Re: [Freesurfer] intensity normalization and GM exclusion

[Meaghan Perdue]

​
 ta7029.zip

​Hi Bruce,

Thank you for your prompt response. I added an expert.opts file with the
line "mris_make_surfaces -max_gray_at_csf_border 60 -max_csf 35" and ran
recon-all -s ta7029 -autorecon2 -autorecon3 -expert
ta7029/scripts/expert.opts -3T -qcache  for one of the affected subjects,
but it doesn't seem to have corrected the pial surface. I have attached the
subject folder here. If you have time to take a look and try a couple of
things, I would really appreciate it!

Thanks,
Meaghan

On Wed, Mar 22, 2017 at 11:21 AM, Bruce Fischl 
wrote:

> Hi Meaghan
>
> it looks like the white surface is pretty accurate but the gm doesn't get
> out far enough. I would play with some of the expert options to
> mris_make_surfaces like max_gray_at_csf_border. If you upload a subject I
> can try it out and see if I can improve things and get back to you.
>
> cheers
> Bruce
>
>
>
> On Wed, 22 Mar 2017, Meaghan Perdue wrote:
>
>
>>   Hello,
>>
>>   I attended the September 2016 Freesurfer training course, and I am
>> seeking help to resolve a consistent issue with white and pial surface
>> extraction
>>   that seems to be rooted in poor intensity normalization. Our lab is
>> working with a pediatric dataset acquired on a 3T scanner and recon-all was
>> run in
>>   Freesurfer v5.3. Throughout the dataset, we have found that the
>> surfaces are cutting off white matter and excluding a significant amount of
>> gray
>>   matter, particularly in the lateral temporal lobes.  I have
>> attached several images to illustrate the problem. As you can see in the
>> images, the pial
>>   surface in the lateral temporal lobes hugs close to the white/gray
>> boundary and excludes gray matter.
>>
>>   We have used the -3T flag when running recon-all for all subjects,
>> and we have manually changed the smoothing distance in mi_nu_correct to 30
>> for
>>   several subjects in an attempt to improve this, but we did not get
>> a better result. We are hesitant to address this problem using control
>> points
>>   because it would require adding many control points across many
>> slices in nearly all the subjects, and we would like to avoid the
>>   reliability/replicability issues of so much manual editing. (Not to
>> mention the time required to do such heavy editing). Is there any way to
>> address
>>   this automatically through the recon pipeline?
>>
>>
>>   Many thanks,
>>
>>   Meaghan Perdue
>>
>>
>>
>>
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Re: [Freesurfer] intensity normalization and GM exclusion

[Bruce Fischl]

Hi Meaghan

it looks like the white surface is pretty accurate but the gm doesn't get 
out far enough. I would play with some of the expert options to 
mris_make_surfaces like max_gray_at_csf_border. If you upload a subject I 
can try it out and see if I can improve things and get back to you.


cheers
Bruce


On Wed, 22 Mar 2017, Meaghan Perdue wrote:



  Hello,

  I attended the September 2016 Freesurfer training course, and I am 
seeking help to resolve a consistent issue with white and pial surface 
extraction
  that seems to be rooted in poor intensity normalization. Our lab is 
working with a pediatric dataset acquired on a 3T scanner and recon-all was run 
in
  Freesurfer v5.3. Throughout the dataset, we have found that the surfaces 
are cutting off white matter and excluding a significant amount of gray
  matter, particularly in the lateral temporal lobes.  I have attached 
several images to illustrate the problem. As you can see in the images, the pial
  surface in the lateral temporal lobes hugs close to the white/gray 
boundary and excludes gray matter.

  We have used the -3T flag when running recon-all for all subjects, and we 
have manually changed the smoothing distance in mi_nu_correct to 30 for
  several subjects in an attempt to improve this, but we did not get a 
better result. We are hesitant to address this problem using control points
  because it would require adding many control points across many slices in 
nearly all the subjects, and we would like to avoid the
  reliability/replicability issues of so much manual editing. (Not to 
mention the time required to do such heavy editing). Is there any way to address
  this automatically through the recon pipeline? 


