Sent: Friday, August 19, 2022 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA - preprocessing error
External Email - Use Caution
Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop
External Email - Use Caution
Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/sc
External Email - Use Caution
Hi,
I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am
getting the following error
ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni
I don’t see the mni folder created in my files… I am trying to only reco
: [Freesurfer] TRACULA preprocessing error
External Email - Use Caution
Hello,
I have been attempting to run TRACULA on the sample practice data using the
sample configuration file listed here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula. I am using Free
Surfer 6.
I
External Email - Use Caution
Hello,
I have been attempting to run TRACULA on the sample practice data using the
sample configuration file listed here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula. I am using
Free Surfer 6.
I receive an error message at the first s
Thanks, Ameen. We'll look into this and let you know.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Al Qadi, Ameen
Sent: Wednesday, January 29, 2020 11:04:46 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA Preprocessing
you downloaded?
>
> Thanks!
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen <
> ameen.alq...@icahn.mssm.edu>
> *Sent:* Tuesday, January 28, 2020 5:38 PM
> *To:* freesurfer@n
on behalf of Al Qadi, Ameen
Sent: Tuesday, January 28, 2020 5:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA Preprocessing Error
External Email - Use Caution
Hi Freesurfer Developers,
I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and
External Email - Use Caution
Hi Freesurfer Developers,
I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and
encountered a number of issues:
1. When running trac-all, I get the following error:
trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutor
Hi Doug - This post from the archives addresses the same error message.
Please check if this fixes it for you, too:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37920.html
Best,
a.y
On Mon, 9 Nov 2015, Douglas Merkitch wrote:
Hey D,
I also had the same error in the same
Hello D,
Thanks for the advice! Your suggestion did the trick!
I remember reading about properly formatting the bval/bvec files, but I
apparently forgot to do so...
Thanks,
Doug
Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Ema
Hi Douglas,
I actually solved it! So, if yours is the same problem, you need to change
your bval and bvec file format. I used mricron to convert from dicom to
nifti, then used the bvec and bval files it produced for me. What it gives
as output doesn't match with tracula's format.
bvec file should
Hey D,
I also had the same error in the same spot, although I'm using an earlier
version of tracula and Mac OS. This is my first time using tracula for DWI
processing so I am a little confused as to how to best troubleshoot this issue.
Any help from the experts would be great!
Thanks,
Doug
Dear all,
I am running Tracula preprocessing on NIFTI files.
After running the command: trac-all -prep -c
I get the error:
...
processing
/data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_tmp0032
mv -f /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs
/data_a
Hi Anastasia,
Found it, I'll replace it right away, thanks :)
Best,Elia.
Date: Tue, 17 Jun 2014 09:29:14 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Check the email archives for a r
4.X
Either from script or command line.
Best,
Elia.
Date: Tue, 17 Jun 2014 09:17:58 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the
: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the epidewarp.fsl command
give you any specific error message, or does it just not create an output?
a.y
On Tue, 17 Jun 2014, Elia S. wrote:
> Hi Anastasia,
> Yes, launchi
4 07:21:28 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created:
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.
f but right now I don't have
the correct images to test it.
Best,Elia.
Date: Sun, 15 Jun 2014 07:21:28 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file
Hi Elia - It looks like this file didn't get created:
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
The command that was supposed to create it was epidewarp.fsl. You can find
the command line that begins with "epidewarp.fsl" in the log file that you
sent m
Dear Freesurfer community,
Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and
the following command line:
trac-all -prep -no-isrunning -c
'/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config
It stops, giving me errors like these:
niiRead(): error opening
ou please clarify which is used, and if these differences can be ignored?
>
> Thanks and best wishes,
> Colm.
>
>
> -Original Message-
> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
> Sent: 11 March 2014 00:39
> To: McGinnity, Colm
> Cc: free
gt;> ignored?
>>
>> Thanks and best wishes,
>> Colm.
>>
>>
>> -Original Message-
>> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
>> Sent: 11 March 2014 00:39
>> To: McGinnity, Colm
>> Cc: freesurfer@nmr.mgh.harv
0.3311 0.2141
Can you please clarify which is used, and if these differences can be ignored?
Thanks and best wishes,
Colm.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harva
ease clarify which is used, and if these differences can be ignored?
Thanks and best wishes,
Colm.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA pr
gh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
Hi Colm - Note that the information in the tutorial (particularly the part
where gradient tables can be formatted in 3 rows or 3
nnity
King's College London
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
Hi Colm - Not
Hi Colm - Note that the information in the tutorial (particularly the part
where gradient tables can be formatted in 3 rows or 3 columns) pertains to
the latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
You're using an older version that only supports th
Dear Experts,
I am very new to TRACULA, I apologise for what is probably a silly question.
I've got the following error on running trac-all -prep (FreeSurfer 5.2.0):
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or
directory)
mri_concat --i
/home/k1193186/FreeSurfer/T
Hi Michael - Two things: First, in the dmrirc that you attached
previously, the bvecfile and bvalfile lines are commented out. Second,
these files need to be in column, not row format, as shown in the
tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
Im of the understanding that X11 and XQuartz will not conflict. Many
users running Mac OSX Snow Leopard have both applications installed on
their systems. But if you are extremely weary of potential issues than I
suppose you could create a symbolic link from /opt/X11 to /usr/X11.
Additional sym
Hello,
I installed XQuartz and the processing gets a little bit farther than it
did before. However, I now run into an error about not being able to move
the bvecs file. To my knowledge I specified the bvecs file correctly (in
the same log file I attached previously), and it is in a format that h
The XQuartz website you linked makes it sound like it is identical to X11,
is it different in some way? I have X11 already and it works flawlessly
with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K wrote:
> Mike,
>
> You need to install XQuartz:
> http://xquart
Mike,
You need to install XQuartz:
http://xquartz.macosforge.org/landing/
Also see the following troubleshooting page:
http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
-Zeke
On 10/28/2013 03:17 PM, Michael Datko wrote:
> Hi Anastasia,
> I've attached my configuration file,
Hi Anastasia,
I've attached my configuration file, and below is pasted the contents of
the error log. Below that, I've pasted the last few lines of the trac-all
log (not the error log), because it says something about a "dyld" that
cannot be loaded...might be related to the problem.
Thanks,
Mike
Hi Mike - I'll need to see the configuration file and trac-all.log.
Thanks,
a.y
On Mon, 21 Oct 2013, Michael Datko wrote:
Hello,I am running into a tracula error very early in the preprocessing steps.
I have data that was already somewhat preprocessed (reconstruction, eddy
correction and mag
Hello,
I am running into a tracula error very early in the preprocessing steps. I
have data that was already somewhat preprocessed (reconstruction, eddy
correction and magnetic field inhomogeneity correction) that I'm trying to
use as an input. I have turned off those steps in the tracula
configu
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