Hi David - Every time you run trac-all, the results get appended to this
file, so you need to look for error messages only in the more recent
invocation of trac-all. The first error there seems to be:
Error: bvecs and bvals don't have the same number of entries
Do you have the same number of b-values and gradient vectors and volumes
in your DWI series?
a.y
On Tue, 6 Aug 2013, Soto, David wrote:
hi
I upgraded to FS 5.3 but still encountering issues with
trac-all prep.
The log is attached, things I noted after inspecting it
1) INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb
not valid
3) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5) ERROR: Could not read
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but despite all this it says:
trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013
thanks for your help
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.
Also, in the future please attach any log files as separate attachments
instead of pasting them into the body of your email - this causes the body
of the email to exceed the limit allowable on the list.
Thanks,
a.y
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