Does a file called "dmri/dwi_motion.txt" get created? That's the output of
the QA step. This is explained in the tutorial, under "Outputs from
quality assessment":
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs
On Fri, 12 Dec 2014, Anri WATANABE wrote:
Thanks, Anastasia.I'm worried about that a quality assessment step is not run
because there are no
presentation about "-qa" when I type "trac-all" in terminal (other steps are
presented.)
Do you mean QA step will be run even if no mention about it?
Thanks in advance,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2014-12-12 4:48 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
Hi Anri - This is not a command itself, it's an option of the trac-all
command. So you need to
run:
trac-all -qa -c the_name_of_your_configuration_file
Or, if you just run the entire preprocessing:
trac-all -prep -c the_name_of_your_configuration_file
then the motion QA measures will be computed by default as one of the
many steps of the
preprocessing.
You can run "trac-all" without any arguments to see usage information on
all the the different
options.
Hope this helps,
a.y
On Tue, 9 Dec 2014, Anri WATANABE wrote:
Thank you, Anastasia.
I had downloaded the updated software and unzipped it, but I
couldn't find
the command "-qa."
I found "-qa" in the trac-all text file in the updated software.
However there are no "-qa" in terminal when I run "trac-all."
Do I have to move the file somewhere?
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2014-11-22 7:22 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Anri - See here, and follow the link "software update":
http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments
The -qa option was added after 5.3 was released.
a.y
On Mon, 10 Nov 2014, Anri WATANABE wrote:
Dear FreeSurfer experts,
I'm running pre-processing steps in TRACULA
separatelly and could neither find the context about
quality
assessment step nor run the command 'trac-all -qa -c
<configulation file>.
I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion
(64-bit).
Could anyone solve this problem?
Thank you.
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
WATANABE ANRI
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine
**********************************************************************
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