Hi Colm - The final version used is bvecs. The eddy current correction
step registers each DWI to the first b=0 image, and the same
transformation is applied to the corresponding gradient vector. This is a
standard procedure when doing eddy current correction by registration.
Hope this helps,
a.y
On Fri, 16 May 2014, McGinnity, Colm wrote:
Hi Anastasia,
Many thanks for your help.
I did reply but don't see the email on the forum.
I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit
confused - I've created a 3-column bvecs format file (I had been using for
version 5.2.0).
After running several I've noticed the 'bvecs' file in the dmri folder is
slightly different from the input file, whereas the 'bvecs.norot' file matches
the input file extactly.
For example:
File 2:
0.9200842 0.3251221 0.2185593
File 2:
0.919 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.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 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 the 3-column format. I have no
idea if this is what's causing the error without looking at your trac-all.log,
but this would be a first guess.
a.y
On Mon, 10 Mar 2014, McGinnity, Colm wrote:
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/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
--mean --o /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
niiRead(): error opening file /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
Can anyone tell me what this means and how to fix this, please?
I’m guessing I’ve set up my configuration wrong or have the files in
the wrong place?
Many thanks!
Best wishes,
Colm.
King's College London
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