MF4-L0Tf8FsDLFXiWNz-KnU-re_mqlz-AXa2mAnoH8hvKI6IJ23ANyNMGBis5RO1oMhTy5yDaI833kgeGvPVzrc3UXngF13YAI3utqkrkb0ssut4jifFVnS-uAlo1HkadPcWDYYEsre38v2YeJ7XQTOanc719223QJmCY28ugu02PGBxFplISpgGt8DWtq6RSKnosmxtFNVPUXPLSCWLjQ8b1R/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>


-- 


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
  wo os...@gmail.com

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Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi FreeSurfers,

I wanted to follow up on my post.  I am still receiving this error when running 
the preprocessing step of TRACULA.  We have run our files without the thalamic 
nuclei included, however, that is not ideal because we are interested in tracts 
that end nearby.

I believe this is a bug in the code because otherwise the following TRACULA 
steps run all the way through with no error.

If you have any suggests we would really appreciate it!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lauren Stephens 

Sent: Friday, October 6, 2023 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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[Freesurfer] Freesurfer TRACULA Error

[Stylianos Charalampous]

External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to apply TRACULA for the reconstruction of white matter pathways 
but I am getting an error when running the trac-all command which I haven’t 
managed to resolve. The TRACULA is applied on an MRI sample from the ADNI 
dataset that has been preprocessed using recon-all.

I've searched the list but I was not able to found a similar error. Does anyone 
have any thoughts on how to trouble-shoot this one?
I have also attached the trac-all.log in case it's of any use.

1) FreeSurfer version: 7.3.2
2) Platform: Ubuntu 22.04
3) trac-all.log: see attached

Kind regards,
Stylianos Charalampous



trac-all.log
Description: trac-all.log
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Re: [Freesurfer] Tracula error in path construction

[Yendiki, Anastasia]

Hi Oshadi - Is this the same subject as before, the one that runs on your 
workstation but not on the cluster? Did the first error message (killed when 
loading the bedpostx samples) get solved?

More generally, it's hard to tell what caused an error just by looking at the 
last few lines of output. Please attach your entire trac-all.log file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, July 25, 2022 3:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Hi Anastasia
Thanks so much for the reply.
My trac-path worked until last step-it says dmric path done but it exited 
without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat 
etc for individual tracts
The error I get is:
fslmaths 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/path.pd.nii.gz
 -thr 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/tmp.nii.gz
Error: no output filename specified!
I am not sure if I am supposed to specify a output file name in the 
configuration file ( in addition to output directory)

Also, I have used a similar configuration file for other subjects -their 
pre-processing is done without errors but they miss nodif_brain_mask.nii so I 
can't run bedpostx

Any suggestion on what I can try for both these issue is really appreciated
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


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Re: [Freesurfer] Tracula error in path construction

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia
Thanks so much for the reply.
My trac-path worked until last step-it says dmric path done but it exited 
without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat 
etc for individual tracts
The error I get is:
fslmaths 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/path.pd.nii.gz
 -thr 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/tmp.nii.gz
Error: no output filename specified!
I am not sure if I am supposed to specify a output file name in the 
configuration file ( in addition to output directory)

Also, I have used a similar configuration file for other subjects -their 
pre-processing is done without errors but they miss nodif_brain_mask.nii so I 
can't run bedpostx

Any suggestion on what I can try for both these issue is really appreciated
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30018
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii
set bvecfile = 30018/bvecs.txt
set bvalfile = 30018/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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Re: [Freesurfer] Tracula error in path construction

[Yendiki, Anastasia]

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] Tracula error in path construction

[Shanika Jayakody]

External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30018
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii
set bvecfile = 30018/bvecs.txt
set bvalfile = 30018/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hi Mona - It's hard to tell from the 2 lines of output that you sent. Do you 
see any other output?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Wednesday, December 15, 2021 11:15 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

Hello,

I wanted to follow up on this question. I appreciate it much if you could 
suggest me any solutions. I checked my space and I have 3.5 T free space, so 
It’s definitely not a space problem.

Thanks,
Mona


On Dec 14, 2021, at 12:59 PM, Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Yes, here it is:

Volume information for data.nii.gz
  type: nii
dimensions: 120 x 120 x 69 x 132
   voxel sizes: 2.00, 2.00, 2.00
  type: SHORT (4)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -69.0, zend: 69.0
TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 132
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-1.7665
  : x_a =  -0., y_a =   1., z_a =  -0., c_a =-0.6018
  : x_s =   0., y_s =   0., z_s =   1., c_s =-5.1718
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.   0.  -0.   118.2335
   -0.   2.  -0.  -120.6018
0.   0.   2.   -74.1718
0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:
   -0.5000  -0.  -0.59.1168
   -0.   0.5000  -0.60.3009
   -0.  -0.   0.500037.0859
   -0.  -0.  -0. 1.


On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Is there a dmri/data.nii.gz? Can you run mri_info on it please?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks,
Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Any chance you're low on disk space?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Hello,

I wanted to follow up on this question. I appreciate it much if you could 
suggest me any solutions. I checked my space and I have 3.5 T free space, so 
It’s definitely not a space problem.

Thanks,
Mona


On Dec 14, 2021, at 12:59 PM, Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Yes, here it is:

Volume information for data.nii.gz
  type: nii
dimensions: 120 x 120 x 69 x 132
   voxel sizes: 2.00, 2.00, 2.00
  type: SHORT (4)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -69.0, zend: 69.0
TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 132
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-1.7665
  : x_a =  -0., y_a =   1., z_a =  -0., c_a =-0.6018
  : x_s =   0., y_s =   0., z_s =   1., c_s =-5.1718
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.   0.  -0.   118.2335
   -0.   2.  -0.  -120.6018
0.   0.   2.   -74.1718
0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:
   -0.5000  -0.  -0.59.1168
   -0.   0.5000  -0.60.3009
   -0.  -0.   0.500037.0859
   -0.  -0.  -0. 1.


On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Is there a dmri/data.nii.gz? Can you run mri_info on it please?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks,
Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Any chance you're low on disk space?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Frees

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Yes, here it is:

Volume information for data.nii.gz
  type: nii
dimensions: 120 x 120 x 69 x 132
   voxel sizes: 2.00, 2.00, 2.00
  type: SHORT (4)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -69.0, zend: 69.0
TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 132
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-1.7665
  : x_a =  -0., y_a =   1., z_a =  -0., c_a =-0.6018
  : x_s =   0., y_s =   0., z_s =   1., c_s =-5.1718
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.   0.  -0.   118.2335
   -0.   2.  -0.  -120.6018
0.   0.   2.   -74.1718
0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:
   -0.5000  -0.  -0.59.1168
   -0.   0.5000  -0.60.3009
   -0.  -0.   0.500037.0859
   -0.  -0.  -0. 1.


On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Is there a dmri/data.nii.gz? Can you run mri_info on it please?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks,
Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Any chance you're low on disk space?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Is there a dmri/data.nii.gz? Can you run mri_info on it please?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks,
Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Any chance you're low on disk space?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

_

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

How much space would I need to run this?

Thanks,
Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Any chance you're low on disk space?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

___
Fr

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Any chance you're low on disk space?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Yes.

dmri.bedpostX has these files in it:

diff_slices  empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281






Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent t

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hard to tell from the two lines. Did any files get created in bedpostX output 
directory?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I 
appreciate it much if you please let me know what the issue is.

Thanks,
Mona


- Bedpostx Monitor -
An error ocurred. Please check file 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769
Killed

bedpostx_pre.e9769:
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77:  9819 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data
/usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78:  9837 Illegal 
instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask





On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[fsbuild]

External Email - Use Caution

Hello Jürgen,
Try running the bash shell from the terminal, e.g., before running anything 
type,
$ bash
- and then try your command again.
If that works then I would set your login shell to bash (as the default is 
dash).

- R.
On Dec 7, 2021, at 01:46, juergen.haen...@upd.unibe.ch 
wrote:External Email - Use 
CautionDear Anastasiathank a 
lot for the answer.We use Ubuntu 18.04..6 LTS.When we run the command directly 
in the terminalbedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmriwe
 get the sane error/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwhen we run 
the command you sent in your last email, i.e. fslver=(`cat 
$FSLDIR/etc/fslversion | sed 's/\./ /g’`)we get the following errorBadly placed 
()’s.Thanks in advanceRegardsJürgenAm 03.12.2021 um 00:02 schrieb Yendiki, 
Anastasia <ayend...@mgh.harvard.edu>:Hi Jürgen - I haven't 
been able to replicate your error locally. What operating system are you 
running it on? And what do you see if you try run the line that errors out 
directly on the command line? The line is:fslver=(`cat $FSLDIR/etc/fslversion | 
sed 's/\./ 
/g'`)Thanks,Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf 
of juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>Sent: Thursday,
 November 25, 2021 1:40 
AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiacat 
$FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the newest version 
availableThanksJürgenAm 24.11.2021 um 15:53 schrieb Yendiki, Anastasia 
<ayend...@mgh.harvard.edu>:Hi Jürgen - Can you check what's in this file: 
$FSLDIR/etc/fslversion 
?Thanks,Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf 
of juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>Sent: Wednesday,
 November 24, 2021 12:53 
AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiawhen I 
type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.this is 
the right path where fsl is installed.however, I can start FSL GUI and also 
other FSL commands.Best JürgenAm 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
<ayend...@mgh.harvard.edu>:Hi Jürgen - What's your $FSLDIR set 
to?Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf 
of juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>Sent: Tuesday,
 November 23, 2021 9:36 
AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiathank you 
for the new option. It works. Now we were able to finish trac-all -prep without 
any further problem.However, when we try to run trac-all -bedp, the following 
error occurred:--trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txtINFO:
 SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjectsINFO:
 Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720Actual
 FREESURFER_HOME /usr/local/freesurferln -sf 
.../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gzWARN:
 Running bedbostx locally - this might take a whileWARN: It is recommended to 
run this step on a clusterbedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/usr/local/freesurfer/bin/bedpostx_mgh:
 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" 
unexpected——we have found this message from 2014 MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/18T9Slnh9GWxjhAdkDbh-RBVdxl_EEto9Zyi1RBkLvNdMSM528wxx0DwvoXJvimRoQPNeWwMfDW27kRTu5zblRhBH7LYQ5b62Lkv_u826S0xvdMGDvPTvjE_vqLT27vcDbs8CqPJkN_i3FItV3Vin4zMDjki43kHFB5VR2tYOlDSiM2xbEvXyMBL3I8H48x8J4UQIjYKD0wbLnwbv93I-5Vpr

Re: [Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu> 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Tracula error

[Nasiriavanaki, Zahra,M.D.]

