Re: [Freesurfer] Trac-all error assistance

[Yendiki, Anastasia]

Hi Emmanuel - Not sure if you saw my earlier response, but the infant stream is 
under construction and not currently supported.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emmanuel Rodríguez Silva 

Sent: Monday, June 13, 2022 12:39 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Trac-all error assistance


External Email - Use Caution

Hello, freesurfer developers
I was running the trac-all command for infant images. But I got an error during 
the cst processing. I've already checked the mailbox to find similar issues, 
but it seems that there are several logic errors. I will appreciate any 
assistance on this matter. I' m attaching my trac-all.log file for reference. 
Thank you.

This is the exact error:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid
Abort (core dumped)

best,
Emmanuel from Mexico

--
Saludos cordiales
Emmanuel Rodríguez Silva


Contacto: (044) 55 59 97 76 18

Licenciado en Manejo Sustentable de Zonas Costeras
UNAM
[https://secure-web.cisco.com/1cNbEZQlhdfIEUxiqcxEsMm9hLKF76H8fbAIIAl4-Gj9OVh67QLId37gMusA7k5OI3h7TMVzBG4eneoNwE1xilPCKmzqIUY3efr61fcjchJNuBxkOPfXFKv0i7rkOh4ZWUy2XYa2mDXj6Mdb0Ay0YwB-9hjDm8bmbiGOk6YOv0U2dRGBeEel9hSEPXkHfuO4ywdWy6FFbMD-xAnDTwVnAjYqApi1stC69qZmMNI8zIS_0i7J6vxEkV9Id5bPSTl6l5NvZMPDQq_Nj6NT-VPymtJ0my5FW3pAUkaApSWaQ2s4JTTHHpKQd7eMZtbmcGzgb9is_z2viNqr3ddcK2BSiRg/https%3A%2F%2Fdocs.google.com%2Fuc%3Fexport%3Ddownload%26id%3D0B5vV8VGxH26nNzd4YTc2bHFqRjQ%26revid%3D0B5vV8VGxH26nNjY3OWIxM2FzbHdtY3RDeFRkZmNHYVJwbFlBPQ][https://secure-web.cisco.com/10x58ceCV8utm8rOGTRKLQFTN5kgOzUu2_gLdMiSeLdX49Jb32I3U0aa6X_4EbnwslLQLkg1QkK_Mo17y6-RIv9Km8avPsXGKpMbo6b1TirHMx27UYBoMAGYSa1YZURMbWNk6NJOXsS2XStLWsGUtjGpl7avP1tawvfiePNuEJUITupS6eqNfjUCZVTni2DlVEG_2k29AbbxTSWFkns4qR-39zFXdpiK3QRKqdvZhq_xy9lR23lXMxGF5fRmyT2Fx5dFpCgnVtzB2q7zphL7P8A5W5LGfsEqQYqfmhp3UhFG6G8ds8i8g0--6o0r2JGVP7vMdrfDl4CC2ZdfEKY65lg/https%3A%2F%2Fdocs.google.com%2Fuc%3Fexport%3Ddownload%26id%3D0B5vV8VGxH26nNTJyNXVVcm9TYk0%26revid%3D0B5vV8VGxH26nSmhYSGdtU1ZkUy9oSExhY3JSZENITTJVWnlNPQ]
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Re: [Freesurfer] Trac-All Error

[Hua, Jessica]

External Email - Use Caution

Hi Dr. Yendiki,

Thanks! That fixed the issue I was having.

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Trac-All Error

[Yendiki, Anastasia]

Hi Jessica - A couple of things to fix. The bvecs file has commas in it. The 
bvals file, if you view it with the more command on linux, you'll see that 
instead of line changes it has "^M" in between the values. This can happen if 
it's saved in a windows text editor. You can open it in a linux text editor and 
save it again.

Hope this helps!

a.y



From: Hua, Jessica 
Sent: Tuesday, April 14, 2020 4:38 PM
To: freesurfer@nmr.mgh.harvard.edu ; Yendiki, 
Anastasia 
Subject: Re: Trac-All Error


External Email - Use Caution

Attached are bvecs and bvals.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Trac-All Error

[Hua, Jessica]

External Email - Use Caution

Attached are bvecs and bvals.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
0,0,0 
0,0,0 
0,0,0 
0,0,0 
0,0,0 
   1,  0,0 
   0.166, 0.986, 0 
   -0.110, 0.664, 0.740 
  0.901, -0.419, -0.110 
  -0.169, -0.601, 0.781 
  -0.815, -0.386, 0.433 
  0.656, 0.366, 0.660 
  0.582, 0.800, 0.143 
  0.900, 0.259, 0.350 
  0.693, -0.698, 0.178 
  0.357, -0.924, -0.140 
  0.543, -0.488, -0.683 
  -0.525, -0.396, 0.753 
  -0.639, 0.689, 0.341 
  -0.330, -0.013, -0.944 
  -0.524, -0.783, 0.335 
  0.609, -0.065, -0.791 
  0.220, -0.233, -0.947 
  -0.004, -0.910, -0.415 
  -0.511, 0.627, -0.589 
  0.414, 0.737, 0.535 
  -0.679, 0.139, -0.721 
  0.884, -0.296, 0.362 
  0.262, 0.432, 0.863 
  0.088, 0.185, -0.979 
  0.294, -0.907, 0.302 
  0.887, -0.089, -0.453 
  0.257, -0.443, 0.859 
  0.086, 0.867, -0.491 
  0.863, 0.504, -0.025 0
0
0
0
0
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
800
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Re: [Freesurfer] Trac-All Error

[Yendiki, Anastasia]

Can you please also send your bvecs and bvals files? I can't see anything else 
going wrong, so I'm guessing it has to do with those.

From: Hua, Jessica 
Sent: Monday, April 13, 2020 12:10 PM
To: Yendiki, Anastasia ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: Trac-All Error


External Email - Use Caution

Hi Dr. Yendiki,

I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed 
your work email. Attached is my full configuration file  as well as my error 
log.

Best,

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Trac-All Error

[Hua, Jessica]

External Email - Use Caution

Hi Dr. Yendiki,

I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed 
your work email. Attached is my full configuration file  as well as my error 
log.

