Re: [Freesurfer] mri_cnr and bash

2015-01-26 Thread Jacek Manko 
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 subjects' names contain the expression 3T, so if someone would like 
to use it, just adjust it properly)

The second loop gives me a single txt. file with the list of cnr value only 
(that is 'total CNR'). However, without subjects ID. I couldnt figure it out 
yet, how to do this.

for i in $(find . -name *cnr.txt); do awk 'NR==8 {print $4}' $i  
cnr_sample.txt; done

But all in all, I would say the problem is more or less solved, so thanks 
everybody for your input.


Cheers,
Jacek




 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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  --
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  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: 
  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
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Re: [Freesurfer] mri_cnr and bash

2015-01-22 Thread Jacek Manko 
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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  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:

Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Jacek Manko 
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
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
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Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Jacek Manko 
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
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
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 e-mail
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Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Bruce Fischl 

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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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Douglas N Greve 

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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 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Bruce 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


cheers
Bruce

On Wed, 21 Jan 2015, 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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Re: [Freesurfer] mri_cnr and bash

2015-01-21 Thread Douglas N Greve 

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 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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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] mri_cnr and bash

2015-01-21 Thread Jacek Manko 
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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