External Email - Use Caution
Tcsh and other programs/files freesurfer uses are not installed by default on
Ubuntu linux. So to install fresurfer and also have the system install
what freesurfer needs to run, you should use one of the freesurfer .deb
package installers availabl
: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you
corrected?
best regards
Woo-Suk, Tae
On Tue, Oct 31, 2023
t;
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.
: (650)-725-1716
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Woo-Suk Tae
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.
#chage codes from
set cmd = mri_binarize
set cmd = (
External Email - Use Caution
Hi FreeSurfers,
I wanted to follow up on my post. I am still receiving this error when running
the preprocessing step of TRACULA. We have run our files without the thalamic
nuclei included, however, that is not ideal because we are interested in tr
es of output. Please attach your entire trac-all.log file.
Thanks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Monday, July 25, 2022 3:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error in
shadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error in path construction
Could be that you reached a memory limit? If the
Could be that you reached a memory limit? If the same analysis runs fine on
your computer, then it's probably a cloud issue, not a TRACULA issue.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Thursday, July 21, 2022 3:58 PM
To
urfer support list
Subject: Re: [Freesurfer] Tracula error
Hello,
I wanted to follow up on this question. I appreciate it much if you could
suggest me any solutions. I checked my space and I have 3.5 T free space, so
It’s definitely not a space problem.
Thanks,
Mona
On Dec 14, 2021, at 12:
2:41 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error
How much space would I need to run this?
Thanks,
Mona
On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> w
Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error
How much space would I need to run this?
Thanks,
Mona
On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Any chance you're low on disk spa
Is there a dmri/data.nii.gz? Can you run mri_info on it please?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
reesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject:
Any chance you're low on disk space?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
Yes.
dmri.bedpost
esday, December 14, 2021 11:40 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error
Hello,
I was running the "trac-all -bedp” section, when I got the below error. I
appreciate it much if you please let me know wha
;>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error
Hi Anastasia,
I did add the ANTs to my path, but
ehalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error
Hi Anastasia,
I did add the ANTs to my path, but am still getting that s
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
Hi Anastasia,
I did add the ANTs to my path, but am still getting that same error.
I adde the path : setenv ANTSPATH /usr/pubs
half
of juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>Sent: Thursday,
November 25, 2021 1:40
AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re:
[Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals
file External Email - Use
Caution
Hi Anastasia,
I did add the ANTs to my path, but am still getting that same error.
I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the
.csh file which has all the TRACULA configuration info, and also to the bash
script that I’m running the trac-all from: export
ANTSPATH
Hi Mona - You need to add the location of the ANTs executables to your path.
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subjec
Hi Stephanie - Please send along your configuration file and the log file from
scripts/trac-all.log. It's hard to guess just by seeing the error message.
Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Stephanie Otto
Sent: Thursda
anks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
juergen.haen...@upd.unibe.ch
Sent: Thursday, November 25, 2021 1:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
Exter
.ch<mailto:juergen.haen...@upd.unibe.ch>
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Wednesday, November 24, 2021 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt
d.edu
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also othe
u>>
on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>
mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Hi Jürgen - What's your $FSLDIR set to?
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
juergen.haen...@upd.unibe.ch
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA erro
reesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem
surfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem occurred wrt the field map for which we did not
find any so
Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case
when you have 1 DWI run only. I committed a bug fix for this. For now you can
get it from here (and it should get merged into the dev version in a couple of
days):
https://raw.githubusercontent.com/ayendiki/freesurfe
support list
Subject: Re: [Freesurfer] TRACULA error: missing output volume name
Hi Shanika - Can you try separating the "=" signs from the variable names in
the config file with a space?
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on
Freesurfer support list
Subject: Re: [Freesurfer] TRACULA error: missing output volume name
External Email - Use Caution
External Email - Use Caution
Hi Anastasia
Thanks so much for your reply. I have attached herewith the scripts/log file
-please let me know if you need any
, Anastasia
Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA error: missing output volume name
Hi Shanika - Can you please send the full log file from scripts/trac-all.log?
It's hard to figure out what causes the error without seeing the
Hi Shanika - Can you please send the full log file from scripts/trac-all.log?
It's hard to figure out what causes the error without seeing the full output.