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA error

[Yendiki, Anastasia]

Hi Stephanie - Please send along your configuration file and the log file from 
scripts/trac-all.log. It's hard to guess just by seeing the error message. 
Thanks!

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Stephanie Otto 

Sent: Thursday, December 2, 2021 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA error


External Email - Use Caution

Hello Freesurfer Team,

I am trying to get TRACULA running on two different machines (Macbook Pro OS 
11.6 and Mac desktop OS 10.14.6). I get the same error message on both devices, 
which is:


domainname: Command not found.

ERROR: for B0 distortion correction with reverse-polarity DWIs

ERROR: or for model-based eddy-current distortion correction,

ERROR: must specify PE direction

I can't find an answer as to how to correct this in the email support archive 
or through Google. If anyone could assist me, I would greatly appreciate it. 
Thanks in advance for all your help.

Best,
Stephanie Otto
Doctoral Candidate, Cognitive and Brain Sciences Program
Department of Psychology, MSS 424/MS0296
University of Nevada, Reno
so...@nevada.unr.edu<mailto:so...@nevada.unr.edu>

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[Yendiki, Anastasia]

Hi Jürgen - I haven't been able to replicate your error locally. What operating 
system are you running it on? And what do you see if you try run the line that 
errors out directly on the command line? The line is:

fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`)

Thanks,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
juergen.haen...@upd.unibe.ch 
Sent: Thursday, November 25, 2021 1:40 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file


External Email - Use Caution

Dear Anastasia

cat $FSLDIR/etc/fslversion reported

6.0.5.1:57b01774

I guess its the newest version available

Thanks
Jürgen

Am 24.11.2021 um 15:53 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?

Thanks,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Wednesday, November 24, 2021 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also other FSL commands.

Best Jürgen

Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - What's your $FSLDIR set to?

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cis

[Freesurfer] TRACULA error

[Stephanie Otto]

External Email - Use Caution

Hello Freesurfer Team,

I am trying to get TRACULA running on two different machines (Macbook Pro
OS 11.6 and Mac desktop OS 10.14.6). I get the same error message on both
devices, which is:

domainname: Command not found.

ERROR: for B0 distortion correction with reverse-polarity DWIs

ERROR: or for model-based eddy-current distortion correction,

ERROR: must specify PE direction

I can't find an answer as to how to correct this in the email support
archive or through Google. If anyone could assist me, I would greatly
appreciate it. Thanks in advance for all your help.

Best,
Stephanie Otto
Doctoral Candidate, Cognitive and Brain Sciences Program
Department of Psychology, MSS 424/MS0296
University of Nevada, Reno
so...@nevada.unr.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[juergen.haenggi]

External Email - Use Caution

Dear Anastasia

cat $FSLDIR/etc/fslversion reported

6.0.5.1:57b01774

I guess its the newest version available

Thanks
Jürgen

Am 24.11.2021 um 15:53 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?

Thanks,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Wednesday, November 24, 2021 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also other FSL commands.

Best Jürgen

Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - What's your $FSLDIR set to?

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/18xjBXjYrSIh4g0qz-fFXlwJgDIeIMDfSbkhPM8uvqPPGcVddtCIhZ8ABN_w7isJwzI_wtuWS2yidSZFU4q07wxeimacwy7Hwlw2cHtizyTigkC2RY15tCO8--P4hYg05IjKCEdRWO8_sz3oKZmtBJnC3yj-UcwySpWQ623hKCzJmNOOvni7-FYPMR1QCeHavw_HnA-7VY2RWR4M5vGJtcwVl0Y2Q2B5AJlPAxKT9EEcDjEmB2rEqzn4AO_DCDsjETnxU6RbUJNBNzN_0dJd1-UyIz3gCX_h9s2vI3DIzTypIs49fyF5AlCLzk9Irt8RQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1WFfJGWlfR-CHru05HKAhlQNPmzcDrEz1dQ3p9REyaVrGRqKzyHFg-xHFCaF_j4WnB6b_PlOyWnm1ir1ROhk0Xy1gmDeYyh8OGeQJxFcQDVu156I2rdFKn2pc3LGZBYg5nCwfjCzBTUgCSNV6jNUToL0hOdnMGIk7gMJ6O4sTNPqm8hJGVhEcaEbc

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[Yendiki, Anastasia]

Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?

Thanks,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
juergen.haen...@upd.unibe.ch 
Sent: Wednesday, November 24, 2021 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file


External Email - Use Caution

Dear Anastasia

when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also other FSL commands.

Best Jürgen

Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - What's your $FSLDIR set to?

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc<https://secure-web.cisco.com/1Y4QR7zMqS-P5ZMuFX5CW29WQG7q8VdLfH5Xj6op25PoQPb5cz8IOhb_ze2LaFMa_EDKXa9XOjy6ZjoLM4uTXjxAvfeInswYAPJClnZiR-R9F10WB2wT9Y0hO0Hci3vHQEBH2b981DSDPisct-IaANfoRoiItgBqQkYx-H__novSCl8nW_lcy8OXaBSqrXy6qjHSdn-sWYa43HZHwOqBheaTd2iqJt8wAS0ba5VrCWxq22Tg_PmwuhF1puRtKvGhFDL-NVvGJwHN4338vS94oi-w37RqEr_D5AJQw9nF5aybKZOaxAcDUr1O0W8YKkwEQ/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>

>From now on the dTE from the config file will supersede the one from the DICOM 
>header. Thanks for finding this and let us know if there are any other issues.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesur

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[juergen.haenggi]

External Email - Use Caution

Dear Anastasia

when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also other FSL commands.

Best Jürgen

Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - What's your $FSLDIR set to?

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/13zK0Djkg62WdCAybVGjaCxhgZNPuk7EoYlAUJL4U0Vy0Tmg5JUsOZYEjDDRd7IGoJli2IcfLJklmggJ4cXp3IZ-fzZ7ZZ9b0Q4VTnAgvDu13R7pvc74ST80MsZM1vs_RYcG42HSoo_6iXt9pSDNuHruR9AJiYdETrSfd66th3JWtjstX3Lt8AIQJAl7baTDUsK7JnbbC3-VN6NzFNdV-_fxPgZnI4UA3K4JvcNzJKR_cE7AgH1L-7yNXpfPd8Qjpu71cJlhYXh6YtTNKzo_2iSIsK3LAUKSyHw8BMXM9bfomNgCTVZ7aYNz1tK-L1xEf/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1OxzZvFvolcg9BuBExqA2Qy2vj9Y5FcY13wmWMjCwANRN0sGmUimrjM-mM2SuPhpNB-lo3IQszPtQYmwo_KfSFOX4JOkdiI_tQDF8hIex5yT_HxtMm7nqUU-BQgG3DebfeOLaqacF45AkpGBSYc_qWthEAYhcKSiQ6wsKIxfzFN5JCvJr56FnDTCZjofKar_FQYYashUz4IcTWsCApJR9So1FzofoxJ7n0XLwgSFIldc31kTFEbpIrLa2aKwjtOawMEdU4TOzAIfRLgqMrw0Bpi9ktm2Dq2zp5-M4AU7QRS4BAMD56dnLkhvlatV-npdx/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc<https://secure-web.cisco.com/1Y4QR7zMqS-P5ZMuFX5CW29WQG7q8VdLfH5Xj6op25PoQPb5cz8IOhb_ze2LaFMa_EDKXa9XOjy6ZjoLM4uTXjxAvfeInswYAPJClnZiR-R9F10WB2wT9Y0hO0Hci3vHQEBH2b981DSDPisct-IaANfoRoiItgBqQkYx-H__novSCl8nW_lcy8OXaBSqrXy6qjHSdn-sWYa43HZHwOqBheaTd2iqJt8wAS0ba5VrCWxq22Tg_PmwuhF1puRtKvGhFDL-NVvGJwHN4338vS94oi-w37RqEr_D5AJQw9nF5aybKZOaxAcDUr1O0W8YKkwEQ/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>

>From now on the dTE from the config file will supersede the one from the DICOM 
>header. Thanks for finding this and let us know if there are any other issues.

Anastasia.

From: 
freesurfe

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[Yendiki, Anastasia]

Hi Jürgen - What's your $FSLDIR set to?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
juergen.haen...@upd.unibe.ch 
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file


External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc<https://secure-web.cisco.com/1Y4QR7zMqS-P5ZMuFX5CW29WQG7q8VdLfH5Xj6op25PoQPb5cz8IOhb_ze2LaFMa_EDKXa9XOjy6ZjoLM4uTXjxAvfeInswYAPJClnZiR-R9F10WB2wT9Y0hO0Hci3vHQEBH2b981DSDPisct-IaANfoRoiItgBqQkYx-H__novSCl8nW_lcy8OXaBSqrXy6qjHSdn-sWYa43HZHwOqBheaTd2iqJt8wAS0ba5VrCWxq22Tg_PmwuhF1puRtKvGhFDL-NVvGJwHN4338vS94oi-w37RqEr_D5AJQw9nF5aybKZOaxAcDUr1O0W8YKkwEQ/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>

>From now on the dTE from the config file will supersede the one from the DICOM 
>header. Thanks for finding this and let us know if there are any other issues.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem occurred wrt the field map for which we did not 
find any solution yet:

-
writing to 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...
mri_probedicom --i 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
 > 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat
ERROR: Need dTE for field map 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[juergen.haenggi]

External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all 
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:

--
trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——

we have found this message from 2014

https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html

is it meanwhile possible to run bedpostx_mgh also locally or do we have to run 
bedpostx directly as suggested in the link?

Best
Jürgen


Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� 
One more bug fix, in the same place (and then in the dev version):
https://secure-web.cisco.com/1Y4QR7zMqS-P5ZMuFX5CW29WQG7q8VdLfH5Xj6op25PoQPb5cz8IOhb_ze2LaFMa_EDKXa9XOjy6ZjoLM4uTXjxAvfeInswYAPJClnZiR-R9F10WB2wT9Y0hO0Hci3vHQEBH2b981DSDPisct-IaANfoRoiItgBqQkYx-H__novSCl8nW_lcy8OXaBSqrXy6qjHSdn-sWYa43HZHwOqBheaTd2iqJt8wAS0ba5VrCWxq22Tg_PmwuhF1puRtKvGhFDL-NVvGJwHN4338vS94oi-w37RqEr_D5AJQw9nF5aybKZOaxAcDUr1O0W8YKkwEQ/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc

>From now on the dTE from the config file will supersede the one from the DICOM 
>header. Thanks for finding this and let us know if there are any other issues.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear Anastasia

thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem occurred wrt the field map for which we did not 
find any solution yet:

-
writing to 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...
mri_probedicom --i 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
 > 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat
ERROR: Need dTE for field map 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
Linux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18 
13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021
---

For some reasons, dTE cannot be extracted from the b0info.dat file (see 
attachment). Indeed, there is only one echo time entry (EchoTime 7.38) in the 
b0info.dat file maybe due to the fact that there is also only one echo time 
entry (EchoTime 7.38) in the DICOM header.