Best,

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


DTIConfigurationFile.tutorial
Description: DTIConfigurationFile.tutorial


trac-all.log
Description: trac-all.log
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Re: [Freesurfer] Trac-all Error

[Yendiki, Anastasia]

Hi Jessica - Please send us your trac-all.log file as an attachment. It's hard 
to guess what went wrong just from the output of one command, without seeing 
the output of all commands before it. Thanks!

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hua, Jessica 

Sent: Sunday, April 12, 2020 12:38 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Trac-all Error


External Email - Use Caution

Hi FreeSurfer,

I am running trac-all prepocessing using a configuration file. I tried 
preprocessing a couple of participants, and I keep getting this error:


#-

#@# Tensor fit Sat Apr 11 21:29:36 PDT 2020

dtifit -k /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dwi.nii.gz -m 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
-r /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvecs -b 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvals -o 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dtifit

libc++abi.dylib: terminating with uncaught exception of type std::logic_error: 
Mat::operator(): index out of bounds

Abort

This is my configuration file:

set dtroot = /Volumes/HuaExternal/DTI_FS
set subjlist = ( S11018a_LGI )
set dcmroot = /Volumes/HuaExternal/DTI
set dcmlist = ( S11018a.nii )
set bvecfile = /Volumes/HuaExternal/DTI/bvecsSPACE.txt
set bvalfile = /Volumes/HuaExternal/DTI/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 mnitemp = /Volumes/HuaExternal/DTI/MNI152_T1_1mm_brain.nii.gz
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)

Do you know what is going wrong, and how I would fix this issue?

Best,

 Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] trac-all error

[nayan wadhwani]

External Email - Use Caution

I followed your given link and ran sudo -E fs_update
and came up with the following error just wanted to know is this error
related to SIP or is it a some other issue.

PILEPSY:subjects eoilepsyosirixadmin$ sudo -E fs_update

 Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c


   Running this will update some of your freesurfer binaries.


 Shall I proceed? [y/n/Abort]: y


rsync -zbrlv --progress --suffix=.1571729614_bak rsync://
surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
/Applications/freesurfer

receiving incremental file list

rsync: change_dir
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"
(in pub) failed: No such file or directory (2)


sent 8 bytes  received 163 bytes  31.09 bytes/sec

total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors)
(code 23) at main.c(1679) [Receiver=3.1.3]

Thanks and Regards
Nayan Wadhwani


On Mon, Oct 21, 2019 at 11:46 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> The error message in your log file ("dyld: Symbol not found...") has been
> addressed here:
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61247.html
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <
> nayanw...@gmail.com>
> *Sent:* Tuesday, October 22, 2019 2:32 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] trac-all error
>
>
> External Email - Use Caution
>
> I have attached the log-file from the trac-all command
> Thanks and Regards
> Nayan Wadhwani
>
>
> On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Please attach your log file from scripts/trac-all.log.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <
> nayanw...@gmail.com>
> *Sent:* Tuesday, October 22, 2019 1:13 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] trac-all error
>
>
> External Email - Use Caution
>
> Hello Freesurfer,
>
> I did changes asked by you but still error persists.
> While i am using dicom images why it is asking for NIFTI format.
> I checked the lib folder also and checked and all the files mention above
> are there in the folder.
> Do i need to check something else.
>
> Sent from my iPhone
>
> On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia 
> wrote:
>
> Hi Nayan - Try using /Applications instead of $Applications everywhere.
> Also, the config file seems to be in rich text format - not sure how
> that'll work. Try converting it to plain text (if you use mac, from the
> Format menu of the text editor).
>
> Best,
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <
> nayanw...@gmail.com>
> *Sent:* Saturday, October 19, 2019 1:36 AM
> *To:* Freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] trac-all error
>
>
> External Email - Use Caution
>
> Hello Freesurfer,
>
> After running recon all script which completed successfully, I ran
> trac-all command which exited with error and tried running it with dicom
> files.
>
> 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
>
>
> Abort
>
> ERROR: input file must be in NIfTI format
>
> Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25
> PST 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019
>
>
> And please help me the correct config the one I created, I am attaching it
> below to try it with .nii files
> Thanks and Regards
> Nayan Wadhwani
>
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Re: [Freesurfer] trac-all error

[Yendiki, Anastasia]

The error message in your log file ("dyld: Symbol not found...") has been 
addressed here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61247.html

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of nayan wadhwani 

Sent: Tuesday, October 22, 2019 2:32 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] trac-all error


External Email - Use Caution

I have attached the log-file from the trac-all command
Thanks and Regards
Nayan Wadhwani


On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Please attach your log file from scripts/trac-all.log.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of nayan wadhwani mailto:nayanw...@gmail.com>>
Sent: Tuesday, October 22, 2019 1:13 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] trac-all error


External Email - Use Caution

Hello Freesurfer,

I did changes asked by you but still error persists.
While i am using dicom images why it is asking for NIFTI format.
I checked the lib folder also and checked and all the files mention above are 
there in the folder.
Do i need to check something else.

Sent from my iPhone

On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, 
the config file seems to be in rich text format - not sure how that'll work. 
Try converting it to plain text (if you use mac, from the Format menu of the 
text editor).

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 nayan wadhwani mailto:nayanw...@gmail.com>>
Sent: Saturday, October 19, 2019 1:36 AM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> 
mailto:Freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all error


External Email - Use Caution

Hello Freesurfer,

After running recon all script which completed successfully, I ran trac-all 
command which exited with error and tried running it with dicom files.

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


Abort

ERROR: input file must be in NIfTI format

Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 
2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019


And please help me the correct config the one I created, I am attaching it 
below to try it with .nii files

Thanks and Regards
Nayan Wadhwani
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Re: [Freesurfer] trac-all error

[Yendiki, Anastasia]

Please attach your log file from scripts/trac-all.log.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of nayan wadhwani 

Sent: Tuesday, October 22, 2019 1:13 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] trac-all error


External Email - Use Caution

Hello Freesurfer,

I did changes asked by you but still error persists.
While i am using dicom images why it is asking for NIFTI format.
I checked the lib folder also and checked and all the files mention above are 
there in the folder.
Do i need to check something else.

Sent from my iPhone

On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, 
the config file seems to be in rich text format - not sure how that'll work. 
Try converting it to plain text (if you use mac, from the Format menu of the 
text editor).

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 nayan wadhwani mailto:nayanw...@gmail.com>>
Sent: Saturday, October 19, 2019 1:36 AM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> 
mailto:Freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all error


External Email - Use Caution

Hello Freesurfer,

After running recon all script which completed successfully, I ran trac-all 
command which exited with error and tried running it with dicom files.