  Many thanks,

  Meaghan Perdue



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Re: [Freesurfer] Intensity normalization in longitudinal processing

[Jaiashre Sridhar]

Martin,

Thank you for your response. I ran the subject completely (cross and long) in 
v6.0 and the white matter intensity distribution in the long brain looks 
similar to the one run with the mixed versions (v5.1 cross and v6.0 long). 
Since the surfaces also look fine, I understand that this is not an issue.

Thank you again,
Jaiashre.
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Re: [Freesurfer] Intensity normalization in longitudinal processing

[Martin Reuter]

Hi Jaiashre, 

generally we advise against mixing version. It may work, but it may also fail. 
We do not test these combinations. I know for example that people did run 5.3 
base and long on top of 5.1 cross successfully (at least they claim). I don’t 
know how mixing with 6.0 behaves. 

I am wondering where the problem comes from as it should not be caused by the 
longitudinal stream, maybe by some changes in the regular stream between 5.3 
and 6.0 or maybe due to your special way of running things. 

Please just re-run this one subject completely from scratch through the full 
6.0 pipeline (cross, base and long) and see if it remains. 

Best, Martin

> On 13 Mar 2017, at 15:48, Jaiashre Sridhar 
>  wrote:
> 
> Bruce,
>  
> We had previously addressed an issue with creating the bases from 5 
> timepoints in v5.1 where mri_robust_register failed. We were advised by Dr. 
> Martin Reuter to either replace mri_robust_register & mri_robust_template 
> binary with the ones from v5.3 or to run all the bases and longs in v5.3. We 
> chose to run the longitudinal stream in v6.0 as it was released by then.
> If it is not safe to mix versions (cross in v5.1; base-long in v6.0), could 
> you clarify if it is alright to just use the binaries from v5.3/v6.0?
>  
> Thank you very much,
> Jaiashre. 
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Re: [Freesurfer] Intensity normalization in longitudinal processing

[Jaiashre Sridhar]

Bruce,

We had previously addressed an issue with creating the bases from 5 timepoints 
in v5.1 where mri_robust_register failed. We were advised by Dr. Martin Reuter 
to either replace mri_robust_register & mri_robust_template binary with the 
ones from v5.3 or to run all the bases and longs in v5.3. We chose to run the 
longitudinal stream in v6.0 as it was released by then.
If it is not safe to mix versions (cross in v5.1; base-long in v6.0), could you 
clarify if it is alright to just use the binaries from v5.3/v6.0?

Thank you very much,
Jaiashre.
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Re: [Freesurfer] Intensity normalization in longitudinal processing

[Bruce Fischl]

HI Jaiashre

is there a reason to mix versions? We always advise against this

cheers
Bruce
On Fri, 10 
Mar 2017, Jaiashre Sridhar wrote:




Hello FreeSurfer Team,

 

For a longitudinal study, we processed the cross-sectional scans through FS
v5.1 and ran the longitudinal stream in FS v6.0. The voxel intensities in
wm.mgz of the long timepoints are variable and are much lower (not in the
range of 110).

 

I have attached the image of a longitudinal timepoint created in v6.0 and
compared it to the one created in v5.1 (The cross brain recons for both of
them were done in v5.1). The white and pial surfaces look similar across
versions but the long created in v6.0 does not have a uniform intensity
compared to the one created in v5.1. Should this matter as long as the
surfaces look fine?

 

I tried to use expert options with ‘mri_normalize –gentle’ while creating
the long in v6.0 but it did not help. Any suggestions to achieve a better
intensity normalization?

 

Thank you,

Jaiashre.

 


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Re: [Freesurfer] Intensity normalization issues leading to improper segmentation

[Bruce Fischl]

Hi Élodie

if you upload your subject we will take a look

cheers
Bruce
On Fri, 1 Jul 2016, Elodie 
Cauvet wrote:



Dear Freesurfer list,

Sorry to bother by posting again, but I am bit stuck by this issue and would
be really glad to get some help on that issue. Of course I can upload some
data if needed.