Specifying dTE = 2.46 in the config file does not solve the problem, neit

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[Yendiki, Anastasia]

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out ?? 
One more bug fix, in the same place (and then in the dev version):
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc

>From now on the dTE from the config file will supersede the one from the DICOM 
>header. Thanks for finding this and let us know if there are any other issues.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
juergen.haen...@upd.unibe.ch 
Sent: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file


External Email - Use Caution

Dear Anastasia

thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem occurred wrt the field map for which we did not 
find any solution yet:

-
writing to 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...
mri_probedicom --i 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
 > 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat
ERROR: Need dTE for field map 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
Linux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18 
13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021
---

For some reasons, dTE cannot be extracted from the b0info.dat file (see 
attachment). Indeed, there is only one echo time entry (EchoTime 7.38) in the 
b0info.dat file maybe due to the fact that there is also only one echo time 
entry (EchoTime 7.38) in the DICOM header.

Specifying dTE = 2.46 in the config file does not solve the problem, neither 
with NIFTI nor DICOM file format for the field map.
In a former email, you mentioned that this should be possible.

The log and config file are also attached.

Is there any work around for this problem?

Thanks in advance
Best,
Jürgen



Am 20.11.2021 um 18:11 schrieb Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>:

Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case 
when you have 1 DWI run only. I committed a bug fix for this. For now you can 
get it from here (and it should get merged into the dev version in a couple of 
days):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc<https://secure-web.cisco.com/1l0klX-YanhXQKwsaHZLsP2jyZS1-cdJ_xY-FMa2uG__1HM8l3SLLeLQZuMu-2cvUofKMq-vD-wUvzIVynW1T0Em5IOaD2qQSclP2b6o3k_3hZ7Fwv5ACz79H_LQ74LLXgbvm-3WtcytqQtgssL52R_2e4I7kWwGmLUHlQ7aO2b-_15ehHxVs_hhhECG0MjMvGsNK99qQCVwhJ8CM0R0FQR4X1WWEGF49sRvxkehr2TbddfuoOK2TTsuBK0My3m60bmnIIJOhFtHQ82K-GLbV0RAExDaZV2caJG4Wp8W1ODbVvzZGGvjx5Vl4H06KJ1XC/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>

Can you please save this version of trac-preproc to your $FREESURFER_HOME/bin/ 
and tell us if it fixes the problem? Thank you for bringing this to our 
attention.

Best,
Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> 
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Wednesday, October 27, 2021 8:19 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution

Dear TRACULA experts

I try to run TRACULA FS7.2 on a Linux machine and get the following error (see 
below). A similar problem has already been reported in the archives, but I 
found no solution.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71032.html<https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[Yendiki, Anastasia]

Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case 
when you have 1 DWI run only. I committed a bug fix for this. For now you can 
get it from here (and it should get merged into the dev version in a couple of 
days):
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc

Can you please save this version of trac-preproc to your $FREESURFER_HOME/bin/ 
and tell us if it fixes the problem? Thank you for bringing this to our 
attention.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
juergen.haen...@upd.unibe.ch 
Sent: Wednesday, October 27, 2021 8:19 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file


External Email - Use Caution

Dear TRACULA experts

I try to run TRACULA FS7.2 on a Linux machine and get the following error (see 
below). A similar problem has already been reported in the archives, but I 
found no solution.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71032.html<https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71032.html>

Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“  
earlier in the run

mv -f 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals
 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals

it cannot be found by awk and as a result, I guess, the index.txt file is empty 
and therefore eddy_openmp terminated.

How can I fix this problem?

The terminal output, log and config files are attached.

Thank you for any advise in advance
Regards
Jürgen


—— error 

awk: fatal: cannot open file 
`/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals'
 for reading (No such file or directory)
eddy_openmp 
--imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
 
--mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz
 
--bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
 
--bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
 
--acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt
 
--index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
 --data_is_shelled 
--out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError:  Error when attempting to read --index file 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 
20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021

upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
——


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[Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

[juergen.haenggi]

External Email - Use Caution

Dear TRACULA experts

I try to run TRACULA FS7.2 on a Linux machine and get the following error (see 
below). A similar problem has already been reported in the archives, but I 
found no solution.

https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71032.html

Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“  
earlier in the run

mv -f 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals
 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals

it cannot be found by awk and as a result, I guess, the index.txt file is empty 
and therefore eddy_openmp terminated.

How can I fix this problem?

The terminal output, log and config files are attached.

Thank you for any advise in advance
Regards
Jürgen


—— error 

awk: fatal: cannot open file 
`/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals'
 for reading (No such file or directory)
eddy_openmp 
--imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
 
--mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz
 
--bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
 
--bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
 
--acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt
 
--index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
 --data_is_shelled 
--out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError:  Error when attempting to read --index file 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 
20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021

upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
——


upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
 trac-all -prep -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example.txt
INFO: SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/dmrirc.local
 -log 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.log
 -cmd 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Wed Oct 27 13:41:01 CEST 2021
rm -f 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals
 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm
 
/mnt/981dac6a

Re: [Freesurfer] TRACULA error: missing output volume name

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

It is working!-thanks so much for your help.

Regards,
Shanika

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, March 18, 2021 12:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name

Hi Shanika - Can you try separating the "=" signs from the variable names in 
the config file with a space?

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, March 18, 2021 9:55 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Hi Anastasia

Thanks so much for your reply. I have attached herewith the scripts/log file 
-please let me know if you need anything else.

Regards,


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name

Hi Shanika - Can you please send the full log file from scripts/trac-all.log? 
It's hard to figure out what causes the error without seeing the full output. 
Nothing looks unusual in the config file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Dear FreeSurfer team

I have been running TRACULA for some time now but recently, I come across a 
message "missing output volume name" and I cannot do preprocessing in new or 
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format 
that I have been using.

Any advice on this is appreciated. I have attached one of the configuration 
files.
Thanks,
Shanika
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Re: [Freesurfer] TRACULA error: missing output volume name

[Yendiki, Anastasia]

Hi Shanika - Can you try separating the "=" signs from the variable names in 
the config file with a space?

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, March 18, 2021 9:55 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Hi Anastasia

Thanks so much for your reply. I have attached herewith the scripts/log file 
-please let me know if you need anything else.

Regards,


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name

Hi Shanika - Can you please send the full log file from scripts/trac-all.log? 
It's hard to figure out what causes the error without seeing the full output. 
Nothing looks unusual in the config file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Dear FreeSurfer team

I have been running TRACULA for some time now but recently, I come across a 
message "missing output volume name" and I cannot do preprocessing in new or 
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format 
that I have been using.

Any advice on this is appreciated. I have attached one of the configuration 
files.
Thanks,
Shanika
___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] TRACULA error: missing output volume name

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks so much for your reply. I have attached herewith the scripts/log file 
-please let me know if you need anything else.

Regards,


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error: missing output volume name

Hi Shanika - Can you please send the full log file from scripts/trac-all.log? 
It's hard to figure out what causes the error without seeing the full output. 
Nothing looks unusual in the config file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Dear FreeSurfer team

I have been running TRACULA for some time now but recently, I come across a 
message "missing output volume name" and I cannot do preprocessing in new or 
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format 
that I have been using.

Any advice on this is appreciated. I have attached one of the configuration 
files.
Thanks,
Shanika
Wed Mar 17 15:41:52 EDT 2021
/home/helena/Documents/freesurfer/subjects
/home/helena/Documents/freesurfer/bin/trac-all
-prep -c Configurationfile_Osh.txt
Subject 30024
SUBJECTS_DIR /home/helena/Documents/freesurfer/subjects
FREESURFER_HOME /home/helena/Documents/freesurfer
Actual FREESURFER_HOME /home/helena/Documents/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
helena
peter-ThinkStation-P520
Linux peter-ThinkStation-P520 4.15.0-137-generic #141~16.04.1-Ubuntu SMP Wed Feb 24 10:47:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  642289 
maxlocks unlimited
maxsignal642289 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:  164636836 4208204   156505448  104888 3923184   158875624
Swap:   1000444   0 1000444


Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/03/17-19:41:52-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: peter-ThinkStation-P520  Platform: Linux  PlatformVersion: 4.15.0-137-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/03/17-19:41:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena 

Re: [Freesurfer] TRACULA error: missing output volume name

[Yendiki, Anastasia]

Hi Shanika - Can you please send the full log file from scripts/trac-all.log? 
It's hard to figure out what causes the error without seeing the full output. 
Nothing looks unusual in the config file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error: missing output volume name


External Email - Use Caution

External Email - Use Caution

Dear FreeSurfer team

I have been running TRACULA for some time now but recently, I come across a 
message "missing output volume name" and I cannot do preprocessing in new or 
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format 
that I have been using.

Any advice on this is appreciated. I have attached one of the configuration 
files.
Thanks,
Shanika
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] TRACULA error: missing output volume name

[Shanika Jayakody]

External Email - Use Caution

Dear FreeSurfer team

I have been running TRACULA for some time now but recently, I come across a 
message "missing output volume name" and I cannot do preprocessing in new or 
old subjects (even subjects who completed preprocessing without error)
I have not made any change to the configuration files. It is the same format 
that I have been using.

Any advice on this is appreciated. I have attached one of the configuration 
files.
Thanks,
Shanika
setenv SUBJECTS_DIR /home/helena/Documents/freesurfer/subjects
set dtroot = /home/helena/Documents/freesurfer/subjects
set subjlist = 30024

set dcmlist=  
$SUBJECTS_DIR/30024/30024_WIP_110_DTI66d_2mm_SF3_SENSE_20200228131759_701.nii

set bveclist= $SUBJECTS_DIR/30024/bvecs_30024.txt

set bvallist= $SUBJECTS_DIR/30024/bvals.txt

set runlist = 1
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set pathlist = ( lh.cst_AS rh.cst_AS \
 lh.ilf_AS rh.ilf_AS \
 lh.unc_AS rh.unc_AS \
 fmajor_PP fminor_PP \
 lh.atr_PP rh.atr_PP \
 lh.cab_PP rh.cab_PP \
 lh.ccg_PP rh.ccg_PP \
 lh.slfp_PP rh.slfp_PP \
 lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
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Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia- Thank you for your reply! I will try another subject and see.

Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, November 2, 2020 11:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

Hi Oshadi - That does not sound normal. Is there anything wrong with the 
FreeSurfer segmentation of this subject?

Anastasia.

From: Shanika Jayakody 
Sent: Monday, November 2, 2020 10:33 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Hi Anastasia

Thanks so much- I think I got the error due to the format of the bvecs and bvals
Trac-all is running but for one person it is running for almost 5 days now- I 
assume that can't be normal?
It says 8/18 tracts are completed but these iterations I have attached in the 
text files are running for 5 days
I wonder if I should let it run or kill the process
thanks,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, October 28, 2020 12:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns 
are:
0 -0.793264
0 -0.394167
0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:
0  -0.793264  -0.453844
-0.2799370.976579   0.920768

Which one is the correct version?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
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External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
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Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Yendiki, Anastasia]

Hi Oshadi - That does not sound normal. Is there anything wrong with the 
FreeSurfer segmentation of this subject?

Anastasia.

From: Shanika Jayakody 
Sent: Monday, November 2, 2020 10:33 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Hi Anastasia

Thanks so much- I think I got the error due to the format of the bvecs and bvals
Trac-all is running but for one person it is running for almost 5 days now- I 
assume that can't be normal?
It says 8/18 tracts are completed but these iterations I have attached in the 
text files are running for 5 days
I wonder if I should let it run or kill the process
thanks,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, October 28, 2020 12:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns 
are:
0 -0.793264
0 -0.394167
0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:
0  -0.793264  -0.453844
-0.2799370.976579   0.920768

Which one is the correct version?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

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Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula<https://secure-web.cisco.com/18c10Fvl1Ui8giMqtzr7W2v4SHmyp_t3hCxViwBQ3ZXsUZEicgaxpNtrTU6gHJGeJxWFlE5wmgor6Jw6JFhwnYQt-G4ny6HpuESTsxijb156iE8Dto7jtPQm7j7CEi5_0r5fLA3PVaFOBxm-hkbDuBoznUFrbe4CWRHg7_rM-3TF2un2Cgx8F_q2b7XEjmbiRF13Hoz8xVl0ImfE9KRibNA/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FRunningTracula%26data%3D04%257C01%257Cshanika.jayakody%2540einsteinmed.org%257C0753eb6c20fa48735e9908d87af7b98a%257C9c01f0fd65e040c089a82dfd51e62025%257C0%257C0%257C637394551681983427%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D6VAL6DtX%252F%252FxJ2BaHKhLZaW438KJ3mqIrz69Iwb%252FkNJA%253D%26reserved%3D0>

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: fr

Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hi Michele - Do you get any other output on the screen? Can you attach your 
configuration file and trac-all.log? Thanks!

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Sent: Friday, October 30, 2020 12:44 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error


External Email - Use Caution

Hello all,
I am trying to run Tracula for one of my subjects and after creating the 
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.

I have run the SetUpFreeSurfer.sh script and echo $FSLDIR prints my fls 
directory. Adding export FSLDIR=/my/fls/path also does not fix the error,

Any suggestions?

Thank you very much,
Michele
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks so much- I think I got the error due to the format of the bvecs and bvals
Trac-all is running but for one person it is running for almost 5 days now- I 
assume that can't be normal?
It says 8/18 tracts are completed but these iterations I have attached in the 
text files are running for 5 days
I wonder if I should let it run or kill the process
thanks,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Wednesday, October 28, 2020 12:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns 
are:
0 -0.793264
0 -0.394167
0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:
0  -0.793264  -0.453844
-0.2799370.976579   0.920768

Which one is the correct version?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
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External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://secure-web.cisco.com/1J5hh7AgcOj1tdo-va-kiSPXCzMxQmIMchhFPavlfopBQeNsljgRr15qwXdJKiq-GyUoFj01HRTpMKbUBlbqVNubXcCD8OaX5wCfcmEE0TlUkI44o6fVTe-ixCwx3l4_fI_IfT1itkeTyVxJxLfaPgUEfb99U8jwPOalr652P99SNCUADnPujazS9OzxK9yHMJjmf1AVRY6Yk6iunpV_npQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula<https://secure-web.cisco.com/146GojQy4RiAvlA_6zW8bT2ny-knf7zanWC8SrvCeKZ-CR_2OUpWP5UDeNRcx3aIZH6-15JLfEJpvg9t75ZtsTYRMyjiAFzwmL0KJcumHCDsjsshLweBsuT8c7_HQvs_iz-brFCBH1XxZHnJIykqFyIstp69xv3rrCnSOedkMWD1bd42wRk3m-pc9W5iEAl90qSK_rdcNFuofSWbPeFfDFA/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FRunningTracula%26data%3D04%257C01%257Cshanika.jayakody%2540einsteinmed.org%257C0753eb6c20fa48735e9908d87af7b98a%257C9c01f0fd65e040c089a82dfd51e62025%257C0%257C0%257C637394551681983427%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D6VAL6DtX%252F%252FxJ2BaHKhLZaW438KJ3mqIrz69Iwb%252FkNJA%253D%26reserved%3D0>

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject l

[Freesurfer] Tracula error

[Michele Valotti]

External Email - Use Caution

Hello all,
I am trying to run Tracula for one of my subjects and after creating the
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.

I have run the SetUpFreeSurfer.sh script and echo $FSLDIR prints my fls
directory. Adding export FSLDIR=/my/fls/path also does not fix the error,

Any suggestions?

Thank you very much,
Michele
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Yendiki, Anastasia]

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns 
are:
0 -0.793264
0 -0.394167
0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:
0  -0.793264  -0.453844
-0.2799370.976579   0.920768

Which one is the correct version?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C365d1f7e99384045bef308d87aa85f54%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394211236261729%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=t48AibkW%2FzZPCiHBgie9eGu4ag7rM8P%2Fh2WCT1mwzW0%3D&reserved=0>

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi
_

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C365d1f7e99384045bef308d87aa85f54%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394211236261729%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=t48AibkW%2FzZPCiHBgie9eGu4ag7rM8P%2Fh2WCT1mwzW0%3D&reserved=0>

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurf

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C2c61f34fe1ea4e1aab4d08d87aa7c4e2%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394208616072027%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=NCzjceGf1ddPm6iE0h9zOL2kfuJal6LwI0IxrMeOAbc%3D&reserved=0>

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It wa

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi


Configurationfile
Description: Configurationfile


bvecs_Oshadi
Description: bvecs_Oshadi


bvals_Oshadi
Description: bvals_Oshadi


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

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

External Email - Use Caution


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi


Tracula_logfile_Oshadi Jayakody
Description: Tracula_logfile_Oshadi Jayakody


Configurationfile
Description: Configurationfile


20190911_600196579_1002_DIFF_SAG_bvals
Description: 20190911_600196579_1002_DIFF_SAG_bvals


20190911_600196579_1002_DIFF_SAG_bvecs
Description: 20190911_600196579_1002_DIFF_SAG_bvecs
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Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi
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[Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi
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Re: [Freesurfer] Tracula error

[Hasimoglu, Yasemin]

Hi Anastasia,

Removing the trailing spaces fixed the problem, thank you so much!

Best,
Yasemin

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, October 1, 2020 4:16 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error

Hi Yasemin - It looks like the unix shell doesn't like that there are spaces 
after the "\" in a few lines:

1723_base \

1741_base \

1725-2/eddy_with_repol.nii.gz \

Best,
Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hasimoglu, Yasemin 

Sent: Tuesday, September 29, 2020 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error

Hi,

I am trying to run trac-all using a configuration file for 30 subjects with 
longitudinal data, and keep getting the following errors:
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I looked through my file line by line and looked at similar posts on the 
archives but could not find a solution. I'm attaching the configuration file 
here. There's no trac-all.log file since this is happening at the very 
beginning. Any help would be greatly appreciated!

Best,
Yasemin

Yasemin Hasimoglu
Research Technician
Department of Neurology
Massachusetts General Hospital
149 13th St, Suite 10130B
Charlestown, MA 02129
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Re: [Freesurfer] Tracula error

[Yendiki, Anastasia]

Hi Yasemin - It looks like the unix shell doesn't like that there are spaces 
after the "\" in a few lines:

1723_base \

1741_base \

1725-2/eddy_with_repol.nii.gz \

Best,
Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hasimoglu, Yasemin 

Sent: Tuesday, September 29, 2020 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error

Hi,

I am trying to run trac-all using a configuration file for 30 subjects with 
longitudinal data, and keep getting the following errors:
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I looked through my file line by line and looked at similar posts on the 
archives but could not find a solution. I'm attaching the configuration file 
here. There's no trac-all.log file since this is happening at the very 
beginning. Any help would be greatly appreciated!

Best,
Yasemin

Yasemin Hasimoglu
Research Technician
Department of Neurology
Massachusetts General Hospital
149 13th St, Suite 10130B
Charlestown, MA 02129
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[Freesurfer] Tracula error

[Hasimoglu, Yasemin]

Hi,

I am trying to run trac-all using a configuration file for 30 subjects with 
longitudinal data, and keep getting the following errors:
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I looked through my file line by line and looked at similar posts on the 
archives but could not find a solution. I'm attaching the configuration file 
here. There's no trac-all.log file since this is happening at the very 
beginning. Any help would be greatly appreciated!

Best,
Yasemin

Yasemin Hasimoglu
Research Technician
Department of Neurology
Massachusetts General Hospital
149 13th St, Suite 10130B
Charlestown, MA 02129


dmrirc2
Description: dmrirc2
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Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors

[Yendiki, Anastasia]

Hi Maria Gabriela - This does not look like a diffusion dicom:
PulseSeq  tfl_me3d4_16ns
Protocol  T1

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Figueiro Longo, Maria 
Gabriela 
Sent: Monday, April 27, 2020 9:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of 
gradient vectors

Hi,

I have been trying different ways to troubleshooting this error without 
success. I am pasting here the whole error when I try to run  "trac-all -prep 
-c"  in the Dev version:

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon
INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
trac-preproc -c 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local
 -log 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log
 -cmd 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd
 ; trac-preproc -c 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ;
#-
/usr/local/freesurfer/dev/bin/trac-preproc
#-
#@# Image corrections Mon Apr 27 09:37:59 EDT 2020
mri_convert --bvec-voxel 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
mri_convert --bvec-voxel 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
reading from 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010...
Getting Series No
INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715
INFO: Scanning for Series Number 102
Scanning Directory
INFO: found 140 files in series
INFO: loading series header info.

RunNo = 101
INFO: sorting.
sdfiSameSlicePos() eps = 0.01

WARNING: file 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 does not contain a Siemens ASCII header
has this file been anonymized?
Proceeding as best as I can ...

