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
: 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
harvard.edu> on behalf of Woo-Suk Tae <
> woos...@gmail.com>
> *Sent:* Saturday, October 28, 2023 10:34 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation
> aparc+aseg+thalnuc.nii.gz
>
>
> External Email -
: (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 = (
@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi FreeSurfers,
I am trying to troubleshoot an error during TRACULA preprocessing and the issue
seems related to the creation of aparc+aseg+thalnuc.nii.gz
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
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
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
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
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
: [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
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
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
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
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:
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
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
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
.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
on behalf of
juergen.haen...@upd.unibe.ch
Sent: Wednesday, October 27, 2021 8:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear TRACULA experts
I try to run TRACULA FS7.2 on a Linux machine an
External Email - Use Caution
Dear TRACULA experts
I try to run TRACULA FS7.2 on a Linux machine and get the following error (see
below). A similar problem has already been reported in the archives, but I
found no solution.
https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn
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
d.edu
on behalf of Shanika Jayakody
Sent: Wednesday, March 17, 2021 4:04 PM
To: Freesurfer support list
Subject: [Freesurfer] TRACULA error: missing output volume name
External Email - Use Caution
External Email - Use Caution
Dear FreeSurfer team
I have been running TRACUL
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
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
: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
External Email - Use Caution
Hi Anastasia
Thanks so much- I think I got the error due to the format of the bvecs and bvals
Trac-all is running but for one person it is running for almost 5 days now- I
assume that can
: 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
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
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
: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
CAUTION: This email comes from an external source; the attachments and/or links
may compromise our secure environment. Do not open or click on suspicious
emails. Please click on the “Phish Alert” button on the top right of
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.
___
arvard.edu
on behalf of Shanika Jayakody
Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error: run list is longer than subject list
External Email - Use Caution
Hello,
I have been trying to run trac-all on a DWI of a participant
External Email - Use Caution
Hello,
I have been trying to run trac-all on a DWI of a participant, but I keep
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one
subject so I am not sure what the err
: [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
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:
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
: 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
Hello Dear Freesurfer Developers,
I am attempting to run Tracula in the last to subject of my study (I had
processed all the other subjects using the same script without problems).
However, when I try to run the scrip bellow, I am having the error:
" ERROR: Must specify input table of gradient
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
21, 2019 9:11 AM
To: Freesurfer Support List
Subject: [Freesurfer] tracula error gradient vectors too many ('s
External Email - Use Caution
Dear FreeSurfer experts:
I am trying to run tracula in 4 subjects of a public dataset. I have
encountered one error. I leave the output of terminal
External Email - Use Caution
Dear FreeSurfer experts:
I am trying to run tracula in 4 subjects of a public dataset. I have
encountered one error. I leave the output of terminal below. I also attach the
configuration file. I hope you can follow from there.
Sincerely,
Andrade.
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
*Sent:* Thursday, October 10, 2019 9:01:25 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] TRACULA error - MRISread could not open file
>
>
> External Email - Use Caution
>
> Hello,
>
> I am running tracula on some of my DTI data and have had no issu
Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list
Subject: [Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution
Hello,
I am running tracula on some of my DTI data and have had no issues for most of
my subjects. However, for on
External Email - Use Caution
Hello,
I am running tracula on some of my DTI data and have had no issues for most
of my subjects. However, for one of them I get the following error after
mri_segreg
MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
open file
@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
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_
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 all,
I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is
exiting with the output below. Most notably, I think, is the section of the
output that says "R: Subscript out of range.” repeatedly and then the section
afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9
, 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
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
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
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
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
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
.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
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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
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
...@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
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
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 everyone,
I’m reposting my problem if someone could help me I would really appreciate it.
I have some problems trying to run TRACULA on some DWI data. It is a mosaic
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and
bval files.
Then I run the trac-all -prep -c c
Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and
bval files.
Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not
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
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