Thanks a lot!

Maybe I am hoping for a miracle with my question, but I am bit desperate
after unsuccessfully trying things around for over a year.
In a nutshell, I need advice on the intensity normalization options.

We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner
with a 32 channel coil (IR-FSPGR 3D volume). This coil has a huge problem in
a field inhomogeneity resulting in strong occipital hypersignal and frontal
hyposignal, from which I believe all my problems originate.

- The standard pipeline provide an incomplete temporal and frontal
segmentation (white and pial surfaces do not include enough) while over
including in occipital and parietal.
- We tried using the watershed 40 value from the skulltrip to get more of
the occipital (we had a few subjects having holes in occipital within the
brain segmentation). This option changed also the segmentation resulting in
better segmentation for temporal and frontal but worse in parietal and
occipital.
- We tried control points as well, without success (as you can imagine due
to the fronto-occipital inhomogeneity). We also tried manually removing
extra voxels from the white surface to correct it. But unfortunately, this
is not an option because we have about 200 scans to process.
- We tried using N4 intensity bias correction on the raw images before
feeding it to freesurfer, but the segmentation did not run through for all
participants (stuck in fixing topology for more than a week) and for those
working, the pial surface did not include enough grey matter.

I am now thinking about playing with the option of intensity normalization
(mri_ca_normalize) within freesurfer but would like to have your expert
opinion on that before roaming. Any advice on how to set up mri_ca_normalize
to retrieve a good white matter homogeneity? Or any other functions I should
be playing around with?

Thanks a lot in advance for your help,
Kind regards,

Élodie


Élodie CAUVET | PhD  

Karolinska Institutet Center of Neurodevelopmental Disorders
(KIND)  

Gävlegatan 22B, floor 8 | 113 30 Stockholm

+46 (0)8 514 527 10 | +46 (0)728 774 058
elodie.cau...@ki.se

http://ki.se/en/kind/startpage

http://elodiecauvet.wordpress.com/

Karolinska Institutet – a medical university

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Re: [Freesurfer] Intensity Normalization

[Bruce Fischl]

glad to hear it
On Sat, 6 Apr 2013, Dan LaFreniere wrote:

> Hi Bruce,
> 
> Apologies for the delay - was having some issues with the automatic
> moderator approval.
> 
> That's good to hear, thank you for your help. You're spot on, the right
> temporal lobes appear to be in worse shape than the left. Control points
> certainly help a great deal with these images. The surfs seem pretty good -
> I've attached a screen of the surfs for you from the same subject and same
> slice (these are following an -autorecon2-cp run). No major problems from
> what I can see.
> 
> Cheers,
> 
> Dan
> 
> 
> On Fri, Apr 5, 2013 at 11:09 AM, Bruce Fischl 
> wrote:
>   Hi Dan
>
>   if the surfs look good you are all set. Does it go from left to
>   right or right to left? Rightmost temporal lobes look the
>   darkest to me. I would have thought you would still need some
>   control points, but if not that's great
>   Bruce
> 
>
>   On Fri, 5 Apr 2013, Dan LaFreniere wrote:
>
> Dear Experts,
>
> I've been working on cleaning up some 4T nifti
> images for cortical thickness analysis. Initially
> our images were quite dark inferiorly due to the
> nature of the RF coil used (it doesn't extend much
> further than the temples resulting in signal
> drop-off).
>
> I've managed to find what appears to be a decent fix
> for the problem by running a higher number of
> -nuiterations during -autorecon1; usually 20-50
> does the trick. Because I'm quite new to this, I was
> wondering if this is an acceptable fix? Just wanted
> to double-check with the experts before
> moving forward.
>
> I've attached a screenshot contrasting image quality
> of default iterations, 10, 20, and 50 iterations.
>
> It's also worth mentioning that -surfs appear to be
> quite accurate especially after I lay down some
> control points after an initial autorecon2
> run.
>
> Thank you very much for your help and patience,
>
> Dan
> 
> 
> 
> 
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Re: [Freesurfer] Intensity Normalization

