Hi all,
We ran tracula prep stage and it exited with errors: 'Selected streamline has
fewer than 5 points'. We have attached the log and error files if needed.
Thank you in advance!
Skyler
--
Skyler G. Shollenbarger
Graduate Student - UWM Brain Lab
Clinical Psychology & Neurospychology
U
Hello,
I am running into the following error when I try to run trac-all:
set: No match.
ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several
attempts at debugging it.
I was wondering if you had any suggestions? Attached
Hi:
I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I
tried to run the command "trac-all -bedp -c dmrirc", I got the error:
ln -sf
/usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz
/usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif
Dear fellow researchers,
I am running tracula pre-processing step, and the computer showed an error
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP F
Hi,
I'm running tracula using the following command:
(Note: I'm replacing actual paths with made up paths)
trac-all -prep -c /path/to/my/config.sh
And for some reason it stops running while working on the first subject
(creates the folder for the first subject), with this error:
if: Expression
External Email - Use Caution
Hello Freesurfer Team,
I am trying to get TRACULA running on two different machines (Macbook Pro
OS 11.6 and Mac desktop OS 10.14.6). I get the same error message on both
devices, which is:
domainname: Command not found.
ERROR: for B0 distortion corr
Hello,
I’ve been running the trac-all -prep step and I faced this error:
ConvertTransformFile 3
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
--hm --ras
ConvertTransformFile:
Hi,
I am trying to run trac-all using a configuration file for 30 subjects with
longitudinal data, and keep getting the following errors:
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects
I looked through my file line by line and looked at similar posts on the
archives but could
External Email - Use Caution
Hello all,
I am trying to run Tracula for one of my subjects and after creating the
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.
I have run the SetUpFreeSurfer.sh script and ec
Hi Skyler - How does the brain mask look like? Any major chunks of brain
missing in the area of the left uncinate? That's the tract where the error
occurs, and based on this info in the log file, I'm guessing it's a
masking issue:
[...]
INFO: Rejected 4221 streamlines for straying off mask
INF
t.
>
> Would you consider this subject a loss or are there other fixes you suggest?
>
> Thanks again!
> Skyler
>
>
> - Original Message -
> From: "Anastasia Yendiki"
> To: sholl...@uwm.edu
> Cc: freesurfer@nmr.mgh.harvard.edu
> Sent: Tuesday, Ma
Hi Emily - You're using "*" to specify all the dicom files in the series.
You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This
dmrirc looks like it might have been adapted from an older version of the
tutorials. If so, I highly recommend d
i727056.MRDC.1, the first dicom
image
Jon
- Original Message -
From: "Anastasia Yendiki"
To: ebell...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 22, 2013 10:09:13 AM
Subject: Re: [Freesurfer] Tracula Error
Hi Emily - You're using "*"
.63 i727127.MRDC.72
> i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc
>
>
>
> so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom
> image
>
> Jon
>
> - Original Message -
> From: "Anastasia Yendiki"
> To: ebell..
elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: "freesurfer" , "ebelleau"
Sent: Tuesday, October 22, 2013 12:24:22 PM
Subject: Re: [Freesurfe
19455034689828982 )
>
>
>
>
> Jon
>
>
>
>
>
> - Original Message -
> From: "Anastasia Yendiki"
> To: "Jon Wieser"
> Cc: "freesurfer" , "ebelleau"
>
> Sent: Tuesday, October 22, 2013 12:24:22 PM
&
e names are assumed be relative to the directory specified in dcmroot
> above.
>
>
> Jon
>
> - Original Message -
> From: "Anastasia Yendiki"
> To: "Jon Wieser"
> Cc: "ebelleau" , "freesurfer"
>
> Sent: Tuesday,
.edu
> Sent: Tuesday, October 22, 2013 2:05:35 PM
> Subject: Re: [Freesurfer] Tracula Error
>
>
> There is no * character in the example on the wiki. What do you think
> should change?