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


Abort

ERROR: input file must be in NIfTI format

Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 
2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019


And please help me the correct config the one I created, I am attaching it 
below to try it with .nii files

Thanks and Regards
Nayan Wadhwani
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Re: [Freesurfer] trac-all error

[nayan wadhwani]

External Email - Use Caution

Hello Freesurfer,

I did changes asked by you but still error persists.
While i am using dicom images why it is asking for NIFTI format.
I checked the lib folder also and checked and all the files mention above are 
there in the folder.
Do i need to check something else.

Sent from my iPhone

> On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia  
> wrote:
> 
> Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, 
> the config file seems to be in rich text format - not sure how that'll work. 
> Try converting it to plain text (if you use mac, from the Format menu of the 
> text editor).
> 
> Best,
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of nayan wadhwani 
> 
> Sent: Saturday, October 19, 2019 1:36 AM
> To: Freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] trac-all error
>  
> External Email - Use Caution
> 
> Hello Freesurfer,
> After running recon all script which completed successfully, I ran trac-all 
> command which exited with error and tried running it with dicom files.
> 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
> 
> Abort  
> ERROR: input file must be in NIfTI format
> Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 
> 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64
> 
> trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019
> 
> And please help me the correct config the one I created, I am attaching it 
> below to try it with .nii files
> Thanks and Regards
> Nayan Wadhwani
> ___
> 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

Re: [Freesurfer] trac-all error

[Yendiki, Anastasia]

Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, 
the config file seems to be in rich text format - not sure how that'll work. 
Try converting it to plain text (if you use mac, from the Format menu of the 
text editor).

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of nayan wadhwani 

Sent: Saturday, October 19, 2019 1:36 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] trac-all error


External Email - Use Caution

Hello Freesurfer,

After running recon all script which completed successfully, I ran trac-all 
command which exited with error and tried running it with dicom files.

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


Abort

ERROR: input file must be in NIfTI format

Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 
2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019


And please help me the correct config the one I created, I am attaching it 
below to try it with .nii files

Thanks and Regards
Nayan Wadhwani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Trac-all error

[Daniel Callow]

External Email - Use Caution

Thank you for the reply. I guess it is possible that there were some issues
with compiling, however I have been using it for a while without issue. I
will look into that issue further. Thanks for all your help and feedback!

Best,
Daniel Callow

On Thu, Jul 4, 2019 at 8:42 AM Yendiki, Anastasia 
wrote:

> It's not an issue of compatibility. The tkregister2 executable doesn't
> exist in whatever version you're sourcing when you run tracula. As far as I
> can see, it should be there in both the stable6 and dev versions. Any
> chance that something went wrong when you built the dev version on your
> system and tkregister2 did not compile?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Thursday, July 4, 2019 8:24:32 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Trac-all error
>
>
> External Email - Use Caution
>
> When running on freesurfer 6.0 I get the following pop-up screen as well.
>
> *“tkregister2.bin” is not optimized for your Mac and needs to be updated.*
>
> This software will not work with future versions of macOS and needs to be
> updated to improve compatibility. Contact the developer for more
> information.
>
>
> Just FYI. It does work on the freesurfer 6.0 version despite the pop-up.
> It seems like trac-all is not compatible with the development version then?
>
>
> 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, Jul 4, 2019 at 8:08 AM Daniel Callow  wrote:
>
> Hello Anastasia,
>
> I was running this on freesurfer's dev version. I will try running it on
> freesurfer 6.0.
>
> Best,
> *Daniel Callow*
> *PhD Student, Neuroscience and Conitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
>
>
> On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not
> found." What version of freesurfer are you using?
>
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Wednesday, July 3, 2019 2:06:27 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Trac-all error
>
>
> External Email - Use Caution
>
> Hello,
>
> I am running trac-all preproc with the following code
>
> setenv FREESURFER_HOME /Applications/freesurfer_dev
>
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> *#Must set SUBJECTS_DIR to where data is or else uses what was set up when
> installing freesurfer*
>
> setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons
>
>
> *#Must set up configuration file - see trac-all-config-file in
> dti_analysis compository*
>
> *#In configuration file can change number of subject to perform analysis
> on each cluster*
>
>
> *#RUN FIRST*
> trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh
>
>
> *and the attached configuration file. *
>
> *However, I get the following error.*
>
> #@# Intra-subject registration Tue Jul  2 18:21:42 EDT 2019
>
> mri_convert
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
>
> mri_convert
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
>
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz...
>
> TR=9.62, TE=3.90, TI=450.00, flip angle=12.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (0, 1, 0)
>
> writing to
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...
>
> orientLAS
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
>
> INFO: input image orientation is LIA
>
> INFO: input image determinant is -1
>
> mri_convert -o

Re: [Freesurfer] Trac-all error

[Yendiki, Anastasia]

It's not an issue of compatibility. The tkregister2 executable doesn't exist in 
whatever version you're sourcing when you run tracula. As far as I can see, it 
should be there in both the stable6 and dev versions. Any chance that something 
went wrong when you built the dev version on your system and tkregister2 did 
not compile?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, July 4, 2019 8:24:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all error


External Email - Use Caution

When running on freesurfer 6.0 I get the following pop-up screen as well.


“tkregister2.bin” is not optimized for your Mac and needs to be updated.

This software will not work with future versions of macOS and needs to be 
updated to improve compatibility. Contact the developer for more information.


Just FYI. It does work on the freesurfer 6.0 version despite the pop-up. It 
seems like trac-all is not compatible with the development version then?


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, Jul 4, 2019 at 8:08 AM Daniel Callow 
mailto:ddcc2...@gmail.com>> wrote:
Hello Anastasia,

I was running this on freesurfer's dev version. I will try running it on 
freesurfer 6.0.

Best,
Daniel Callow
PhD Student, Neuroscience and Conitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298


On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not 
found." What version of freesurfer are you using?


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: Wednesday, July 3, 2019 2:06:27 PM
To: Freesurfer support list
Subject: [Freesurfer] Trac-all error


External Email - Use Caution

Hello,

I am running trac-all preproc with the following code

setenv FREESURFER_HOME /Applications/freesurfer_dev

source $FREESURFER_HOME/SetUpFreeSurfer.csh

#Must set SUBJECTS_DIR to where data is or else uses what was set up when 
installing freesurfer

setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons


#Must set up configuration file - see trac-all-config-file in dti_analysis 
compository

#In configuration file can change number of subject to perform analysis on each 
cluster


#RUN FIRST

trac-all -prep -c 
/Volumes/DANIEL/dmrirc.long.MCIP.example.sh<http://dmrirc.long.MCIP.example.sh>


and the attached configuration file.