INFO: (256 256 140), nframes = 1, ismosaic=0
sdfi->UseSliceScaleFactor 0
INFO: rescale not needed
datatype = 4, short=4, float=3
PE Dir ROW ROW
FileName 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
Identification
NumarisVersyngo MR E11
ScannerModel  Prisma_fit
PatientName   3LT050_s1_170715
Date and time
StudyDate 20170715
StudyTime 092536.87
SeriesTime100956.32
AcqTime   093429.902500
Acquisition parameters
PulseSeq  tfl_me3d4_16ns
Protocol  T1
PhEncDir  ROW
EchoNo1
FlipAngle 7
EchoTime  1.69
InversionTime 1100
RepetitionTime2530
PhEncFOV  0
ReadoutFOV0
Image information
RunNo 101
SeriesNo  102
ImageNo   139
NImageRows256
NImageCols256
NFrames   1
SliceArraylSize   0
IsMosaic  0
ImgPos 54.1349  92.6115 176.0819
VolRes  1.   1.   1.
VolDim256  256  140
Vc  0.0934  -0.9338  -0.3453
Vr  0.0226   0.3487  -0.9370
Vs  0.4326   0.3520  -0.8301
VolCenter  99.2585  42.3521 -46.1506
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00
i_ras = (0.0933703, -0.933839, -0.345291)
j_ras = (0.0225973, 0.348705, -0.93696)
k_ras = (0.432568, 0.35197, -0.830061)
writing to 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz...
mri_probedicom --i 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 > 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat
ERROR: Must specify input table of gradie

Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors

[Figueiro Longo, Maria Gabriela]

Hi,

I have been trying different ways to troubleshooting this error without 
success. I am pasting here the whole error when I try to run  "trac-all -prep 
-c"  in the Dev version:

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon
INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
trac-preproc -c 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local
 -log 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log
 -cmd 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd
 ; trac-preproc -c 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ;
#-
/usr/local/freesurfer/dev/bin/trac-preproc
#-
#@# Image corrections Mon Apr 27 09:37:59 EDT 2020
mri_convert --bvec-voxel 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
mri_convert --bvec-voxel 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
reading from 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010...
Getting Series No
INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715
INFO: Scanning for Series Number 102
Scanning Directory
INFO: found 140 files in series
INFO: loading series header info.

RunNo = 101
INFO: sorting.
sdfiSameSlicePos() eps = 0.01

WARNING: file 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 does not contain a Siemens ASCII header
has this file been anonymized?
Proceeding as best as I can ...

INFO: (256 256 140), nframes = 1, ismosaic=0
sdfi->UseSliceScaleFactor 0
INFO: rescale not needed
datatype = 4, short=4, float=3
PE Dir ROW ROW
FileName 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
Identification
NumarisVersyngo MR E11
ScannerModel  Prisma_fit
PatientName   3LT050_s1_170715
Date and time
StudyDate 20170715
StudyTime 092536.87
SeriesTime100956.32
AcqTime   093429.902500
Acquisition parameters
PulseSeq  tfl_me3d4_16ns
Protocol  T1
PhEncDir  ROW
EchoNo1
FlipAngle 7
EchoTime  1.69
InversionTime 1100
RepetitionTime2530
PhEncFOV  0
ReadoutFOV0
Image information
RunNo 101
SeriesNo  102
ImageNo   139
NImageRows256
NImageCols256
NFrames   1
SliceArraylSize   0
IsMosaic  0
ImgPos 54.1349  92.6115 176.0819
VolRes  1.   1.   1.
VolDim256  256  140
Vc  0.0934  -0.9338  -0.3453
Vr  0.0226   0.3487  -0.9370
Vs  0.4326   0.3520  -0.8301
VolCenter  99.2585  42.3521 -46.1506
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00
i_ras = (0.0933703, -0.933839, -0.345291)
j_ras = (0.0225973, 0.348705, -0.93696)
k_ras = (0.432568, 0.35197, -0.830061)
writing to 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz...
mri_probedicom --i 
/autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.301707150016462772010
 > 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat
ERROR: Must specify input table of gradient vectors
Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020

#-
/usr/local/freesurfer/dev/bin/trac-preproc
#-
#@# Inter-subject registration (base template) Mon Apr 27 09:39:14 EDT 2020
cp 
/autofs/cluster/guptagp/gabi/tracula/Output/3LT0

[Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors

[Figueiro Longo, Maria Gabriela]

Hello Dear Freesurfer Developers,

I am attempting to run Tracula in the last to subject of my study (I had 
processed all the other subjects using the same script without problems). 
However, when I try to run the scrip bellow, I am having the error:

" ERROR: Must specify input table of gradient vectors "

 I am reviewed the associated DICOM images and couldn't find any problem with 
the images. I reviewed a couple emails in the list, but couldn't find a clear 
reason for keeping having this error.

I am using the Freesurfer Dev version.

I really appreciate any help.

Thank you, Gabriela



# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)
#
set subjlist = ( 3LT050_s1_170715 )

# Longitudinal base template subject IDs (one for each time point above)
#
set baselist = ( 3LT050 )

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
# set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data
set dcmlist = ( 
3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 )




Gabriela Longo, MD, MSc.


Emergency Radiology Clinical Fellow, Emergency Radiology Division

Massachusetts General Hospital (MGH)

mfigueirolo...@mgh.harvard.edu

Phone: +1 857 214 0568
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[Freesurfer] tracula error too many ('s

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:

I mentioned an error that I still cannot fix. I don’t think is the “\” because 
as you can see in the file attached everything seems correct. I cannot fix the 
issue with TRACULA I attach the configuration file so you can check in effect 
is correct. 



dmrirc.IXI
Description: Binary data


Sincerely, 
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Re: [Freesurfer] tracula error gradient vectors too many ('s

[Yendiki, Anastasia]

Hi Andrade - You have some forward slashes ("/") at the ends of lines in the 
config file that should be backslashes ("\") instead.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Renew Andrade 

Sent: Saturday, December 21, 2019 9:11 AM
To: Freesurfer Support List 
Subject: [Freesurfer] tracula error gradient vectors too many ('s


External Email - Use Caution

Dear FreeSurfer experts:
I am trying to run tracula in 4 subjects of a public dataset. I have 
encountered one error. I leave the output of terminal below. I also attach the 
configuration file. I hope you can follow from there.
Sincerely,
Andrade.


root@andraderenew:/usr/local/freesurfer/subjects# trac-all -prep -c 
/usr/local/freesurfer/subjects/dmrirc.IXI
Too many ('s.
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
INFO: Diffusion root is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/dmrirc.local -log 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.log -cmd 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc
#-
#@# Image corrections sáb dic 21 15:06:13 CET 2019
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
ERROR: Must specify input table of gradient vectors
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at sáb dic 21 15:06:13 CET 2019

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[Freesurfer] tracula error gradient vectors too many ('s

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I am trying to run tracula in 4 subjects of a public dataset. I have 
encountered one error. I leave the output of terminal below. I also attach the 
configuration file. I hope you can follow from there. 
Sincerely, 
Andrade. 


root@andraderenew:/usr/local/freesurfer/subjects# trac-all -prep -c 
/usr/local/freesurfer/subjects/dmrirc.IXI
Too many ('s.
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
INFO: Diffusion root is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/dmrirc.local -log 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.log -cmd 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections sáb dic 21 15:06:13 CET 2019
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
ERROR: Must specify input table of gradient vectors
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at sáb dic 21 15:06:13 CET 2019


dmrirc.IXI
Description: Binary data
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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Yendiki, Anastasia]

It appears to be a bbregister error:
bbregister --s APOE.269 --init-fsl --dti --mov 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/dwi.nii.gz --reg 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/anatorig2diff.bbr.dat --fslmat 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/diff2anatorig.bbr.mat

Make sure that SUBJECTS_DIR is correct in the config file. If the problem 
persists, please email about the bbregister problem separately and perhaps Doug 
can assist you. Note that I'll be traveling and may not be responding to email 
in the next 10 days.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, October 10, 2019 9:20 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

It isn't an error with recon-all, at least I don't think it is. Recon-all ran 
without error and the file that Tracula is trying to access seems to be where 
it is supposed to be. It seems like Tracula is having an issue opening the 
lh.white file. I just included the recon-all log for that subject to show that 
recon-all hadn't had any issues. Do you still think it would have to do with 
recon-all? It seems to have to do with the way Tracula is trying to read the 
file?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298


On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error" 
in the subject line if you want the developers of the structural stream to look 
into it.

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Daniel Callow mailto:ddcc2...@gmail.com>>
Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most of 
my subjects. However, for one of them I get the following error after mri_segreg


MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open 
file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in that 
exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders   rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labelsrh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H   rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofixrh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv  rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file for 
recon-all and trac-all the subject in case it might help.


Thank you,

Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Daniel Callow]

External Email - Use Caution

Hello,

It isn't an error with recon-all, at least I don't think it is. Recon-all
ran without error and the file that Tracula is trying to access seems to be
where it is supposed to be. It seems like Tracula is having an issue
opening the lh.white file. I just included the recon-all log for that
subject to show that recon-all hadn't had any issues. Do you still think it
would have to do with recon-all? It seems to have to do with the way
Tracula is trying to read the file?

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia 
wrote:

> Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula
> error" in the subject line if you want the developers of the structural
> stream to look into it.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Thursday, October 10, 2019 9:01:25 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] TRACULA error - MRISread could not open file
>
>
> External Email - Use Caution
>
> Hello,
>
> I am running tracula on some of my DTI data and have had no issues for
> most of my subjects. However, for one of them I get the following error
> after mri_segreg
>
> MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
> open file
>
> Loading mov
>
> Extracting frame 0
>
> Projecting LH Surfs
>
> Loading lh.white surf
>
> No such file or directory
>
>
> It doesn't make sense that I am getting this error because when looking in
> that exact folder I see the following
>
>
> [255a-280:freesurfer_pin/APOE.269/surf] amos% ls
>
> lh.area lh.smoothwm.FI.crv  rh.area
> rh.smoothwm.FI.crv
>
> lh.curv lh.smoothwm.H.crv   rh.curv
> rh.smoothwm.H.crv
>
> lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders
> rh.smoothwm.K.crv
>
> lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull
> rh.smoothwm.K1.crv
>
> lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labels
> rh.smoothwm.K2.crv
>
> lh.inflated lh.smoothwm.S.crv   rh.inflated
> rh.smoothwm.S.crv
>
> lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H
> rh.smoothwm.nofix
>
> lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere
>
> lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc
>
> lh.orig lh.sulc rh.orig rh.white.H
>
> lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K
>
> lh.qsphere.nofixlh.white.K  rh.qsphere.nofix
> rh.white.preaparc
>
> lh.smoothwm lh.white.preaparc   rh.smoothwm
> rh.white.preaparc.H
>
> lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv
> rh.white.preaparc.K
>
> lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv
>
>
> It looks like the file it can't open is there? I have attached the log
> file for recon-all and trac-all the subject in case it might help.
>
>
> Thank you,
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
> ___
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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Yendiki, Anastasia]

Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error" 
in the subject line if you want the developers of the structural stream to look 
into it.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most of 
my subjects. However, for one of them I get the following error after mri_segreg


MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open 
file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in that 
exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders   rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labelsrh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H   rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofixrh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv  rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file for 
recon-all and trac-all the subject in case it might help.