>
> On Tue, 22 Oct 2013, Jon Wieser wrote:
>
>> that makes perfect sense, but you
Thank you for your help! We were able to work out the issue!
Emily
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 22, 2013 2:21:49 PM
Subject: Re: [Freesurfer] Tracula Error
Jon - Thank you
ead in the dicom's okay now
Jon
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 22, 2013 2:21:49 PM
Subject: Re: [Freesurfer] Tracula Error
Jon - Thank you for your suggestion. However, the
Hi Gonzalo - This has come up a few times recently. Please see here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html
Hope this helps,
a.y
On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote:
> Hi:
>
> I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I
> tr
Hi Anastasia:
And, which options do you think I must use with bedpostx ?... The default ?...
Sincerely,
Gonzalo Rojas Costa
On Mon, Jul 30, 2012 at 5:36 PM, Anastasia Yendiki wrote:
>
> Hi Gonzalo - This has come up a few times recently. Please see here:
> http://www.mail-archive.com/fre
Yes, default is fine! Just run bedpostx with the path to the dmri
directory as the only argument, that should work.
On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote:
> Hi Anastasia:
>
> And, which options do you think I must use with bedpostx ?... The default
> ?...
>
> Sincerely,
>
>
> Gonzal
Hi Freesurfers,
Could you help me interpret this error message? I am attempting to run
TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3
helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1
INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI
IN
i" mailto:l...@union.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, August 7, 2017 at 12:00 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Fr
Monday, August 7, 2017 at 12:00 AM
> To: "freesurfer@nmr.mgh.harvard.edu"
> Subject: [Freesurfer] TRACULA ERROR!!
>
> Dear fellow researchers,
>
> I am running tracula pre-processing step, and the computer showed an error
> message:
> Location of aparc+aseg's relative to b
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
, 2017 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA - error
Hi,
I’m running tracula using the following command:
(Note: I’m replacing actual paths with made up paths)
trac-all -prep -c /path/to/my/config.sh
And for some reason it stops running while working on the
Dear Freesurfer Staff,
I encountered the following error while running tracula - longitudinal:
ERROR: flag ; unrecognized
The exact command line i ran is the following one:
trac-all -prep -c
'/home/elia/scripts/Tracula/LCL/dcmTimePoints_tar-2/tracula.config'
I will attach the complete erro
External Email - Use Caution
Hi list,
Im using TRACULA in a dataset of 60 subjects.
for 56 subjects everything is fine, but for 4 subjects I had the following
error:
>> ncpts: Subscript out of range.
For these subjects TRACULA does not reconstruct the file
dpath/merged_avg33_mni_
Sent: Thursday, December 2, 2021 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA error
External Email - Use Caution
Hello Freesurfer Team,
I am trying to get TRACULA running on two different machines (Macbook Pro OS
11.6 and Mac desktop OS 10.14.6). I get the same
Subject: [Freesurfer] Tracula error
Hello,
I’ve been running the trac-all -prep step and I faced this error:
ConvertTransformFile 3
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error
Hello,
I’ve been running the trac-all -prep step and I faced this error:
ConvertTransformFile 3
/autofs/cluster/gu
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
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
: [Freesurfer] Tracula error
Hello,
I was running the "trac-all -bedp” section, when I got the below error. I
appreciate it much if you please let me know what the issue is.
Thanks,
Mona
- Bedpostx Monitor -
An error ocurred. Please check file
/autofs/cluster/guptagp/zn025/ALD/subje
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
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
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:
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
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
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
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:
imoglu, Yasemin
Sent: Tuesday, September 29, 2020 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error
Hi,
I am trying to run trac-all using a configuration file for 30 subjects with
longitudinal data, and keep getting the following errors:
Too many ('s.
ERROR:
: [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
: Freesurfer support list
Subject: [Freesurfer] Tracula error
External Email - Use Caution
Hello all,
I am trying to run Tracula for one of my subjects and after creating the
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.