However, I get the following error.


#@# Intra-subject registration Tue Jul  2 18:21:42 EDT 2019

mri_convert 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz

mri_convert 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz

$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $

reading from 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz...

TR=9.62, TE=3.90, TI=450.00, flip angle=12.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...

orientLAS 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

INFO: input image orientation is LIA

INFO: input image determinant is -1

mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 
-6.32147 -1.97853 6.55573 -rt nearest 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 
-6.32147 -1.97853 6.55573 -rt nearest 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $

reading from 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...

TR=9.62, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0

Re: [Freesurfer] Trac-all error

[Daniel Callow]

External Email - Use Caution

Hello Anastasia,

I was running this on freesurfer's dev version. I will try running it on
freesurfer 6.0.

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Conitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia 
wrote:

> Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not
> found." What version of freesurfer are you using?
>
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Wednesday, July 3, 2019 2:06:27 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Trac-all error
>
>
> External Email - Use Caution
>
> Hello,
>
> I am running trac-all preproc with the following code
>
> setenv FREESURFER_HOME /Applications/freesurfer_dev
>
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> *#Must set SUBJECTS_DIR to where data is or else uses what was set up when
> installing freesurfer*
>
> setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons
>
>
> *#Must set up configuration file - see trac-all-config-file in
> dti_analysis compository*
>
> *#In configuration file can change number of subject to perform analysis
> on each cluster*
>
>
> *#RUN FIRST*
> trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh
>
>
> *and the attached configuration file. *
>
> *However, I get the following error.*
>
> #@# Intra-subject registration Tue Jul  2 18:21:42 EDT 2019
>
> mri_convert
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
>
> mri_convert
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
>
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from
> /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz...
>
> TR=9.62, TE=3.90, TI=450.00, flip angle=12.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (0, 1, 0)
>
> writing to
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...
>
> orientLAS
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
>
> INFO: input image orientation is LIA
>
> INFO: input image determinant is -1
>
> mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1
> -oc -6.32147 -1.97853 6.55573 -rt nearest
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
>
> mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1
> -oc -6.32147 -1.97853 6.55573 -rt nearest
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
>
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...
>
> TR=9.62, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (0, 1, 0)
>
> Reslicing using nearest
>
> writing to
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz...
>
> tkregister2 --mov
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
> --targ
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
> --regheader --noedit --fslregout
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat
> --reg
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat
>
> tkregister2: Command not found.
>
> Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11
> 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Tue Jul  2 18:21:47 EDT 2019
>
>
> #-
>
> /Applications/freesurfer_dev/bin/trac-preproc
>
> #-
>
> #@# Inter-subject registration (base template) Tue Jul  2 18:21:49 EDT
> 2019
>
> cp
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat
> /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat
> 

Re: [Freesurfer] Trac-all error

[Yendiki, Anastasia]

Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not 
found." What version of freesurfer are you using?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Wednesday, July 3, 2019 2:06:27 PM
To: Freesurfer support list
Subject: [Freesurfer] Trac-all error


External Email - Use Caution

Hello,

I am running trac-all preproc with the following code

setenv FREESURFER_HOME /Applications/freesurfer_dev

source $FREESURFER_HOME/SetUpFreeSurfer.csh

#Must set SUBJECTS_DIR to where data is or else uses what was set up when 
installing freesurfer

setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons


#Must set up configuration file - see trac-all-config-file in dti_analysis 
compository

#In configuration file can change number of subject to perform analysis on each 
cluster


#RUN FIRST

trac-all -prep -c 
/Volumes/DANIEL/dmrirc.long.MCIP.example.sh


and the attached configuration file.

However, I get the following error.


#@# Intra-subject registration Tue Jul  2 18:21:42 EDT 2019

mri_convert 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz

mri_convert 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz

$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $

reading from 
/Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz...

TR=9.62, TE=3.90, TI=450.00, flip angle=12.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...

orientLAS 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

INFO: input image orientation is LIA

INFO: input image determinant is -1

mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 
-6.32147 -1.97853 6.55573 -rt nearest 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 
-6.32147 -1.97853 6.55573 -rt nearest 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz

$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $

reading from 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz...

TR=9.62, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

Reslicing using nearest

writing to 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz...

tkregister2 --mov 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz
 --targ 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz
 --regheader --noedit --fslregout 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat
 --reg 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat

tkregister2: Command not found.

Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 
18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 
x86_64


trac-preproc exited with ERRORS at Tue Jul  2 18:21:47 EDT 2019


#-

/Applications/freesurfer_dev/bin/trac-preproc

#-

#@# Inter-subject registration (base template) Tue Jul  2 18:21:49 EDT 2019

cp 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat
 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat
 /Volumes/DANIEL/dti_freesurf_MCIP/trac/base_MCIP0006/dmri/xfms

cp: 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat:
 No such file or directory

cp: 
/Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat:
 No such file or directory

Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 
18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 
x86_64


trac-preproc exited with ERRORS at Tue Jul  2 18:21:49 EDT 2019

What might be causing the issue? Does it seem like 

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

[Yendiki, Anastasia]

Hi Hao - This will also be fixed in the new version. For now, if you do not 
have them as dicoms, please do your testing without a field map.

Thanks,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Tuesday, December 20, 2016 1:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom


Hello:

More information to give, I think the problem is from the format of the 
magnitude and phase image for the registration-based B0-inhomogeneity 
compensation, I tried to comment the registration-based B0-inhomogeneity 
compensation, and it seems to work, So:


In TRACULA, we can not define the magnitude and phase image to be nii.gz???


Thanks



De : Hao wen
Envoyé : mardi 20 décembre 2016 18:44
À : freesurfer@nmr.mgh.harvard.edu
Objet : RE: trac-all error with .nii.gz images, mri_probedicom


Sorry, the command is not

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txtt,

it is :

trac-all -prep -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt


Thanks

Hao


De : Hao wen
Envoyé : mardi 20 décembre 2016 18:42
À : freesurfer@nmr.mgh.harvard.edu
Objet : trac-all error with .nii.gz images, mri_probedicom


Hello, FreeSurfer experts:

I know that we are going to have a new version of FS 6.0.0, but with the curent 
newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) 
for FS5.3.0, I am working on UBUNTU14.0.