Nothing looks unusual in the config file.
Thanks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
Hi Oshadi - That does not sound normal. Is there anything wrong with the
FreeSurfer segmentation of this subject?
Anastasia.
From: Shanika Jayakody
Sent
ndiki, Anastasia
Sent: Wednesday, October 28, 2020 12:12 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
The two formats that you sent are not equivalent.
In the version where the gradient vectors saved in columns, the first 2 co
Hi Michele - Do you get any other output on the screen? Can you attach your
configuration file and trac-all.log? Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Michele Valotti
Sent: Friday, October 30, 2020 12:44 PM
To: Freesurfer
AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
The two formats that you sent are not equivalent.
In the version where the gradient vectors saved in columns, the first 2 columns
are:
0 -0.793264
0 -0.394167
0 0.464074
In the ve
pport list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
Hi Oshadi - Yes.
For future reference, if you have any doubts about command line usage, you can
1. run "trac-all", without any arguments, and/or 2. read the tutorial:
MailScanner has detected a possibl
get the same error
Thank you very much,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject
hat causes this.
If you have any suggestion please let me know
Thanks,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
External Email - Use Caution
I am double checking so the command i
: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
What goes after "-c" in the trac-all command should be the configuration file,
not the nifti file.
From: Shanik
ething-looking forward to hear from you.
Many thanks,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is lon
ggest something-looking forward to hear from you.
Many thanks,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run
anika Jayakody
Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
CAUTION: This email comes from an external source; the attachments and/or links
may compromise our secure environment. Do not open or
External Email - Use Caution
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error: run list is longer
t: Re: [Freesurfer] Tracula error: run list is longer than subject list
Make sure to use "subjlist", not "sublist". If that is not the issue, then
please attach your log file and configuration file - it's hard to guess the
issue without more information.
Best,
Anastasia.
___
Make sure to use "subjlist", not "sublist". If that is not the issue, then
please attach your log file and configuration file - it's hard to guess the
issue without more information.
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sha
: [Freesurfer] Tracula error
Hi Yasemin - It looks like the unix shell doesn't like that there are spaces
after the "\" in a few lines:
1723_base \
1741_base \
1725-2/eddy_with_repol.nii.gz \
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.h
Hi Yasemin - It looks like the unix shell doesn't like that there are spaces
after the "\" in a few lines:
1723_base \
1741_base \
1725-2/eddy_with_repol.nii.gz \
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hasimoglu, Yasemin
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of
gradient vectors
Hi,
I have been trying different ways to troubleshooting this error without
success. I am pasting here the whole error when I try to run "trac-all -prep
-c" in the D
Hi,
I have been trying different ways to troubleshooting this error without
success. I am pasting here the whole error when I try to run "trac-all -prep
-c" in the Dev version:
INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon
INFO: Diffusion root is /autofs/cluster/guptagp/gabi/trac
Hi Andrade - You have some forward slashes ("/") at the ends of lines in the
config file that should be backslashes ("\") instead.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Saturday, December 21, 2019 9:11 AM
To: Freesur
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Thursday, October 10, 2019 9:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution
Hello,
It isn't an error with rec
External Email - Use Caution
Hello,
It isn't an error with recon-all, at least I don't think it is. Recon-all
ran without error and the file that Tracula is trying to access seems to be
where it is supposed to be. It seems like Tracula is having an issue
opening the lh.white file.
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error"
in the subject line if you want the developers of the structural stream to look
into it.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Thursday,
Hi Lorenzo - If you are still having this problem, please send the trac-all.log
file from one of the 4 subjects.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lorenzo Pini
Sent: Friday, May 10, 2019 4:35:50 PM
To: freesurfer@nmr.mgh.harvard.
Hi all,
sorry for reviving this super old thread, but it came up here as well
with Freesurfer 6.0.0.
> This is an Ubuntu-related error that has surfaced recently because in
> Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
> edit the first line of the scripts $FREESURFE
Hi Batool - Please send over your (actual and not made up :) config file and
trac-all.log.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool
[br2...@cumc.columbia.edu]
Sent: Tuesday, October 10,
support list
Subject: Re: [Freesurfer] TRACULA ERROR!!
Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons were
found in SUBJECTS_DIR in my configuration file. Thanks.
best,
Ariel
On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia
mailto:ayend
Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons
were found in SUBJECTS_DIR in my configuration file. Thanks.
best,
Ariel
On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia wrote:
> Hi Ariel – Have you run freesurfer on the structural images of your
> su
Hi Ariel – Have you run freesurfer on the structural images of your subjects?
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in
your configuration file?
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Lin, Yizhi" mailto:l...@union.edu
Hi Marisa – Did you check the archives of this email list? I believe this error
has come up before.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Marissa Pifer
mailto:marissapi...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
D
Hi Alex,
Try setting the FSLDIR to when same value as FSL_DIR. So you command
would be something like:
export FSLDIR=$FSLDIR
Then try rerunning TRACULA. Hopefully this solves the issue.
-Zeke
On 11/29/2016 01:53 PM, Yendiki, Anastasia wrote:
> Hi Alex - Have you run the freesurfer setup sc
Hi Alex - Have you run the freesurfer setup script?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alexander Zent
[az...@p
Hi Kristina - I suspect there's some misregistration, or part of the brain
mask (and hence the anatomical segmentation) missing or something like
that. Do you mind uploading the tracula directories of this subject for me
to take a look at?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
You get the same error as trac-all because trac-all runs mri_convert. I'd
send the mri_convert error in a new email with mri_convert somewhere in
the title, so that someone else can help you.
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Also when I run mir_convert on the DICOMs I get the same
Also when I run mir_convert on the DICOMs I get the same error as the one I got
when I used DICOMs :
WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERR
It says 1 … I don’t understand why I get that knowing that when I open the
nifti I can go through the frames …
Ismail
> On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
> wrote:
>
>
> I do not know why the dicoms do not work. When you run mri_info on your
> nifti, what is the number of frames
I do not know why the dicoms do not work. When you run mri_info on your
nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So
this shouldn’t be the reason.
A
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?
Thanks,
Ismail
> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki
> wrote:
>
>
> Hi Ismail - You can see from the log
Hi Ismail - You can see from the log file that the command that causes the
error is this:
mri_convert --frame 31
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd fram
Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
> wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not th
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks,
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I t
Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you understand
more.
I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.36800
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic
> Siemens DWI.
Hi Scott - The gradient table produced by dcm2nii is formatted in 3 rows,
rather than 3 columns. If you want to use gradient tables formatted in
rows, you have to download the tracula update described here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
a.y
On Tue, 7 Apr 20
Hi Tadeu - The files appear to have the problem described here:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg20513.html
That's probably was causing them not to be converted correctly.
a.y
On Thu, 6 Nov 2014, Tadeu Kubo wrote:
Dear FS Experts,
I'm trying to work with the
Hi,
Thanks a lot.
I corrected the files as you suggested and now it finished without error.
Best,
Pedro Rosa.
On Jul 4, 2014, at 7:24 AM, Anastasia Yendiki
wrote:
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the gradient table should have 1
Thank you once again!
Yes, that is true.
The bval and bvec file were doubled, so I removed half the values (and also the
empty spaces) and the fMRIframe: frame >= nframes stopped from happening.
A converted the dcm to nii using dcm2nii software, and used its bval and bvec
files as input to TRAC
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the gradient table should have
130*3 entries (one x,y,z direction vector for each b-value). This error
means that there are fewer entries in the gradient table than there should
be. Run wc -w on
The error message is "data and bvals/bvecs do not contain the same number
of entries". This doesn't necessarily mean that the bvecs and bvals don't
agree with each other, but that the bvecs and bvals don't agree with the
DWI data.
Based on this line in the log file, there are 130 frames in t
Hi Pedro - Have you specified not to do eddy current compensation? It
looks like it's being skipped. In that case, you need to also skip the QA
step (by adding -noqa to your trac-all command line). That's because the
QA step requires the output of the eddy current compensation to assess how
mu
Anastasia,
I was finding the same error as Jun, and your help fixed it. Thank you very
much.
However, I am now finding a new error (attached).
Can you help me?
Thank you again.
Regards,
Pedro Rosa.
On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote:
> Hi Anastasia,
>
> You are right!