I
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to apply TRACULA for the reconstruction of white matter pathways
but I am getting an error when running the trac-all command which I haven’t
managed to resolve. The TRACULA is applied on an MRI sample from the
External Email - Use Caution
Hi FreeSurfers,
I am attempting to run tracula on longitudinal DTI data however during trac-all
-prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz
from mri_concat.
#-
/Applications/f
Hi Anastasia,
I've got this error when running -prep Tracula step.
/usr/local/freesurfer/bin/dmri_motion: error while loading shared
libraries: libnetcdf.so.6: cannot open shared object file: No such file or
directory
We have RedHat 6 (I tried in 2 different machines). Do you think it is some
mi
Hi,
I have a problem running TRACULA in the pre-processing stage.
The error message is the following;
Loading streamline start ROI from
/usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
niiRead(): error opening file
/usr/local/fre
I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
Variable. I have looked at the answers to this question that have been
previously posted but cannot seem to remedy this problem. I'm running
freesurfer 5.3 via virtualbox on windows. I have applied for a license and
added that
.harvard.edu>>
Date: Friday, July 21, 2017 at 9:41 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] tracula error message
___emutls_get_address
___
Freesurfer mailing list
Freesurfer@n
Hi Elia - This issue was fixed in the last update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
FYI, there will be another tracula update soon (after ISMRM) that will
further improve the longitudinal stream specifically.
a.y
On Fri, 9 May 2014, Elia S. wrote:
Dear Free
Thanks, it works fine now, i missed that update.
Best,Elia.
Date: Fri, 9 May 2014 11:24:02 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer-Tracula Error
Hi Elia - This issue was fixed in the last update:
http
@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error -path
External Email - Use Caution
Hi list,
Im using TRACULA in a dataset of 60 subjects.
for 56 subjects everything is fine, but for 4 subjects I had the following
error:
>> ncpts: Subscript out of range.
For these subjects TRACULA do
Hi Gari - This is coming from the new code in the update that I posted
recently. Which build of freesurfer 5.3 and which build of the tracula
update do you have? Using our Centos 6 build, I was not able to replicate
your error.
a.y
On Wed, 11 Dec 2013, Garikoitz Lerma-Usabiaga wrote:
> Hi An
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 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
...@pdx.edu]
Sent: Wednesday, November 23, 2016 6:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA Error in virtualbox
I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
Variable. I have looked at the answers to this question that have been
previously posted
on behalf of Alexander Zent
> [az...@pdx.edu]
> *Sent:* Wednesday, November 23, 2016 6:12 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] TRACULA Error in virtualbox
>
> I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
> Variable. I have
Dear Anastasia and Freesurfer experts,
I am trying to set up an analysis of motion parameters using the flag -q
from a set of DTI Dicoms located on the Martinos cluster, but I am facing
problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to
Freesurfer5.3 and FSL.
What am I doing
Dear All,
I am trying to run a single subject in TRACULA (trac-all -prep -c
dmrirc), but exited with ERRORS.
ERROR: fMRIframe: frame >= nframes
The attached file is a log file.
Can anyone help me?
Thank you in advance.
Regards,
Jun Shinozaki.
[root@localhost 140518MS]# trac-all -prep -c dmrirc
External Email - Use Caution
Dear FreeSurfer experts:
I mentioned an error that I still cannot fix. I don’t think is the “\” because
as you can see in the file attached everything seems correct. I cannot fix the
issue with TRACULA I attach the configuration file so you can check
External Email - Use Caution
Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without
errors until path reconstruction but exis
Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find
the log file). I try to re-run the fslroi command as follow:
fslroi
/autofs/space/guasha_001/users/phoebe/strab_func
Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's
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
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:
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
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/
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,
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 - 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,
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
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,
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
___
> > > > > > Freesurfer mailing list
> > > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > > (mailto:Freesurfer@nmr.mgh.harvard.edu)
> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu
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
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
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
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
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
External Email - Use Caution
Dear FreeSurfer team
I have been running TRACULA for some time now but recently, I come across a
message "missing output volume name" and I cannot do preprocessing in new or
old subjects (even subjects who completed preprocessing without error)
I hav
58 PM
To: Freesurfer support list
Subject: [Freesurfer] Tracula error in path construction
External Email - Use Caution
Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For
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
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
Hi Phoebe,
The fslroi part extracts all the low-b images from the 4D diffusion data
and creates an average low-b mask.
