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
Unfortunately it doesnt. I was trying to modify the paths, but got always
results like:
MRISread(/surf/lh.white): could not open file
No such file or directory
mri_cnr: could not read surface file /surf/lh.white
No such file or directory
and @Dr. Fischl
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 cat them into a single file
Indeed, but I dont quite get it, how to extract CNR from these values.
Thanks,
Cheers,
Jacek Manko
On 01/21/2015 02:46 PM, Jacek Manko wrote:
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 napisał(a):
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 like
that:
"
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz
processing MRI volume
/homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
gray/white CNR = 2.241, gray/csf CNR = 1.026
lh CNR = 1.633
white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
gray/white CNR = 2.205, gray/csf CNR = 0.937
rh CNR = 1.571
total CNR = 1.602
"
My question is, if there is a way to export the CNR value, that is
1.602, to a seperate file alongside with the subject's ID. I suppose
there are no such bulit-in commands in FreeSurfer, is that right?
Thanks.
Cheers,
Jacek Manko
Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
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 pretty
advanced bash scripting, am I right? If so, has anyone some experience
with that matter?
Thanks.
Cheers,
Jacek Manko
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Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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