[Bruce Fischl]

Hi Dan

if the surfs look good you are all set. Does it go from left to right or 
right to left? Rightmost temporal lobes look the darkest to me. I would 
have thought you would still need some control points, but if not that's 
great
Bruce


On Fri, 5 
Apr 2013, Dan LaFreniere wrote:

> Dear Experts,
> 
> I've been working on cleaning up some 4T nifti images for cortical thickness 
> analysis. Initially our images were quite dark inferiorly due to the
> nature of the RF coil used (it doesn't extend much further than the temples 
> resulting in signal drop-off).
> 
> I've managed to find what appears to be a decent fix for the problem by 
> running a higher number of -nuiterations during -autorecon1; usually 20-50
> does the trick. Because I'm quite new to this, I was wondering if this is an 
> acceptable fix? Just wanted to double-check with the experts before
> moving forward.
> 
> I've attached a screenshot contrasting image quality of default iterations, 
> 10, 20, and 50 iterations.
> 
> It's also worth mentioning that -surfs appear to be quite accurate especially 
> after I lay down some control points after an initial autorecon2
> run.
> 
> Thank you very much for your help and patience,
> 
> Dan
> 
>
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Re: [Freesurfer] Intensity normalization parameters to fix dura included in pial surface

[Bruce Fischl]

Hi Martina
Can you send us one example dataset?
Bruce



On Aug 24, 2011, at 10:52 PM, Martina Ly  wrote:

> Hello freesurfers,
> Dura is being included in the pial surface of the superior section of the 
> brain in about 80% of the subjects (about 200) that I'm processing in fs 
> version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It 
> takes too much time to manually edit the dura and I would not like to do so 
> much manual intervention on the other 2 time points. Adjusting the watershed 
> parameters and the -gcut  flag did not help. Would I be able to adjust 
> nu_correct or  mri_normalize (the intensity normalization steps prior to 
> skull stripping)? 
> 
> I'm also thinking of using another intensity correction software (i.e. 
> unicorr) to put back into the freesurfer pipeline but I would prefer a flag 
> or parameter I can adjust within fs. 
> 
> Any suggestions would be appreciated!
> 
> Best,
> Martina
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Re: [Freesurfer] Intensity Normalization error

[Bruce Fischl]

Hi Antonella,

I'll leave 2) for others. For 1), it's only worth intervening/adding 
control points if the white surface doesn't extend all the way out to the 
end of a white matter strand (or if the gray matter over it doesn't get all 
the way out either)

cheers
Bruce


On Fri, 29 Jul 2011, Antonella Kis wrote:

> Dear Bruce,
> 
> 1). What is the minimum value/the range for the intensity in order to be 
> considered acceptable? I know the value in wm should be very close to
> 110 but what is the accepted value closed to this?
> If is not exactly 110 (foe example if is 101) do I need to add control points 
> in order to normalize the intensity and get the value 110?
> 
> 2). I was trying to create a table with my statistical results (the cortical 
> thickness and the number of vertices) and I was running:
> 
> aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t 
> lh.aparcstas.THICKNESS.txt
> 
> When I tried to also get the number of vertices a table by running: 
> aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t
> lh.aparcstas.VERTICES.txt I got the following error:
> 
> aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose 
> from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
> 
> I Why I don't have an option for the no. of vertices?
> Can I get a table with both data: cortical thickness and no. of vertices?
> 
> Many thanks,
> Antonella
> 
>
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Re: [Freesurfer] intensity normalization fails?

