Hi Prad
if you use the cortex.label is will avoid using the non-cortical regions in
the surface, like the midline, so should be a more accurate measure
cheers
Bruce
On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use Caution
Hi,
I had a question about th
External Email - Use Caution
Hi,
I had a question about the -label flag in mri_cnr.
1) When you do not use the -label option and just use the following
command: mri_cnr $FREESURFER_HOME/subjects/bert/surf
$FREESURFER_HOME/subjects/bert/mri/norm.mgz
The output is as follows
w
Is it possible to get CNR info on a masked region? I have tried these commands
but see only unexpected tiny values or NaN for results:
mri_binarize --i $SUBJECTS_DIR/$subj/mri/aseg.mgz --match $mndx --o $tmpmask
mri_mask $SUBJECTS_DIR/$subj/mri/norm.mgz $tmpmask $norm_tmpmask
mri_cnr $SUBJECTS_D
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
Dear Bruce
Thanks a lot
Cheers
Jürgen
---
-
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
yes, that is correct.
Bruce
On Mon, 10 Nov 2014, Jürgen Hänggi wrote:
Dear FS experts
There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
lo
Dear FS experts
There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
located at the interface between the white and pial surface?
Thanks in adv
"
> Cc: "freesurfer"
> Sent: Monday, June 18, 2012 2:27:29 PM
> Subject: Re: [Freesurfer] mri_cnr
>
> Hi KK
>
> this is something i wrote for myself, but you are welcome to try it out.
> YOu don't need to give it the slope stuff, that is
gt;
> To: "Kushal Kapse" <kka...@mail.med.upenn.edu>
> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Monday, June 18, 2012 2:27:29 PM
> Subject: Re: [Freesurfer] mri_cnr
>
> Hi KK
>
> this is something i wrote for my
thanks Dr. B.that helped a lot
- Original Message -
From: "Bruce Fischl"
To: "Kushal Kapse"
Cc: "freesurfer"
Sent: Monday, June 18, 2012 2:27:29 PM
Subject: Re: [Freesurfer] mri_cnr
Hi KK
this is something i wrote for myself, but you are welcome to
Hi KK
this is something i wrote for myself, but you are welcome to try it out.
YOu don't need to give it the slope stuff, that is optional. The "vol"
command line parms are the volumes that you want to assess CNR in. For
example:
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/n
hi fellas,
i am trying to run mri_cnr command in freesurfer to compute and see CNR for
gray/white/csf the command gives following info as help:
-bash-3.2$ mri_cnr
usage: mri_cnr [options]...
-s
i understand that 'surf directory'= subjects 'surf' folder ; but i am not able
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