: [Freesurfer] trac-preproc error
Hi Yasemin - If you upload all the tracula output files for me here, I'll take
a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Please include all the output directories for this one subject in one zip file.
Thanks!
Anastasia.
From
...@nmr.mgh.harvard.edu
on behalf of Hasimoglu, Yasemin
Sent: Thursday, October 29, 2020 11:47 AM
To: Freesurfer support list
Subject: [Freesurfer] trac-preproc error
Hi,
I'm running Tracula on a longitudinal dataset and it's failing at the preproc
stage for one subject with the following message
Hi,
I'm running Tracula on a longitudinal dataset and it's failing at the preproc
stage for one subject with the following message:
INFO: Distances between consecutive points in test subject's space are 16 13 12
14
WARN: Could not find satisfactory control point fit - try 4967
Finding center
Thank you. It worked. I have been running a few brains and they have been
preprocessed successfully. One brain gave me an error message. Can you
please help me address this:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/mni2diff.bbr.mat
--ncpts
You're welcome. It seems like it can't find this file:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train
I can't tell exactly what's going on without looking at your trac-all.log
in its entirety. Can you please send it?
On Tue, 6 Aug 2013, Alan Francis wrote:
Hi Anastasia:
The problem is solved. thanks so much,
Alan
On Tue, Aug 6, 2013 at 11:21 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
You're welcome. It seems like it can't find this file:
/autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
Data//bin/dmri_train
I
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have
a bvec.txt and bval file in each directory.
thanks for your help,
Alan
The following are the messages:
The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
No such file or directory
Does this file exist?
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited
Hi Anastasia:
Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.
thanks,
Alan
On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
The error says:
Hi Alan - The file doesn't need to have an extension, .txt or other. But
you do need to set bvecfile to the full name of the file, including the
extension, if it has one.
a.y
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes this file does exist but it did not have the *.txt
Hi Tanja,
Are these healthy controls or do they have any lesions etc on the WM? It
looks like most of the training streamlines from the atlas are rejected
for straying off the subject's brain mask.
Can you please check out a similar posting on the list and overlay your
training histogram over
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