[Bruce Fischl]

that's what I thought, but it's the orig, not the nu. I think it's the 
histogram in mri_convert. The mdeft looks like it has a lot of very bright 
vessels in it, maybe more than we ignore

On Fri, 18 Jun 2010, Douglas N Greve wrote:

> This might be a problem with the way we call nu_correct. I had a similar 
> problem a few months ago. I changed mri_nu_correct.mni, and the problem went 
> away, so you may need the new version (attached). Make sure to make a backup.
>
> doug
>
>
> Bruce Fischl wrote:
>> Hi Frank,
>> is it the orig.mgz that is dark, or the nu?
>> 
>> cheers
>> Bruce
>> 
>> On Fri, 18 Jun 2010, Frank Scharnowski wrote:
>> 
>> 
>>> Dear Freesurfers,
>>> 
>>> When importing a 3T MDEFT structural scan into freesurfer with
>>> 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
>>> (see attached tkmedit snapshot).
>>> The results of recon all are suboptimal, probably due to the bad
>>> intensity normalization. In SPM the structural looks just fine.
>>> Is there a way to correct for this?
>>> 
>>> Many thanks for your help,
>>> frank
>>> 
>>> 
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>> 
>
>
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Re: [Freesurfer] intensity normalization fails?

[Douglas N Greve]

This might be a problem with the way we call nu_correct. I had a similar 
problem a few months ago. I changed mri_nu_correct.mni, and the problem 
went away, so you may need the new version (attached). Make sure to make 
a backup.


doug


Bruce Fischl wrote:

Hi Frank,
is it the orig.mgz that is dark, or the nu?

cheers
Bruce

On Fri, 18 Jun 2010, Frank Scharnowski wrote:

  

Dear Freesurfers,

When importing a 3T MDEFT structural scan into freesurfer with
'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
(see attached tkmedit snapshot).
The results of recon all are suboptimal, probably due to the bad
intensity normalization. In SPM the structural looks just fine.
Is there a way to correct for this?

Many thanks for your help,
frank



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#! /bin/tcsh -f

#
# mri_nu_correct.mni
#
# Original Author: Doug Greve
# CVS Revision Info:
#$Author: greve $
#$Date: 2009/12/16 20:15:41 $
#$Revision: 1.12 $
#
# Copyright (C) 2002-2007,
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#

# mri_nu_correct.mni
#
set VERSION = '$Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $';

set InVol = ();
set OutVol = ();
set nIters = 4; # default in recon-all
set HiRes = ();
set nProtoIters = ();
set StopThresh = ();
set Distance = ();
set FWHM = ();
set LF = ();
set UseFloat = 1;

set debug = 0;
set PrintHelp = 0;

set cmdargs = ($argv);
if($#argv == 0)  goto usage_exit;
set n = `echo $argv | egrep -e --version | wc -l`
if($n != 0) then
  echo $VERSION
  exit 1;
endif
set n = `echo $argv | egrep -e --help | wc -l`
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
  exit 1;
endif

# Parse the command-line arguments
goto parse_args;
parse_args_return:

# Check the command-line arguments
goto check_params;
check_params_return:

set OutDir = `dirname $OutVol`;
mkdir -p $OutDir;

if($#LF == 0) set LF = $OutDir/mri_nu_correct.mni.log
if(-e $LF) mv $LF $LF.bak

pwd  | tee -a $LF
which mri_nu_correct.mni | tee -a $LF
echo $cmdargs | tee -a $LF
echo "nIters $nIters" | tee -a $LF
echo $VERSION | tee -a $LF
uname -a | tee -a $LF
date | tee -a $LF
nu_correct -version | tee -a $LF

set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
mkdir -p $tmpdir
echo "tmpdir is $tmpdir" | tee -a $LF

# Convert input to minc
set cmd = (mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc)
if($UseFloat) set cmd = ($cmd -odt float)
pwd |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) then
  echo "ERROR: converting to minc" |& tee -a $LF
  exit 1;
endif

