External Email - Use Caution
Hello,
I am attempting to run white matter tractography using TRACULA, as
described in the tutorial, however, using a brain parcellation acquired
using an external algorithm. I have put the aparc+aseg.mgz file in the
subject directory in folder mri
External Email - Use Caution
Hello,
I am attempting to run white matter tractography using TRACULA, as
described in the tutorial, however, using my own data and brain
parcellation acquired using external algorithm. I have put the
aparc+aseg.mgz file in the subject directory in
External Email - Use Caution
Hi:
I tried to use trac-all using following syntax:
trac-all -prep -s name -i
SIEMENS_DICOM_256_GRADIENTS_TRACTOGRAPHY_FILES_PATH
and I got the following error message:
"ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for
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
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
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
___
Freesurfer mai
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 te
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,
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: Tra
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
ehalf 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 partici
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
> 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 Regard
y, 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
ma
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
erting 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.h
tasia.
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 comp
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
Reference
> 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.
>
>
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 - Us
er-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
---
> *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
>
>
&g
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
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 freesu
[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
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 t
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
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
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 ha
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
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
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.
Hop
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
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
> dow
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 h
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
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
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 el
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
trac-all.o103866
Description: Bina
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 t
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:
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:
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
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-pre
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 repl
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/
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
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 li
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 hel
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
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/dmr
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