fslroi
is the number of 3D low-b volumes to be extracted from the 4D
diffusion volume. For some reason tracula is unable to read the no. of
low-b images from your dicom hea
Hi Priti,
Thank you for your help. I get through the fslroi successfully by setting
the nb0 variable. The lowb.nii.gz looks fine. However, when the process
comes to bet, there's another error prompt for lowb.nii.gz.hdr.
fslmaths
/autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func
Hi Phoebe - I don't have permission to access your files, but do you have
FSLOUTPUTTYPE set to anything other than nifti by any chance?
a.y
On Thu, 14 Jul 2011, pho...@nmr.mgh.harvard.edu wrote:
> Hi Priti,
>
> Thank you for your help. I get through the fslroi successfully by setting
> the nb
Hi, I am trying to get TRACULA running. I have converted the DTI data using dcm2nii (as i was unable to get tracula to read the .ima Siemens DICOM) and have a bevc and bval file output from dcm2nii.The error I get is in bold below (from trac-all.log). I believe that the error is coming from the bev
You may have to transpose the bval and bvec files.
On 07/29/2013 11:17 AM, Borsodi Florian wrote:
Hello,
I have been trying to run tracula on my data and i keep getting the
same kind of error repeatedly.
For my imput I am using dicoms from a Siemens scanner with a stadard
diffusion protocol.
Hello,
Thank you for your quick answer.
I already run tracula with the transposed bvec and bval files but i keep
getting the same kind of error.
With kind regards,
Florian Borsodi
>>> Chris Watson 29.07.13 19.12 Uhr >>>
You may have to transpose the bval and bv
Hi Florian - Do these files exist?
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvecs
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvals
The format of the bvecs and bvals that you sent seems fine, but (and this
has nothing to do with the error y
Hi Anastasia
Thank you for your answer.
Yes, those files exist.
I also extracted the bvec an bval files with anotther software then dcm2nii and
i keep getting the same kind of error.
Also, about the 6 diffusion direction, those data i sent you, are just testdata
for running tracula.
sincer
Hi Anastasia,
Thank you for your help.
I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the
command "xfmrot" changed the dots back to commas. So, I changed our system
language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing
the system language everything
Hi Anastasia,
Yes, i am running this on ubuntu 12.04.
Sincerely,
Florian
>>> Anastasia Yendiki 20.08.13 17.38 Uhr >>>
Hi Florian - Are you running this on an ubuntu system by any chance?
a.y
On Tue, 20 Aug 2013, Borsodi Florian wrote:
> Hi Anastasia,
>
> Thank you for your help.
> I change
Hi Florian - Are you running this on an ubuntu system by any chance?
a.y
On Tue, 20 Aug 2013, Borsodi Florian wrote:
Hi Anastasia,
Thank you for your help.
I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command
"xfmrot" changed the dots back to
commas. So, I chang
This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
"/bin/
Hi Anastasia,
This Ubuntu-related error is a tricky one.
I changed the first line in those files you told me and reran trac-all. All
three steps of trac-all ran without any errrors. I checked the FA maps and the
MNI registration and everything looks fine.
After running trac-all -bedp, the st
Hi Florian - My guess is that everything ran fine and you don't need to
change anything else. Check that all the output files were created in the
dmri.bedpostX directory:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
a.y
On Thu, 22 Aug 2013, Borsodi Florian wrote:
Hi A
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