# Run intensity correction #
@ nthIter = 1;
while($nthIter <= $nIters)
  echo " " |& tee -a $LF
  echo "" |& tee -a $LF
  echo "Iteration $nthIter `date`" |& tee -a $LF
  @ m = $nthIter - 1
  set cmd = (nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc)
  set cmd = ($cmd -tmpdir ${tmpdir}/${m}/ );
  if($#nProtoIters)   set cmd = ($cmd -iterations $nProtoIters);
  if($#StopThresh)set cmd = ($cmd -stop $StopThresh);
  if($#Distance)  set cmd = ($cmd -distance $Distance);
  if($#FWHM)  set cmd = ($cmd -fwhm $FWHM);
  echo $cmd |& tee -a $LF
  $cmd |& tee -a $LF
  if($status) then
echo "ERROR: nu_correct" |& tee -a $LF
exit 1;
  endif
  rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
  @ nthIter = $nthIter + 1;
  echo " " |& tee -a $LF
end
echo " " |& tee -a $LF
echo " " |& tee -a $LF

set numnc = $tmpdir/nu$nIters.mnc

if($UseFloat) then
  # Rescale so that global mean of output = mean of input
  set ones = $tmpdir/ones.mgz
  set cmd = (mri_binarize --i $numnc --min -1 --o $ones);
  echo $cmd | tee -a $LF
  $cmd | tee -a $LF
  if($status) exit 1;

  set cmd = (mri_segstats --id 1 --seg $ones --i $InVol \
--sum $tmpdir/sum.junk --avgwf $tmpdir/input.mean.dat)
  echo $cmd | tee -a $LF
  $cmd | tee -a $LF
  if($status) exit 1;
  set inmean = `cat $tmpdir/input.mean.dat`

  set cmd = (mri_segstats --id 1 --seg $ones --i $numnc \
--sum $tmpdir/sum.junk --avgwf $tmpdir/output.mean.dat)
  echo $cmd | tee -a $LF
  $cmd | tee -a $LF
  if($status) exit 1;
  set outmean = `cat $tmpdir/output.mean.dat`

  set scale = `echo $inmean/$outmean | bc -l`
  set cmd = (mris_calc -

Re: [Freesurfer] intensity normalization fails?

[Frank Scharnowski]

Hi Bruce,
It is the orig.mgz (cannot check right now if the nu is also dark).
Many thanks,
frank


2010/6/18 Bruce Fischl :
> Hi Frank,
> is it the orig.mgz that is dark, or the nu?
>
> cheers
> Bruce
>
> On Fri, 18 Jun 2010, Frank Scharnowski wrote:
>
>> Dear Freesurfers,
>>
>> When importing a 3T MDEFT structural scan into freesurfer with
>> 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
>> (see attached tkmedit snapshot).
>> The results of recon all are suboptimal, probably due to the bad
>> intensity normalization. In SPM the structural looks just fine.
>> Is there a way to correct for this?
>>
>> Many thanks for your help,
>> frank
>>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>



-- 
Dr. Frank Scharnowski
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
United Kingdom
f.scharnow...@fil.ion.ucl.ac.uk
http://sites.google.com/site/scharnowskifrank/
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Re: [Freesurfer] intensity normalization fails?

[Bruce Fischl]

Hi Frank,
is it the orig.mgz that is dark, or the nu?

cheers
Bruce

On Fri, 18 Jun 2010, Frank Scharnowski wrote:

> Dear Freesurfers,
>
> When importing a 3T MDEFT structural scan into freesurfer with
> 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
> (see attached tkmedit snapshot).
> The results of recon all are suboptimal, probably due to the bad
> intensity normalization. In SPM the structural looks just fine.
> Is there a way to correct for this?
>
> Many thanks for your help,
> frank
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] intensity normalization and control points

[Jones, Kathryn L]

Thank you for your quick reply! Based on your suggestion we are going to
re-run the scan through FS with some changes to the input volume. I was
doubtful about using control points but thought maybe I should ask
before we did anything else. Thanks again. Kathy 

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Thursday, April 01, 2010 3:01 PM
To: Jones, Kathryn L
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] intensity normalization and control points

eek, that's pretty low contrast. You could certainly try, but you might 
be better of changing the intensity thresholds. What is your voxel size 
and acquisition parameters?
On Thu, 1 Apr 2010, Jones, Kathryn L wrote:

> Hello FS listers,
>
> I apologize if this has been asked before and I missed it in the
> archives. Can you use control points to correct intensity in overly
> bright scans. I've attached an example pic.
>
> Thanks for your help,
> Kathy
>
>


The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.