Thank you,

Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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[Freesurfer] TRACULA error - MRISread could not open file

[Daniel Callow]

External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most
of my subjects. However, for one of them I get the following error after
mri_segreg

MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
open file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in
that exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area
rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv
rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders
rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull
rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labels
rh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated
rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H
rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofix
rh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm
rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv
rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file
for recon-all and trac-all the subject in case it might help.


Thank you,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


recon-all-status.log
Description: Binary data


trac-all.error
Description: Binary data


trac-all.log
Description: Binary data
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Re: [Freesurfer] Tracula error -path

[Yendiki, Anastasia]

Hi Lorenzo - If you are still having this problem, please send the trac-all.log 
file from one of the 4 subjects.


a.y



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lorenzo Pini 

Sent: Friday, May 10, 2019 4:35:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error -path


External Email - Use Caution

Hi list,

Im using TRACULA in a dataset of 60 subjects.
for 56 subjects everything is fine, but for 4 subjects I had the following 
error:
>> ncpts: Subscript out of range.

For these subjects TRACULA does not reconstruct the file 
dpath/merged_avg33_mni_bbr.mgz and the statistics of the tracts (i.e. 
pathstats.* files)
Freesurfer parcellations look fine

Do you have any suggestions?
Thank you
Lorenzo
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[Freesurfer] Tracula error -path

[Lorenzo Pini]

External Email - Use Caution

Hi list,

Im using TRACULA in a dataset of 60 subjects.
for 56 subjects everything is fine, but for 4 subjects I had the following
error:
>> ncpts: Subscript out of range.

For these subjects TRACULA does not reconstruct the file
dpath/merged_avg33_mni_bbr.mgz and the statistics of the tracts (i.e.
pathstats.* files)
Freesurfer parcellations look fine

Do you have any suggestions?
Thank you
Lorenzo
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Re: [Freesurfer] [tracula] error running trac-all -prep

[Michael Krause]

Hi all,

sorry for reviving this super old thread, but it came up here as well
with Freesurfer 6.0.0.

> This is an Ubuntu-related error that has surfaced recently because in 
> Ubuntu /bin/sh is not a bash shell any more. To get around this, you can 
> edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and 
> $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with 
> "/bin/bash" on the first line of those two scripts.

I believe this is only half the truth. Sure, changing the interpreter to
/bin/bash fixes the issue, but underlying assumption is wrong and should
be addressed with a future release of Freesurfer I think.

Using bash-syntax in a /bin/sh (posix shell) interpreted script is
simply an error and should be fixed by either removing the bashism[1]
(arrays in this case) or by explicitly switching to /bin/bash.


[1]
http://mywiki.wooledge.org/Bashism

best regards
Michael Krause
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dispose of the e-mail.

[Freesurfer] TRACULA error "R: Subscript out of range"

[Anna Mynick]

Hi all, 

I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is 
exiting with the output below. Most notably, I think, is the section of the 
output that says "R: Subscript out of range.” repeatedly and then the section 
afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame 
numbers are between 0 and 0”. Does anyone have thoughts on what might be going 
on here? 

I’ve attached my bvecs and bvals too, in case there is trouble there too. 

Thanks very much for any help. 

Best,
Anna 


0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.99649667739868 0.06475614756346 -0.05292384698987
0.60556709766388 0.42478442192078 0.67293894290924
0.86823248863220 0.03115228191018 -0.49517852067947
0.67013686895370 0.45375373959541 -0.58738726377487
-0.08319617807865 -0.97095906734467 0.22431358695030
0.19819127023220 -0.76370823383331 0.61438584327698
-0.38230711221695 0.40581783652306 0.83015239238739
0.21735191345215 -0.75227254629135 -0.62196791172028
0.02298471517861 0.97281080484390 -0.23045811057091
-0.07650605589151 0.04117560386658 0.99621850252151
-0.14655694365501 0.75338035821915 0.64104521274567
-0.57700997591019 -0.78357273340225 0.23037599027157
0.12379934638739 -0.96946108341217 -0.21170438826084
0.04432926326990 0.02168774046004 -0.99878138303757
0.26761892437935 -0.38499519228935 -0.88326603174210
-0.28756865859032 0.78847736120224 -0.54369783401489
0.38445866107941 0.07492686808109 0.92009633779526
-0.83095681667328 0.54706901311874 0.10112489014864
0.32437109947205 0.77897244691849 0.53664255142212
0.52829635143280 0.79588997364044 -0.29573988914490
-0.16789475083351 0.45606943964958 -0.87396329641342
-0.59607589244843 0.39722976088524 -0.69778358936310
-0.42442059516907 0.90444123744965 -0.04304528608918
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-0.40714001655579 -0.01904341205955 -0.91316711902618
0.36646711826324 0.92621129751205 0.08851362764835
-0.77262413501740 -0.05901937559247 -0.63211452960968
-0.71511095762253 -0.66166228055954 -0.22543147206306
-0.17854259908199 -0.41829714179039 0.89058959484100
-0.88413268327713 -0.43072432279587 0.18106889724731
-0.24447374045849 -0.79100799560547 -0.56083726882935
-0.60315960645676 -0.48198029398918 -0.63552600145340
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-0.68014901876450 0.66064327955246 -0.31772288680077
0.86024975776672 0.48736852407455 -0.14980775117874
-0.19012457132339 -0.44323825836182 -0.87600934505463
-0.52820658683777 0.75576055049896 0.38707065582275
0.13211445510387 0.46795129776001 0.87382322549820
0.89498126506805 -0.39065974950790 -0.21539171040058
0.55196392536163 -0.00862982682884 -0.83382308483124
0.74213677644730 -0.65859544277191 0.12443807721138
-0.34717303514481 -0.92652040719986 -0.14502120018005
-0.75233423709869 0.36954036355019 0.54537409543991
0.28638312220573 -0.37944245338440 0.87977713346481
0.30121210217476 0.39795523881912 -0.86654651165009
0.71197289228439 0.66156578063965 0.23542550206184
-0.98868387937546 0.09445825219154 0.11654109507799
0.55790656805038 -0.78184622526169 -0.27831059694290
0.65419042110443 -0.44598758220673 -0.610843658447270.00
0.00
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0.00
0.00
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700.00
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700.00
700.00
700.00
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——

INFO: SUBJECTS_DIR is 
/mindhive

Re: [Freesurfer] TRACULA - error

[Yendiki, Anastasia]

Hi Batool - Please send over your (actual and not made up :) config file and 
trac-all.log.

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool 
[br2...@cumc.columbia.edu]
Sent: Tuesday, October 10, 2017 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA - error

Hi,
I’m running tracula using the following command:
(Note: I’m replacing actual paths with made up paths)

trac-all -prep -c /path/to/my/config.sh

And for some reason it stops running while working on the first subject 
(creates the folder for the first subject), with this error:

if: Expression Syntax.

It doesn’t show any errors before this line. The line before this one was 
copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt 
path/to/dmri/dwi_orig.bvecs)

Is there something I’m doing wrong?

Thanks,
Batool


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but does not contain patient information, please contact the sender and properly
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[Freesurfer] TRACULA - error

[Rizvi, Batool]

Hi,
I'm running tracula using the following command:
(Note: I'm replacing actual paths with made up paths)

trac-all -prep -c /path/to/my/config.sh

And for some reason it stops running while working on the first subject 
(creates the folder for the first subject), with this error:

if: Expression Syntax.

It doesn't show any errors before this line. The line before this one was 
copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt 
path/to/dmri/dwi_orig.bvecs)

Is there something I'm doing wrong?

Thanks,
Batool


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA ERROR!!

[Yendiki, Anastasia]

What do you see when you run:
ls /media/brain/brains/TN_retro/Tracula/AN01/mri


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lin, Yizhi 
[l...@union.edu]
Sent: Monday, August 07, 2017 3:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA ERROR!!

Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons were 
found in SUBJECTS_DIR in my configuration file. Thanks.

best,

Ariel

On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Ariel – Have you run freesurfer on the structural images of your subjects? 
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in 
your configuration file?

Best,

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Lin, Yizhi" mailto:l...@union.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, August 7, 2017 at 12:00 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA ERROR!!

Dear fellow researchers,

I am running tracula pre-processing step, and the computer showed an error 
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017

I am sure that I have the aparc+aseg file in the right directory but it showed 
that the files are missing.

I would be really appreciated if anyone could please help!!! Thanks so much!!!

PS: I attached trac-all.log as an attachment. Thanks

Sincerely,

Ariel

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA ERROR!!

[Lin, Yizhi]

Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons
were found in SUBJECTS_DIR in my configuration file. Thanks.

best,

Ariel

On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia  wrote:

> Hi Ariel – Have you run freesurfer on the structural images of your
> subjects? Are those freesurfer recons found in what you have defined as
> SUBJECTS_DIR in your configuration file?
>
> Best,
>
> a.y
>
> From:  on behalf of "Lin, Yizhi" <
> l...@union.edu>
> Reply-To: Freesurfer support list 
> Date: Monday, August 7, 2017 at 12:00 AM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] TRACULA ERROR!!
>
> Dear fellow researchers,
>
> I am running tracula pre-processing step, and the computer showed an error
> message:
> Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
> Brain mask for output subject: Segmentation fault (core dumped)
> Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017
>
> I am sure that I have the aparc+aseg file in the right directory but it
> showed that the files are missing.
>
> I would be really appreciated if anyone could please help!!! Thanks so
> much!!!
>
> PS: I attached trac-all.log as an attachment. Thanks
>
> Sincerely,
>
> Ariel
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA ERROR!!

[Yendiki, Anastasia]

Hi Ariel – Have you run freesurfer on the structural images of your subjects? 
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in 
your configuration file?

Best,

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Lin, Yizhi" mailto:l...@union.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, August 7, 2017 at 12:00 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA ERROR!!

