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/

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From: Anastasia Yendiki [ayendiki@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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