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Re: [Freesurfer] intensity normalization and control points

[Bruce Fischl]

eek, that's pretty low contrast. You could certainly try, but you might 
be better of changing the intensity thresholds. What is your voxel size 
and acquisition parameters?
On Thu, 1 Apr 2010, Jones, Kathryn L wrote:

> Hello FS listers,
>
> I apologize if this has been asked before and I missed it in the
> archives. Can you use control points to correct intensity in overly
> bright scans. I've attached an example pic.
>
> Thanks for your help,
> Kathy
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] intensity normalization

[Bruce Fischl]

see if the ?h.white surface is accurate. If it is, then you're all set. 
If it's not then you can add a few control points in the dark wm in those 
regions.


cheers,
Bruce
On Fri, 10 Feb 2006 [EMAIL PROTECTED] wrote:


Hi,
I had been having a lot of trouble with the skull stripping in the newest
dev version (it was taking off the top half of the head and leaving head and
skull on the bottom half). I was able to fix this by redoing the intensity
normalization step from autorecon1 using control points. My question is - In
the brains where I did not have a problem with skull stripping, but after
autorecon1 I have white matter intensity values below 110, should I redo
intensity normalization with control points on them as well?
Thanks!
Kelli



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Re: [Freesurfer] intensity normalization

[Nick Schmansky]

Kelli,

In the newest dev version (Jan28 or Feb 10), certain defaults changed,
which appear possibly not for the better.  Could you try re-running
recon-all on the failed subject, using flags which I'll describe in a
second?

Attached is a new recon-all.  To install, type this from where you have
saved the attachment:

  gunzip recon-all.gz
  chmod a+x recon-all
  cp recon-all $FREESURFER_HOME/bin/

Then, we'd first like you to try adding more iterations to the
nu_correct step, as possibly your subject has large non-uniformities.
Type the following (where  is the name):

  recon-all -s  -autorecon1 -clean -nuiterations 4

This increases the iterations of the 'nu_correct' step from the default
of 2 up to 4.  See if the resulting skull strip is any better.

Note: the -clean flag will delete your control points!  In fact, for
now, please don't use control points! (not just yet anyway)

If the skull-strip still fails, try:

  recon-all -s  -autorecon1 -clean -no-wsatlas

The -no-wsatlas flag bypasses using an atlas during the skull-strip step
(mri_watershed).  We've had mixed results with using this atlas (mostly
for the better), but its possible that it is the source of your
troubles.

Lastly, you can try both flags:

recon-all -s  -autorecon1 -clean -nuiterations 4 -no-wsatlas

If even this fails, then we may want to have a look at the subject
files.

Thank you in advance for your patience!

Nick (and Xiao)



On Fri, 2006-02-10 at 16:49 -0500, [EMAIL PROTECTED] wrote:
> Hi,
> 
> I had been having a lot of trouble with the skull stripping in the
> newest dev version (it was taking off the top half of the head and
> leaving head and skull on the bottom half). I was able to fix this by
> redoing the intensity normalization step from autorecon1 using control
> points. My question is - In the brains where I did not have a problem
> with skull stripping, but after autorecon1 I have white matter
> intensity values below 110, should I redo intensity normalization with
> control points on them as well?
> 
> Thanks!
> 
> Kelli
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


recon-all.gz
Description: GNU Zip compressed data
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RE: [Freesurfer] intensity normalization failure

[Bruce Fischl]

Hi Alex,

the -pvol flag assumes ever border voxel is a linear combination of the 
class that it is labeled as and another class that it borders. The local 
class means are computed by as the sample mean in a local window of all non 
border voxels of that class.