To run tracula in parallel on my machine, here is my config file( for test, I 
have two subjects, and all are recon-alled, I stored all the image into 
.nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the 
magnitude and phase image to do the correction for the B0-inhomogeneity, the 
gradient table format are .bvec and .bval , Here is one of my config file:


### This is to define the CAPS version subjects_dir and subject_id for 
FreeSurfer
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects
set dtroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result
set subjlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0
 )

### This is to point to the dwi original data
set dcmroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test
set dcmlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz)

### This is to define the dwi gradient table(bvel and bvec)
set bvecfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec
set bvalfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval

### This is to define the registration-based B0-inhomogeneity compensation with 
the magnitude and phase map images
set dob0 = 1
set b0mlist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz)
set b0plist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz)

# This is to define Echo spacing for field mapping sequence (from sequence 
printout), only used when doing registration-based B0-inhomogeneity 
compensation.
set echospacing = 0.7

Here is the command to run the preprocessing:

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt

But it gave me some errro from mri_probedicom:

mri_probedicom --i 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz
 > 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016

The error is obvious, because the image here is not a dicom file, but I suppose 
tracula can deal with any format for mri_convert?

In case you need the trac-all.log, I atttached one of them here.

Really need your help, thanks in advance

Hao


___
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 o

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

[Hao wen]

Hello:

More information to give, I think the problem is from the format of the 
magnitude and phase image for the registration-based B0-inhomogeneity 
compensation, I tried to comment the registration-based B0-inhomogeneity 
compensation, and it seems to work, So:


In TRACULA, we can not define the magnitude and phase image to be nii.gz???


Thanks



De : Hao wen
Envoyé : mardi 20 décembre 2016 18:44
À : freesurfer@nmr.mgh.harvard.edu
Objet : RE: trac-all error with .nii.gz images, mri_probedicom


Sorry, the command is not

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txtt,

it is :

trac-all -prep -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt


Thanks

Hao


De : Hao wen
Envoyé : mardi 20 décembre 2016 18:42
À : freesurfer@nmr.mgh.harvard.edu
Objet : trac-all error with .nii.gz images, mri_probedicom


Hello, FreeSurfer experts:

I know that we are going to have a new version of FS 6.0.0, but with the curent 
newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) 
for FS5.3.0, I am working on UBUNTU14.0.


To run tracula in parallel on my machine, here is my config file( for test, I 
have two subjects, and all are recon-alled, I stored all the image into 
.nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the 
magnitude and phase image to do the correction for the B0-inhomogeneity, the 
gradient table format are .bvec and .bval , Here is one of my config file:


### This is to define the CAPS version subjects_dir and subject_id for 
FreeSurfer
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects
set dtroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result
set subjlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0
 )

### This is to point to the dwi original data
set dcmroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test
set dcmlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz)

### This is to define the dwi gradient table(bvel and bvec)
set bvecfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec
set bvalfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval

### This is to define the registration-based B0-inhomogeneity compensation with 
the magnitude and phase map images
set dob0 = 1
set b0mlist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz)
set b0plist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz)

# This is to define Echo spacing for field mapping sequence (from sequence 
printout), only used when doing registration-based B0-inhomogeneity 
compensation.
set echospacing = 0.7

Here is the command to run the preprocessing:

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt

But it gave me some errro from mri_probedicom:

mri_probedicom --i 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz
 > 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016

The error is obvious, because the image here is not a dicom file, but I suppose 
tracula can deal with any format for mri_convert?

In case you need the trac-all.log, I atttached one of them here.

Really need your help, thanks in advance

Hao


___
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.

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

[Hao wen]

Sorry, the command is not

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txtt,

it is :

trac-all -prep -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt


Thanks

Hao


De : Hao wen
Envoyé : mardi 20 décembre 2016 18:42
À : freesurfer@nmr.mgh.harvard.edu
Objet : trac-all error with .nii.gz images, mri_probedicom


Hello, FreeSurfer experts:

I know that we are going to have a new version of FS 6.0.0, but with the curent 
newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) 
for FS5.3.0, I am working on UBUNTU14.0.


To run tracula in parallel on my machine, here is my config file( for test, I 
have two subjects, and all are recon-alled, I stored all the image into 
.nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the 
magnitude and phase image to do the correction for the B0-inhomogeneity, the 
gradient table format are .bvec and .bval , Here is one of my config file:


### This is to define the CAPS version subjects_dir and subject_id for 
FreeSurfer
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects
set dtroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result
set subjlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0
 )

### This is to point to the dwi original data
set dcmroot = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test
set dcmlist = ( 
sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz)

### This is to define the dwi gradient table(bvel and bvec)
set bvecfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec
set bvalfile = 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval

### This is to define the registration-based B0-inhomogeneity compensation with 
the magnitude and phase map images
set dob0 = 1
set b0mlist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz)
set b0plist = 
(sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz)

# This is to define Echo spacing for field mapping sequence (from sequence 
printout), only used when doing registration-based B0-inhomogeneity 
compensation.
set echospacing = 0.7

Here is the command to run the preprocessing:

trac-all -path -c 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt

But it gave me some errro from mri_probedicom:

mri_probedicom --i 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz
 > 
/aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016

The error is obvious, because the image here is not a dicom file, but I suppose 
tracula can deal with any format for mri_convert?

In case you need the trac-all.log, I atttached one of them here.

Really need your help, thanks in advance

Hao


___
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.

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi there - I think I know what it is, but it's a problem that should be 
solved if you have the last tracula update. It means that your LANG 
environment variable needs to be set to en_US.UTF-8, which the update does 
for you.


a.y

On Tue, 5 Jul 2016, Lars M. Rimol wrote:



Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I do

n't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).



Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n

ii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o

/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U
TC 
2015 x86_64 x86_64 x86_64 GNU/Linux


trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula

version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway










sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Lars M. Rimol]

Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and
dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway











sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway


bvals_rows
Description: Binary data


bvec_rows
Description: Binary data


bvals
Description: Binary data


bvecs
Description: Binary data


dwi_orig.mghdti.bvals
Description: Binary data


dwi_orig.mghdti.bvecs
Description: Binary data
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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals 
and dmri/bvecs files that get generated look fine too?


a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Koubiyr, Ismail]

Hi Lars,

I had the same problem. You can notice in your bvec file that there are some 
unusual blank spaces sometimes. Try to look at each space between two numbers 
and make sure it’s fine. You can also make sure about the number of entries by 
running wc -w on each of your bvec or bval file.
Hope it’s gonna help you.