Hi Anastasia,
You are right! There are empty spaces at the end of the lines in
original bvecs and bvals.
I could fix the error and finish trac-preproc without error by
eliminating these spaces.
Thank you so much!
Regards,
Jun Shinozaki
2014-07-02 15:21 GMT+09:00 Anastasia Yendiki :
>
> There are
There are probably some empty spaces at the end of the lines of the
original files that confuses it into introducing those zeros. If you
attach the original files, I can take a look at them.
On Wed, 2 Jul 2014, Jun Shinozaki wrote:
> Hi Anastasia,
>
> I created bvals.txt and bvecs.txt using dc
Hi Anastasia,
I created bvals.txt and bvecs.txt using dcm2nii.
These original files were text files and set in dmrirc profile as
"set bvalfile = /path/to/bvals.txt".
I checked word count for these files
# wc -w bvals.txt bvecs.txt
65 bvals.txt
195 bvecs.txt
260 total
However, when I run "t
Hi Jun - By a simple word count on these files:
% wc -w bvals bvecs
65 bvals
198 bvecs
263 total
As you can see, there are 3 extra entries in the bvecs file. If you then
open the file, you'll see that there is an extra column of zeros in the
end. Not sure if that's what's causing the pr
Hi Anastasia,
Thank you for your e-mail.
I took 65 DWIs (5 b0 volumes and 60 direction DWIs).
I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images.
Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts.
It seems consistent.
I attach bvals and bvecs. These fil
Hi Jun - It's failing at the point where it tries to extract the low-b
images from the DWI series. I suspect that the number of frames in the 4D
DWI volume that is extracted from your dicom does not match the number of
frames that it expects to find based on how many gradient vectors or
b-valu
Hi Anastasia,
Thanks for the reply.
After I edit my .tcshrc file to source the dev, I still get an error message.
glia:shantanu[64] mynmr53
MNE software location set to:/usr/pubsw/packages/mne/stable
MATLAB software not available
/usr/pubsw/packages/mne/stable/bin added to PATH
/usr/pubsw/
thanks.
On Fri, June 13, 2014 12:30 pm, Anastasia Yendiki wrote:
>
> The right one to source is /usr/local/freesurfer/nmr-dev-env
>
>
> On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
>
>> Hi Anastasia,
>>
>> Thanks for the reply.
>>
>> After I edit my .tcshrc file to source the dev, I still get an err
The right one to source is /usr/local/freesurfer/nmr-dev-env
On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
> Hi Anastasia,
>
> Thanks for the reply.
>
> After I edit my .tcshrc file to source the dev, I still get an error message.
>
> glia:shantanu[64] mynmr53
>
> MNE software location set to:
Hi Shantanu - The -qa flag was added in the update to tracula that was
posted after the 5.3 release.
http://freesurfer.net/fswiki/Tracula/#Updates
Martinos Center users can simply switch to the dev version of freesurfer
to take advantage of these updates, in which case you don't need to
Hi Wonsang - The new tutorial data has subjects named elmo.2005,
elmo.2008, and elmo.2012 - not Diff001, which was from the old tutorial
data. So if you're using the new tutorial data you need to set your
configuration file accordingly with the new subject names, as shown on the
tutorial page
Hi Francesco - The bvecs file that you're attaching has only 3 vectors,
while the bvals file has 65 b-values. Are these your original files, or
the ones saved by trac-all in the dmri/ directory?
a.y
On Mon, 13 Jan 2014, Francesco Baldacchini wrote:
> Hi everybody,
> I'm trying to run the trac
Hi Anastasia,
It was solved after reinstalling netCDF and updating the links (and some 64
bit packages missing too), now it is working, many thanks!!
Gari
On Tuesday, December 17, 2013, Anastasia Yendiki wrote:
>
> Hi Gari - This is coming from the new code in the update that I posted
> recently.
Hi Matthieu - This error had to do with a change in bedpostx's command
line arguments after an FSL upgrade. The problem is fixed in the newer
version of tracula. Again, I'd strongly recommend upgrading to the newer
tracula.
Hope this helps,
a.y
On Thu, 12 Dec 2013, Matthieu Vanhoutte wrote:
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