Dear fellow researchers,

I am running tracula pre-processing step, and the computer showed an error 
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017

I am sure that I have the aparc+aseg file in the right directory but it showed 
that the files are missing.

I would be really appreciated if anyone could please help!!! Thanks so much!!!

PS: I attached trac-all.log as an attachment. Thanks

Sincerely,

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] TRACULA ERROR!!

[Lin, Yizhi]

Dear fellow researchers,

I am running tracula pre-processing step, and the computer showed an error
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017

I am sure that I have the aparc+aseg file in the right directory but it
showed that the files are missing.

I would be really appreciated if anyone could please help!!! Thanks so
much!!!

PS: I attached trac-all.log as an attachment. Thanks

Sincerely,

Ariel
Sun Aug  6 18:19:37 EDT 2017
/media/brain/brains/TN_retro/Tracula
/usr/local/freesurfer/bin/trac-all
-prep -c dmrirc
Subject AN01
SUBJECTS_DIR /media/brain/brains/TN_retro/Tracula
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  15430 
maxlocks unlimited
maxsignal15430 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   39716123064872 906740  53912 6797921089976
-/+ buffers/cache:12951042676508
Swap:  4117500  158044101696


Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  15430 
maxlocks unlimited
maxsignal15430 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   39716123068316 903296  53912 6798561092544
-/+ buffers/cache:12959162675696
Swap:  4117500  158044101696

#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Sun Aug

Re: [Freesurfer] tracula error message

[Yendiki, Anastasia]

Hi Marisa – Did you check the archives of this email list? I believe this error 
has come up before.

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Marissa Pifer 
mailto:marissapi...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, July 21, 2017 at 9:41 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] tracula error message

___emutls_get_address
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] tracula error message

[Marissa Pifer]

Hi Freesurfers,

Could you help me interpret this error message? I am attempting to run
TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3

helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1

INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI

INFO: Diffusion root is /Users/CRC/Documents/myprojects/R01_DTI/tracresults

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/dmrirc.local
-log
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.log
-cmd
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-

#@# Image corrections Fri Jul 21 09:28:12 EDT 2017

mri_convert --bvec-voxel
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz

mri_convert.bin --bvec-voxel
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz...

TR=3222.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.997757, 0.0345085, 0.057362)

j_ras = (0.0453079, 0.978915, 0.19918)

k_ras = (0.0492791, -0.201332, 0.978283)

writing to
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz...

cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bvec
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs

cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bval
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals

mv -f
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvecs.tmp
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs

mv -f
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvals.tmp
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals

orientLAS
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig_las.nii.gz

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


Trace/BPT trap

ERROR: input file must be in NIfTI format

Darwin helpdesks-MacBook-Pro-2.local 15.3.0 Darwin Kernel Version 15.3.0:
Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Fri Jul 21 09:29:59 EDT 2017


helpdesks-MacBook-Pro-2:R01_DTI crc$


It says at the end that the input file needs to be in nifty format, but my
input file is in nifty format. Do you guys have any idea what could be
going on here. I attached my dmrirc.example file for your reference as
well.

Thank you,

Marissa


dmrirc.example1
Description: Binary data
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Re: [Freesurfer] TRACULA Error in virtualbox

[Z K]

Hi Alex,

Try setting the FSLDIR to when same value as FSL_DIR. So you command 
would be something like:

   export FSLDIR=$FSLDIR

Then try rerunning TRACULA. Hopefully this solves the issue.

-Zeke

On 11/29/2016 01:53 PM, Yendiki, Anastasia wrote:
> Hi Alex - Have you run the freesurfer setup script?
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
>
> a.y
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alexander Zent
> [az...@pdx.edu]
> *Sent:* Wednesday, November 23, 2016 6:12 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] TRACULA Error in virtualbox
>
> I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
> Variable. I have looked at the answers to this question that have been
> previously posted but cannot seem to remedy this problem. I'm running
> freesurfer 5.3 via virtualbox on windows. I have applied for a license
> and added that to the license.txt file but to no avail. Thank you and I
> look forward to hearing from you.
>
> Thanks,
> Alex
>
>
>
>
> ___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA Error in virtualbox

[Yendiki, Anastasia]

Hi Alex - Have you run the freesurfer setup script?

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alexander Zent 
[az...@pdx.edu]
Sent: Wednesday, November 23, 2016 6:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA Error in virtualbox

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined 
Variable. I have looked at the answers to this question that have been 
previously posted but cannot seem to remedy this problem. I'm running 
freesurfer 5.3 via virtualbox on windows. I have applied for a license and 
added that to the license.txt file but to no avail. Thank you and I look 
forward to hearing from you.

Thanks,
Alex


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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] TRACULA Error in virtualbox

[Alexander Zent]

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
Variable. I have looked at the answers to this question that have been
previously posted but cannot seem to remedy this problem. I'm running
freesurfer 5.3 via virtualbox on windows. I have applied for a license and
added that to the license.txt file but to no avail. Thank you and I look
forward to hearing from you.

Thanks,
Alex
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula Error -preproc Segmentation fault (core dumped)

[Anastasia Yendiki]

Hi Kristina - I suspect there's some misregistration, or part of the brain 
mask (and hence the anatomical segmentation) missing or something like 
that. Do you mind uploading the tracula directories of this subject for me 
to take a look at?


https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks!

a.y

On Thu, 1 Sep 2016, Kristina Jelinkova wrote:



Hello everyone,


I've been using Tracula for a while now with much success (and help from the
archive) but I've run into an error I haven't been able to solve. I have
several subjects for which trac-all -preproc ends with Segmentation fault
(core dumped) 


I don't think it's a mistake with my directories, they appear correct and
I've ran numerous subjects successfully like this already. The dti data and
aparc+aseg also appear normal. I'm attaching the trac-all log and error log
from one of these problematic subjects. Any insight would be greatly
appreciate!


Thank you, 


Kristina Jelinkova


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

You get the same error as trac-all because trac-all runs mri_convert. I'd 
send the mri_convert error in a new email with mri_convert somewhere in 
the title, so that someone else can help you.


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Also when I run mir_convert on the DICOMs I get the same error as the one I
got when I used DICOMs :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.
45306.2014091812330393354083931 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

  On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
   wrote:

It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …

Ismail

  On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
   wrote:


  I do not know why the dicoms do not work. When you run
  mri_info on your nifti, what is the number of frames that
  shows up?

  On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains
64 frames as my bvecs/bvals. So this shouldn’t
be the reason.
Also why the DICOMs wouldn’t work at the
beginning ?

Thanks,
Ismail

  On Jul 4, 2016, at 2:41 PM,
  Anastasia Yendiki
  
  wrote:


  Hi Ismail - You can see from the
  log file that the command that
  causes the error is this:

  mri_convert --frame 31
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

  It's trying to extract the 32nd
  frame of your nifti file, but from
  the error message it looks like
  your nifti file doesn't have a
  32nd frame. So either the nifti
  file has too few volumes, or the
  bvecs/bvals have too many lines.
  You'll have to figure that out.

  a.y

  On Mon, 4 Jul 2016, Koubiyr,
  Ismail wrote:

Hi Anastasia,
Here it is.
But how could the
problem be related to
the nifti volume since
I have errors
when using the DICOMs
too ?
Thanks again,
Ismail
  On Jul 4,
  2016, at
  1:44 PM,
  Anastasia
  Yendiki


wrote:


  Hi Ismail
  - It
  sounds
  like the
  error has
  to do with
  the nifti
  volume,
  not

the bvecs/bvals. Can
you send the log file
from
scripts/trac-all.log?

  Thanks,
  a.y

  On Mon, 4
  Jul 2016,
  Koubiyr,
  Ismail
  wrote:

Hi
Anastasia,
Thank
you
for
getting
back
to
me.
Here
are
more
details
about
my
problem,
I
think
it
should
help
you
understand
more.
I
run
trac-all
-prep
-c

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Also when I run mir_convert on the DICOMs I get the same error as the one I got 
when I used DICOMs :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail 
mailto:ikoub...@bwh.harvard.edu>> wrote:

It says 1 … I don’t understand why I get that knowing that when I open the 
nifti I can go through the frames …

Ismail

On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:


I do not know why the dicoms do not work. When you run mri_info on your nifti, 
what is the number of frames that shows up?

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail

On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:


Hi Ismail - You can see from the log file that the command that causes the 
error is this:

mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the error 
message it looks like your nifti file doesn't have a 32nd frame. So either the 
nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll 
have to figure that out.

a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:


Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?

Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs  and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

   On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
   mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

   Hi everyone,

   I have some problems trying to run TRACULA on some DWI
   data. It is a mosaic Siemens DWI. I first converted the
   DICOM files with dcm2nii to get the bvec and bval files.
   Then I run the trac-all -prep -c command and I get the
   following error :

   WARNING: file /My/path/to/dicom does not contain a Siemens
   ASCII header
   has this file been anonymized?
   ERROR: cannot unpack mosiacs without ASCII header

   I tried to unpack the mosaics with gdcmtar, but I got the
   same error.

   Thank you in advance for your help,

   Ismail
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

It says 1 … I don’t understand why I get that knowing that when I open the 
nifti I can go through the frames …

Ismail

> On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki  
> wrote:
> 
> 
> I do not know why the dicoms do not work. When you run mri_info on your 
> nifti, what is the number of frames that shows up?
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> 
>> This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. 
>> So this shouldn’t be the reason.
>> Also why the DICOMs wouldn’t work at the beginning ?
>> 
>> Thanks,
>> Ismail
>> 
>>> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki 
>>>  wrote:
>>> 
>>> 
>>> Hi Ismail - You can see from the log file that the command that causes the 
>>> error is this:
>>> 
>>> mri_convert --frame 31 
>>> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
>>> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
>>> 
>>> It's trying to extract the 32nd frame of your nifti file, but from the 
>>> error message it looks like your nifti file doesn't have a 32nd frame. So 
>>> either the nifti file has too few volumes, or the bvecs/bvals have too many 
>>> lines. You'll have to figure that out.
>>> 
>>> a.y
>>> 
>>> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>>> 
 Hi Anastasia,
 Here it is.
 But how could the problem be related to the nifti volume since I have 
 errors
 when using the DICOMs too ?
 Thanks again,
 Ismail
> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
  wrote:
> 
> 
> Hi Ismail - It sounds like the error has to do with the nifti volume, not
 the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
> 
> Thanks,
> a.y
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error
 :
>> WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
 0043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional
 space,
>> but when the new bvecs  and bvals are created, they seem messed up. I
 will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>> 
>> On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>  wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>> 
>> Hi everyone,
>> 
>> I have some problems trying to run TRACULA on some DWI
>> data. It is a mosaic Siemens DWI. I first converted the
>> DICOM files with dcm2nii to get the bvec and bval files.
>> Then I run the trac-all -prep -c command and I get the
>> following error :
>> 
>> WARNING: file /My/path/to/dicom does not contain a Siemens
>> ASCII header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> 
>> I tried to unpack the mosaics with gdcmtar, but I got the
>> same error.
>> 
>> Thank you in advance for your help,
>> 
>> Ismail
>> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

I do not know why the dicoms do not work. When you run mri_info on your 
nifti, what is the number of frames that shows up?