Cheers,

Ismail

> On Jul 2, 2016, at 4:27 AM, Lars M. Rimol  wrote:
> 
> Hi,
> 
> Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
> that there are different numbers of entries in the bval and bvec files. I 
> don't understand why, since both have the same number of rows (64). 
> 
> OS = Ubuntu 14.04.4
> Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
> Tracula and FSL (v 5.0.9). 
> 
> 
> Error message:
> 
> #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
> dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>  -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
> Error: bvecs and bvals don't have the same number of entries
> Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 
> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> 
> trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016
> 
> --
> I also tried flipping the bvec/bval files, but got the same error. 
> I don't know if there's anything wrong with the bval/bvec files, or if this 
> error message is indicative of some other problem. Is the updated Tracula 
> version only compatible with the dev version of FS? 
> 
> I have attached the bval/bvec files and the trac-all.log.
> 
> ---
> The contents of the dmric file is:
> 
> setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
> set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
> set subjlist = (4_FS)
> set dcmroot =  /media/lmr2/subjects/DTI
> set dcmlist =   ( 4/5/1.dcm )
> set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
> set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv
> 
> 
> 
> Thank you!
> 
> 
> yours,
> 
> Lars M. Rimol, PhD
> Senior researcher, 
> Norwegian Advisory Unit for functional MRI
> Department of Radiology, 
> St. Olav's University hospital,
> 7006 Trondheim, 
> Norway
> 
> 
> 
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Re: [Freesurfer] Trac-all error

[Emad Ahmadi]

Thank you so much, Zeke! That helped a lot.

Best,
Emad

 On Mar 10, 2015, at 11:43 PM, zkauf...@nmr.mgh.harvard.edu wrote:
 
 Hello Emad,
 
 The download page states that OSX versions of freesurfer require the user
 to download and install XQuartz onto their machine. I have updated the
 download page so it is a little more clear.
 https://surfer.nmr.mgh.harvard.edu/fswiki/Download 
 https://surfer.nmr.mgh.harvard.edu/fswiki/Download
 
 Also, the dev version of freesurfer is in a high degree of flux right now.
 We are undergoing compiler upgrades and other various changes to the
 build. This means I would expect the nightly builds to be unstable for the
 next couple days.
 
 But installing XQuartz should resolve the issue you experienced below.
 
 -Zeke
 
 
 
 Hello Anastasia,
 
 I’m using the nightly-built version for Mac OS Lion; I double checked it
 by the command freesurfer -ver and got this response:
 
 You are running this version of FreeSurfer:
 
  freesurfer-Darwin-lion-dev-20150227
 
 I’m using this version on Mac OS X Yosemite. I tried to re-download a
 nightly built version, but it didn’t let me (presumably because it’s
 workshop time). Please let me know how I should proceed.
 
 Yours,
 Emad
 
 On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote:
 
 
 Hi Emad - The error is:
 dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib
 
 Does the freesurfer build that you're using match the computer that
 you're running it on?
 
 a.y
 
 On Wed, 4 Mar 2015, Emad Ahmadi wrote:
 
 Hello Freesurfers!
 
 I’m trying to use tracheal -prep, and I’m getting an error. Would
 you please help me with figuring out where the problem is? The log file
 is attached.
 
 Thank you very much,
 Emad
 
 
 
 Emad Ahmadi, MD
 ---
 Research Fellow
 Department of Radiology
 Massachusetts General Hospital
 Harvard Medical School
 
 25 New Chardon Street, Suite 400
 Boston, MA 02114
 Tel: 617 726 5237
 Email: e...@nmr.mgh.harvard.edu
 
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Re: [Freesurfer] Trac-all error

[zkaufman]

Hello Emad,

The download page states that OSX versions of freesurfer require the user
to download and install XQuartz onto their machine. I have updated the
download page so it is a little more clear.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download

Also, the dev version of freesurfer is in a high degree of flux right now.
We are undergoing compiler upgrades and other various changes to the
build. This means I would expect the nightly builds to be unstable for the
next couple days.

But installing XQuartz should resolve the issue you experienced below.

-Zeke



 Hello Anastasia,

 I’m using the nightly-built version for Mac OS Lion; I double checked it
 by the command freesurfer -ver and got this response:

 You are running this version of FreeSurfer:

   freesurfer-Darwin-lion-dev-20150227

 I’m using this version on Mac OS X Yosemite. I tried to re-download a
 nightly built version, but it didn’t let me (presumably because it’s
 workshop time). Please let me know how I should proceed.

 Yours,
 Emad

 On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:


 Hi Emad - The error is:
  dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib

 Does the freesurfer build that you're using match the computer that
 you're running it on?

 a.y

 On Wed, 4 Mar 2015, Emad Ahmadi wrote:

 Hello Freesurfers!

 I’m trying to use tracheal -prep, and I’m getting an error. Would
 you please help me with figuring out where the problem is? The log file
 is attached.

 Thank you very much,
 Emad



 Emad Ahmadi, MD
 ---
 Research Fellow
 Department of Radiology
 Massachusetts General Hospital
 Harvard Medical School

 25 New Chardon Street, Suite 400
 Boston, MA 02114
 Tel: 617 726 5237
 Email: e...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Trac -all error

[Alan Francis]

Thanks Anastasia:

Yes that helps. Have a great weekend!

Alan

On Fri, Mar 6, 2015 at 6:30 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Alan - Your culprit is here:

 WARN: Could not find /data/alanf/FreeSurfer_5.3/
 diffusion_recons/105014/mri/aparc+aseg.mgz
 WARN: You will not be able to complete TRACULA processing without it

 You have to make sure your freesurfer recon is there, or define
 SUBJECTS_DIR appropriately if it's elsewhere.

