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solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors
On Fri, 6 Nov 2020 at 11:38, Michele Valotti
wrote:
> Hi all,
> I am trying t
u> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Thursday, April 30, 2020 2:22 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] trac-all -bedp error
>
>
> External Email - Use Caution
>
> Hi,
>
> I run trac-all, the log f
Yes, this is fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Thursday, April 30, 2020 2:22 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -bedp error
External Email - Use Caution
Hi,
I run trac-all, the
External Email - Use Caution
Hi,
I run trac-all, the log file has the following endings.
"Queuing post processing stage"
or
"Queuing post processing stage
59 slices processed
All slices processed
/hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
line 345:
Good to know, thanks for sharing this trick!
On Sat, 3 Sep 2016, Chung, Yoonho wrote:
I found out why it didn't work. One of the script that bedpostx_postproc.sh
calls is written in python2. I set my default to python3 and therefore
caused the error in the last step. After I loaded python2 e
I found out why it didn't work. One of the script that bedpostx_postproc.sh
calls is written in python2. I set my default to python3 and therefore caused
the error in the last step. After I loaded python2 environment, i got the
merged files and finished properly. Thanks for your help as always!
Hi Yoon - It sounds like FSL's bedpostx postprocessing script
failed. You can run it like this:
bedpostx_postproc.sh /path/to/your/subject/dmri
This script merges the results from all the slices. It's possible that
something went wrong with the slices (you ran out disk space for exam
Hi Anastasia,
trac-all -prep completed without error.
I thought trac-all -bedp starts and ends without any error but trac-all path
failed with these messages.
Loading BEDPOST parameter samples from */dmri.bedpostX
niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Co
This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
> Dear Priti
>
> The bedpostx works fine
Dear Priti
The bedpostx works fine on the data if I run it outside of tracula.
The command "/home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/s
Hi Gabor,
If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?
Priti
> Dear all,
>
> I've the following error right after starting trac-all -bedp -c
> configuration_file:
>
> Making bedpostx directory structure
> Queuing preprocessing stages
>
Dear all,
I've the following error right after starting trac-all -bedp -c
configuration_file:
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected opera
Hi Sarina,
Can you check to see what files are there in the dmri.bedpostX directory?
Do you have the merged_*, mean_*, dyads_* files??
Priti
> Hi, tracula users
>
> I run the trac-all bedp process and resulted this error:
>
> 74 slices processed
> 75 slices processed
> 76 slices processed
>
Hi, tracula users
I run the trac-all bedp process and resulted this error:
74 slices processed
75 slices processed
76 slices processed
Queuing post processing stage
80 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
r
Where is the data?
On Thu, 21 Jul 2011, pho...@nmr.mgh.harvard.edu wrote:
> Hi,
>
> I run the trac-all bedp process and it comes up with the following errors:
>
> 56 slices processed
> 56 slices processed
> 57 slices processed
> Queuing post processing stage
> 58 slices processed
> For some reas
Hi,
I run the trac-all bedp process and it comes up with the following errors:
56 slices processed
56 slices processed
57 slices processed
Queuing post processing stage
58 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
res
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