Dear all,
I have come up with a pretty good preliminary solution namely:
I run the first loop that returns me CNR and some other stuff from the command
mri_cnr. It creates one txt. file for each subject.
for i in *3T; do mri_cnr $i/surf $i/mri/norm.mgz > $i/"$i"_cnr.txt; done
(All of my subje
gray/white CNR is the first column
On Thu, 22 Jan 2015, Jacek Manko wrote:
Dear Dr. Greve, dear Dr. Fischl
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr > yourfile
Unfort
Dear Dr. Greve, dear Dr. Fischl
> would something like this work?
>
> set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
> $SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
> echo $subject $cnr > yourfile
Unfortunately it doesnt. I was trying to modify the paths, but got always
actually if you run mri_cnr with -l out.log it will write a line to out.log
of the form:
gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean sqrt(white_var)
sqrt(gray_var) sqrt(csf_var))
so you would create one file for each subject. You could then run a for
loop over your subjects to
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr > yourfile
On 01/21/2015 02:46 PM, Jacek Manko wrote:
> My desirable output would be then a .txt file that consists of merely
My desirable output would be then a .txt file that consists of merely two
columns. The first column is the subject's ID and the second is the CNR value
only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisa
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
Oh, I thought it was already defined. I am referring actually to this thread...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
...and, allowing myself to specify my problem, when I type the command
'mri_cnr' what I become in my terminal is something more or less
how do you want to define CNR?
On 01/21/2015 06:21 AM, Jacek Manko wrote:
> Dear All,
>
> I have been wondering if there is a way (already implemented in the
> FreeSurfer) to export CNR measurement outputs to seperate file, like a table
> or someting. If not, it will possible only via some pret
Dear All,
I have been wondering if there is a way (already implemented in the FreeSurfer)
to export CNR measurement outputs to seperate file, like a table or someting.
If not, it will possible only via some pretty advanced bash scripting, am I
right? If so, has anyone some experience with that
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