 Hope this helps,
 a.y


 On Thu, 26 Feb 2015, Alan Francis wrote:

  Hi Anastasia:
 Sorry to bother you again. I ran trac all  on our cluster but it gave me
 an error message. I have enclosed the text file. I used vim to see
 if I could decipher the error but I am not entirely sure what the problem
 is

 Please advice.

 thanks,

 Alan






 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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-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu ezra_wegbr...@brown.edu
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Re: [Freesurfer] Trac -all error

[Anastasia Yendiki]

Hi Alan - Your culprit is here:

WARN: Could not find 
/data/alanf/FreeSurfer_5.3/diffusion_recons/105014/mri/aparc+aseg.mgz
WARN: You will not be able to complete TRACULA processing without it

You have to make sure your freesurfer recon is there, or define 
SUBJECTS_DIR appropriately if it's elsewhere.


Hope this helps,
a.y

On Thu, 26 Feb 2015, Alan Francis wrote:


Hi Anastasia:
Sorry to bother you again. I ran trac all  on our cluster but it gave me an 
error message. I have enclosed the text file. I used vim to see
if I could decipher the error but I am not entirely sure what the problem is

Please advice.

thanks,

Alan



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Re: [Freesurfer] trac-all error (segmentation fault?)

[Anastasia Yendiki]

Hi Durai - You cannot run all 3 steps of trac-all at the same time. The 3 
steps need to be run separately. Please check the tutorial on the wiki for 
more details.


a.y

On Tue, 24 Jun 2014, Durai Arasan wrote:


Hi Freesurfer experts,
I tried running trac-all with my config file and received the following
error :

Segmentation fault 
Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33
UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Tue Jun 24 11:15:12 EDT 2014

Any help would be greatly appreciated! I am attaching the config file, log
and error files.

Thank you!
Durai


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Re: [Freesurfer] Trac-all Error

[Anastasia Yendiki]

Hi Crystal - This is because of the way the B0 dewarping script is called 
during the pre-processing. It assumes that you have 2 phase images instead 
of the difference of 2 phase images (which is what you have). The next 
version actually accommodates both cases but for now you have 2 options:


1. Edit the script $FREESURFER_HOME/bin/trac-preproc and change this line:
set cmd = ($cmd --ph $dwidir/b0pha.nii.gz)
   to this:
set cmd = ($cmd --dph $dwidir/b0pha.nii.gz)

2. Be lazy and skip B0 dewarping!

Hope this helps,
a.y

On Wed, 24 Oct 2012, Franklin, Crystal G wrote:


Freesurfer,

I am trying to run trac-all –prep and trac-preproc keeps exiting with errors.  
It
keeps saying the unwrappedphasemaps must contain at least two volumes.  My data
only contains one phase image and 2 magnitude images.  Do you know what could be
causing this error or how to get around it?

Thanks in advance,
Crystal

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Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

[Anastasia Yendiki]

Hi Torben - I'm looking at all the invocations of trac-all -prep in your 
log file, and they've both exited with an error (the same bvecs error).

 grep prep trac-all.log
-prep -c /Users/torben/Desktop/tracon/tracon
New invocation of trac-preproc
/Applications/MRSoftware/freesurfer/bin/trac-preproc
trac-preproc exited with ERRORS at Do 21 Jun 2012 20:34:41 CEST
...
-prep -c /Users/torben/Desktop/tracon/tracon
New invocation of trac-preproc
/Applications/MRSoftware/freesurfer/bin/trac-preproc
trac-preproc exited with ERRORS at So 24 Jun 2012 22:37:30 CEST

After that you've ran trac-all -bedp and trac-all -path, but obviously 
these are going to fail if trac-all -prep has failed. I hope this makes 
sense.

a.y

On Fri, 29 Jun 2012, Torben Prokscha wrote:

 Hi Anastasia!

 Yes, we reran trac-all -prep after fixing the bvec issue. I am still
 surprised how you know that the latest failure was due to a bvecs problem,
 because the last error message was the one about the missing tract ...?

 Thank you for your help!

 Best
 Torben



 Hi Torben - I just scrolled to the end of your log file. The last
 invocation of trac-all -prep is the one that failed b/c of the bvecs
 error. Did you rerun trac-all -prep after you fixed the bvecs?

 Thanks,
 a.y

 On Tue, 26 Jun 2012, Torben Prokscha wrote:

 Hi Priti,

 thank you for your reply, but I'm afraid you didn't scroll to the end of
 the log file: Yes, we had that bvecs/bvals error in the first run, but
 we
 corrected it and got the error I reported in my previous mail (it is
 also
 printed at the end of the log file):

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Could you or anybody else please help with this problem which is
 obviously
 related to missing tracts?

 Thanks in advance
 Torben


 Hi Torben,

 Your trac-preproc exited with errors because of the following error.

 Error: bvecs and bvals don't have the same number of entries

 You should check to see if your bvals and bvecs have the same no.of
 lines
 and then rerun trac-all -prep.

 Priti


 Dear all,

 while running trac-all, I got the following error:

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Obviously, a similar problem was discussed before (here:
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html).
 However, no general solution was publicly mailed. Since it was
 requested
 then, I attach the trac-all.log file.

 Thanks in advance for any help!

 Best
 Torben Prokscha

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Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

[Torben Prokscha]

Hi Priti,

thank you for your reply, but I'm afraid you didn't scroll to the end of
the log file: Yes, we had that bvecs/bvals error in the first run, but we
corrected it and got the error I reported in my previous mail (it is also
printed at the end of the log file):

ERROR: Could not open
/Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

Could you or anybody else please help with this problem which is obviously
related to missing tracts?

Thanks in advance
Torben


 Hi Torben,

 Your trac-preproc exited with errors because of the following error.

 Error: bvecs and bvals don't have the same number of entries

 You should check to see if your bvals and bvecs have the same no.of lines
 and then rerun trac-all -prep.

 Priti


 Dear all,

 while running trac-all, I got the following error:

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Obviously, a similar problem was discussed before (here:
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html).
 However, no general solution was publicly mailed. Since it was requested
 then, I attach the trac-all.log file.

 Thanks in advance for any help!

 Best
 Torben Prokscha

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Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

[Anastasia Yendiki]

Hi Torben - I just scrolled to the end of your log file. The last 
invocation of trac-all -prep is the one that failed b/c of the bvecs 
error. Did you rerun trac-all -prep after you fixed the bvecs?

Thanks,
a.y

On Tue, 26 Jun 2012, Torben Prokscha wrote:

 Hi Priti,

 thank you for your reply, but I'm afraid you didn't scroll to the end of
 the log file: Yes, we had that bvecs/bvals error in the first run, but we
 corrected it and got the error I reported in my previous mail (it is also
 printed at the end of the log file):

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Could you or anybody else please help with this problem which is obviously
 related to missing tracts?