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail


On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki  
wrote:


Hi Ismail - You can see from the log file that the command that causes the 
error is this:

mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the error 
message it looks like your nifti file doesn't have a 32nd frame. So either the 
nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll 
have to figure that out.

a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail

On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki

 wrote:



Hi Ismail - It sounds like the error has to do with the nifti volume, not

the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error

:

WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368

0043

.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional

space,

but when the new bvecs  and bvals are created, they seem messed up. I

will

attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

 On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
  wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

 Hi everyone,

 I have some problems trying to run TRACULA on some DWI
 data. It is a mosaic Siemens DWI. I first converted the
 DICOM files with dcm2nii to get the bvec and bval files.
 Then I run the trac-all -prep -c command and I get the
 following error :

 WARNING: file /My/path/to/dicom does not contain a Siemens
 ASCII header
 has this file been anonymized?
 ERROR: cannot unpack mosiacs without ASCII header

 I tried to unpack the mosaics with gdcmtar, but I got the
 same error.

 Thank you in advance for your help,

 Ismail
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail

> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki  
> wrote:
> 
> 
> Hi Ismail - You can see from the log file that the command that causes the 
> error is this:
> 
> mri_convert --frame 31 
> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
> 
> It's trying to extract the 32nd frame of your nifti file, but from the error 
> message it looks like your nifti file doesn't have a 32nd frame. So either 
> the nifti file has too few volumes, or the bvecs/bvals have too many lines. 
> You'll have to figure that out.
> 
> a.y
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> Here it is.
>> But how could the problem be related to the nifti volume since I have errors
>> when using the DICOMs too ?
>> Thanks again,
>> Ismail
>> > On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
>>  wrote:
>> >
>> >
>> > Hi Ismail - It sounds like the error has to do with the nifti volume, not
>> the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>> >
>> > Thanks,
>> > a.y
>> >
>> > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>> >
>> >> Hi Anastasia,
>> >> Thank you for getting back to me.
>> >> Here are more details about my problem, I think it should help you
>> >> understand more.
>> >> I run trac-all -prep -c on some DICOM files but I had the following error
>> :
>> >> WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
>> 0043
>> >> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> >> header
>> >> has this file been anonymized?
>> >> ERROR: cannot unpack mosiacs without ASCII header
>> >> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> >> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> >> previous error but something else weird happened. Now I get :
>> >> ERROR: fMRIframe: frame >= nframes
>> >> I checked the bvecs and bvals files, they seem normal, no additional
>> space,
>> >> but when the new bvecs  and bvals are created, they seem messed up. I
>> will
>> >> attach you all the bvecs and bvals I used and the ones I get too.
>> >> Ideally, the DICOMs should work fine but I have no idea why I get these
>> >> errors.
>> >> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> >> any additional space.
>> >> Thank you in advance for your help.
>> >> Best,
>> >> Ismail
>> >> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>> >>
>> >>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>> >>   wrote:
>> >> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> >> It's
>> >> hard to tell without looking at your configuration file.
>> >> Best,
>> >> a.y
>> >> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>> >>
>> >>  Hi everyone,
>> >>
>> >>  I have some problems trying to run TRACULA on some DWI
>> >>  data. It is a mosaic Siemens DWI. I first converted the
>> >>  DICOM files with dcm2nii to get the bvec and bval files.
>> >>  Then I run the trac-all -prep -c command and I get the
>> >>  following error :
>> >>
>> >>  WARNING: file /My/path/to/dicom does not contain a Siemens
>> >>  ASCII header
>> >>  has this file been anonymized?
>> >>  ERROR: cannot unpack mosiacs without ASCII header
>> >>
>> >>  I tried to unpack the mosaics with gdcmtar, but I got the
>> >>  same error.
>> >>
>> >>  Thank you in advance for your help,
>> >>
>> >>  Ismail
>> >>  ___
>> >>  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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - You can see from the log file that the command that causes the 
error is this:


mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the 
error message it looks like your nifti file doesn't have a 32nd frame. So 
either the nifti file has too few volumes, or the bvecs/bvals have too 
many lines. You'll have to figure that out.


a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,

Ismail



> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
 wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error
:
>> 
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional
space,
>> but when the new bvecs  and bvals are created, they seem messed up. I
will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>>
>>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>   wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>>
>>  Hi everyone,
>>
>>  I have some problems trying to run TRACULA on some DWI
>>  data. It is a mosaic Siemens DWI. I first converted the
>>  DICOM files with dcm2nii to get the bvec and bval files.
>>  Then I run the trac-all -prep -c command and I get the
>>  following error :
>>
>>  WARNING: file /My/path/to/dicom does not contain a Siemens
>>  ASCII header
>>  has this file been anonymized?
>>  ERROR: cannot unpack mosiacs without ASCII header
>>
>>  I tried to unpack the mosaics with gdcmtar, but I got the
>>  same error.
>>
>>  Thank you in advance for your help,
>>
>>  Ismail
>>  ___
>>  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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

Here it is.
But how could the problem be related to the nifti volume since I have errors 
when using the DICOMs too ?
Thanks again,

Ismail



> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki  
> wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not the 
> bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error :
>> WARNING: 
>> file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional space,
>> but when the new bvecs  and bvals are created, they seem messed up. I will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>>
>>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>   wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>>
>>  Hi everyone,
>>
>>  I have some problems trying to run TRACULA on some DWI
>>  data. It is a mosaic Siemens DWI. I first converted the
>>  DICOM files with dcm2nii to get the bvec and bval files.
>>  Then I run the trac-all -prep -c command and I get the
>>  following error :
>>
>>  WARNING: file /My/path/to/dicom does not contain a Siemens
>>  ASCII header
>>  has this file been anonymized?
>>  ERROR: cannot unpack mosiacs without ASCII header
>>
>>  I tried to unpack the mosaics with gdcmtar, but I got the
>>  same error.
>>
>>  Thank you in advance for your help,
>>
>>  Ismail
>>  ___
>>  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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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trac-all.log
Description: trac-all.log
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - It sounds like the error has to do with the nifti volume, not 
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space,
but when the new bvecs  and bvals are created, they seem messed up. I will
attach you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.


  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
   wrote:


Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

  Hi everyone,

  I have some problems trying to run TRACULA on some DWI
  data. It is a mosaic Siemens DWI. I first converted the
  DICOM files with dcm2nii to get the bvec and bval files.
  Then I run the trac-all -prep -c command and I get the
  following error :

  WARNING: file /My/path/to/dicom does not contain a Siemens
  ASCII header
  has this file been anonymized?
  ERROR: cannot unpack mosiacs without ASCII header

  I tried to unpack the mosaics with gdcmtar, but I got the
  same error.

  Thank you in advance for your help,

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



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

Thank you for getting back to me.
Here are more details about my problem, I think it should help you understand 
more.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get the 
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space, but 
when the new bvecs  and bvals are created, they seem messed up. I will attach 
you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any 
additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.


On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:


Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

Hi everyone,

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

Thank you in advance for your help,

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



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bvals
Description: bvals


bvecs
Description: bvecs


bvecs.norot
Description: bvecs.norot


dwi_orig.mghdti.bvecs
Description: dwi_orig.mghdti.bvecs


dwi_orig.mghdti.bvals
Description: dwi_orig.mghdti.bvals
0
1000
1000
1000
1000
1000
1000
1000
1000
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1000
1000
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1000
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1000
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1000
1000
1000
1000
1000
1000
1000
0
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0
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-0.201801 0.940841 -0.272204
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-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
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0 0 0
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0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
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-0.857087 0.178312 0.48333
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0.331016 0.523908 0.784824
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0.979641 0.177715 0.0933861
0 0 0
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - Are you passing the nifti volume as input to trac-all? It's 
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
> Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec 
> and bval files.
> Then I run the trac-all -prep -c command and I get the following error :
>
> WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
> has this file been anonymized?
> ERROR: cannot unpack mosiacs without ASCII header
>
> I tried to unpack the mosaics with gdcmtar, but I got the same error.
>
> Thank you in advance for your help,
>
> Ismail
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>
>
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[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I’m reposting my problem if someone could help me I would really appreciate it.

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

P.S : DTIFIT works on FSL (FDT) but gives a poor quality in the reconstruction 
not as the one expected with Tracula.

Thank you in advance for your help,

Ismail

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[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

Thank you in advance for your help,

Ismail
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Re: [Freesurfer] TRACULA error related to bvec/bval input

[Anastasia Yendiki]

Hi Scott - The gradient table produced by dcm2nii is formatted in 3 rows, 
rather than 3 columns. If you want to use gradient tables formatted in 
rows, you have to download the tracula update described here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

a.y

On Tue, 7 Apr 2015, Scott Quadrelli wrote:


Hi,

I am trying to get TRACULA running. I have converted the DTI data using dcm2nii 
(as i was unable to get tracula to read the .ima Siemens DICOM) and have a bevc 
and bval file output from dcm2nii.

The error I get is in bold below (from trac-all.log). I believe that the error 
is coming from the bevy/bval file however I can’t see what the issue is with 
the data contained within the file. Does the output from dcm2nii need to be 
reformatted for input to TRACULA ?

Cheers,

Scott

-
/Applications/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue  7 Apr 2015 21:43:25 AEST
mri_convert 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz
mri_convert 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz...
TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99802, 0.0188805, 0.0599977)
j_ras = (0.0278771, 0.987856, 0.152851)
k_ras = (0.0563831, -0.154221, 0.986426)
writing to 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz...
cp 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bvec.txt
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs
cp 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bval.txt
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -9.38889
fslswapdim 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz
 x y z 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz
INFO: found 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals,
 converting to FSL format
INFO: found 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs,
 converting to FSL format
mv -f 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvecs
 /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvecs
mv -f 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvals
 /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvals
mv -f 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz
ln -sf 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz
 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/data.nii.gz
mri_concat --i 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz
 --mean --o 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/lowb.nii.gz
niiRead(): error opening file 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading 
/Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz
Darwin Scotts-MacBook-Pro.local 14.1.0 Darwin Kernel Version 14.1.0: Thu Feb 26 
19:26:47 PST 2015; root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64

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