 Thanks in advance
 Torben


 Hi Torben,

 Your trac-preproc exited with errors because of the following error.

 Error: bvecs and bvals don't have the same number of entries

 You should check to see if your bvals and bvecs have the same no.of lines
 and then rerun trac-all -prep.

 Priti


 Dear all,

 while running trac-all, I got the following error:

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Obviously, a similar problem was discussed before (here:
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html).
 However, no general solution was publicly mailed. Since it was requested
 then, I attach the trac-all.log file.

 Thanks in advance for any help!

 Best
 Torben Prokscha

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Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

[Priti Srinivasan]

Hi Torben,

Your trac-preproc exited with errors because of the following error.

Error: bvecs and bvals don't have the same number of entries

You should check to see if your bvals and bvecs have the same no.of lines
and then rerun trac-all -prep.

Priti


 Dear all,

 while running trac-all, I got the following error:

 ERROR: Could not open
 /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

 Obviously, a similar problem was discussed before (here:
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html).
 However, no general solution was publicly mailed. Since it was requested
 then, I attach the trac-all.log file.

 Thanks in advance for any help!

 Best
 Torben Prokscha

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

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Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

[Peter J. Molfese]

Sorry for the delay in responding, I wanted to try every permutation that I 
could think of.  I updated the tracula binaries for snow leopard 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html)
 and that gives me some of the same, and some different issues that may help.  
First, if the bvec file is in the correct format (3 columns), then it copies 
the file correctly and trac-all continues smoothly.  If the file is in the 3 
row format (needing to be transposed), then tracula will only copy the first 9 
numbers out of it giving the error of not having the correct number of bvecs to 
bvals.  So that seems fixable, I just need to reorient all of our bval and bvec 
files into the correct format.  

I'm still a bit unsure why tracula won't create the bvec and bval files during 
the mri_convert stage.  I have been using dcm2nii to create these two files but 
then continue to give tracula the path to the dicom files.  So the orientation 
of this file could be related to how dcm2nii writes the files.  Any suggestions 
would be very welcome.  As it stands, my current workflow is:

1. use dcm2nii to create bvec and bval files
2. reorient bvec and bval files to be 3 column and 1 column format respectively.
3. run trac-all -prep with a config file showing where the dicom images are and 
hand specifying the bvec and bval files

Peter


Peter J. Molfese, Ph.D.
Postdoctoral Associate
Haskins Laboratories
300 George Street, Suite 900
New Haven, CT 06511
peter.molf...@yale.edu


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Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

[Anastasia Yendiki]

Hi Peter - The format for the bvec and bval files is explained in:
$FREESURFER_HOME/bin/dmrirc.example

If you've structured your dmrirc following this example file and you're 
still getting this error, please send the following so I can debug this:
- your exact trac-all command line
- your dmrirc file
- your trac-all.log
- the actual bvecs and bvals files that you specify in your dmrirc

Thanks,
a.y

On Mon, 28 Nov 2011, Peter J. Molfese wrote:

 Sorry for the delay in responding, I wanted to try every permutation that I 
 could think of.  I updated the tracula binaries for snow leopard 
 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html)
  and that gives me some of the same, and some different issues that may help. 
  First, if the bvec file is in the correct format (3 columns), then it copies 
 the file correctly and trac-all continues smoothly.  If the file is in the 3 
 row format (needing to be transposed), then tracula will only copy the first 
 9 numbers out of it giving the error of not having the correct number of 
 bvecs to bvals.  So that seems fixable, I just need to reorient all of our 
 bval and bvec files into the correct format.

 I'm still a bit unsure why tracula won't create the bvec and bval files 
 during the mri_convert stage.  I have been using dcm2nii to create these two 
 files but then continue to give tracula the path to the dicom files.  So the 
 orientation of this file could be related to how dcm2nii writes the files.  
 Any suggestions would be very welcome.  As it stands, my current workflow is:

 1. use dcm2nii to create bvec and bval files
 2. reorient bvec and bval files to be 3 column and 1 column format 
 respectively.
 3. run trac-all -prep with a config file showing where the dicom images are 
 and hand specifying the bvec and bval files

 Peter


 Peter J. Molfese, Ph.D.
 Postdoctoral Associate
 Haskins Laboratories
 300 George Street, Suite 900
 New Haven, CT 06511
 peter.molf...@yale.edu


 CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is 
 for the sole use of the intended recipient(s) and may contain confidential 
 and privileged information. Any unauthorized review, use, disclosure or 
 distribution is prohibited. If you are not the intende d recipient, please 
 contact the sender immediately by reply e-mail and destroy all copies of the 
 original message.





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Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

[Anastasia Yendiki]

Hi Peter - Each of the volumes in your DWI series was acquired with a 
certain b-value and a certain diffusion gradient direction. These have to 
be in the bvals and bvecs files, respectively, in the same order. This 
means for every volume in the DWI series, there'll be 1 number in bvals 
and 3 numbers in bvecs (could be zero in a few cases).


If you suspect that the bvals and bvecs files are not correct, you should 
consult your MR physicist. If you think they're correct but trac-all isn't 
reading them properly, you can attach those 2 files and I can take a look.


a.y

On Fri, 18 Nov 2011, Peter J. Molfese wrote:


Hello,

I'm running trac-all (trac-preproc) on some DTI data and receive the following 
error: 

dtifit -k /Users/pete/Documents/dti/pete/run7/peter/dmri/dwi.nii.gz -m
/Users/pete/Documents/dti/pete/run7/peter/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/Users/pete/Documents/dti/pete/run7/peter/dmri/bvecs -b 
/Users/pete/Documents/dti/pete/run7/peter/dmri/bvals -o
/Users/pete/Documents/dti/pete/run7/peter/dmri/dtifit

Error: bvecs and bvals don't have the same number of entries

I found the following 
thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19747.html but
 when I attempted to add
export LC_ALL=en_US, the problem persists.  I have looked in the files and 
found that they do indeed have different numbers of
entries.  The scans were performed on a Siemens TimTrio 3T scanner.  

Is there something else I should set?  

Peter J. Molfese, Ph.D.
Postdoctoral Associate
Haskins Laboratories
300 George Street, Suite 900
New Haven, CT 06511
peter.molf...@yale.edu


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contain confidential and privileged information. Any unauthorized review, use, 
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e-mail and destroy all copies of the original message. 


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