The mac and linux version should be compatible, as long as you make sure 
they are the same version of the software.


cheers,
Bruce


On Fri, 16 Sep 2005, Fornito, Alexander 
wrote:



Hi,
Just had a couple of questions re: the -pvvol flag in mri_segstats:
How does it take account of partial voluming?
Is there anyway to visualize what the partial volume-corrected volume would 
look like?
Would you recmmoned using this falg routinely to obtain  subcortical volumes?

Finally, on a completely unrelated question, is there any reason to think that 
surfaces created using the same freesurfer distribution on a Mac would be 
incompatible with those created using a Linux machine (ie., would you be able 
to pool them for one study without any problems, and could you start creating 
surfaces on one, and then re-run afdter manual edits on the other?)

Thanks,
Alex


-Original Message-
From:   Doug Greve [mailto:[EMAIL PROTECTED]
Sent:   Thu 9/15/2005 10:11 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang
Subject:RE: [Freesurfer] intensity normalization failure

You should be able to use mri_segstats somehow. You'll need a
segmentation, though. You could tell it to report
on the aseg wm values. You could also use the fill volume (127 and
255?). Check out the --help

doug


On Wed, 14 Sep 2005, Bruce Fischl wrote:


should be easy enough to do in matlab. Just load the wm volume, then find all
the T1 voxels that are nonzero in it.

Bruce
On Thu, 15 Sep 2005, Fornito, Alexander wrote:


Is it possible to obtain and intensity histogram of the wm voxels, or
descriptive stats (eg., Mean, SD) as a quick check?

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, September 15, 2005 3:33 AM
To: Tracy Wang
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] intensity normalization failure

if it succeeds then the intensity in the wm should be exactly 110 over
much of the brain, and 90
Hi

What is a typical example of when the intensity normalization process

fails?

Does the over-all image seem brighter?  What is a good indicator of

success

or failure?

Thanks,
Tracy


Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
[EMAIL PROTECTED]


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RE: [Freesurfer] intensity normalization failure

[Fornito, Alexander]

Hi,
Just had a couple of questions re: the -pvvol flag in mri_segstats: 
How does it take account of partial voluming?  
Is there anyway to visualize what the partial volume-corrected volume would 
look like?
Would you recmmoned using this falg routinely to obtain  subcortical volumes?

Finally, on a completely unrelated question, is there any reason to think that 
surfaces created using the same freesurfer distribution on a Mac would be 
incompatible with those created using a Linux machine (ie., would you be able 
to pool them for one study without any problems, and could you start creating 
surfaces on one, and then re-run afdter manual edits on the other?)

Thanks,
Alex


-Original Message-
From:   Doug Greve [mailto:[EMAIL PROTECTED]
Sent:   Thu 9/15/2005 10:11 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang
Subject:RE: [Freesurfer] intensity normalization failure

You should be able to use mri_segstats somehow. You'll need a
segmentation, though. You could tell it to report
on the aseg wm values. You could also use the fill volume (127 and
255?). Check out the --help

doug


On Wed, 14 Sep 2005, Bruce Fischl wrote:

> should be easy enough to do in matlab. Just load the wm volume, then find all 
> the T1 voxels that are nonzero in it.
>
> Bruce
> On Thu, 15 Sep 2005, Fornito, Alexander wrote:
>
>> Is it possible to obtain and intensity histogram of the wm voxels, or
>> descriptive stats (eg., Mean, SD) as a quick check?
>> 
>> -Original Message-
>> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
>> Sent: Thursday, September 15, 2005 3:33 AM
>> To: Tracy Wang
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] intensity normalization failure
>> 
>> if it succeeds then the intensity in the wm should be exactly 110 over
>> much of the brain, and 90> 
>> Bruce
>> 
>> On Wed, 14 Sep
>> 2005, Tracy Wang wrote:
>> 
>>> Hi
>>> 
>>> What is a typical example of when the intensity normalization process
>> fails?
>>> Does the over-all image seem brighter?  What is a good indicator of
>> success
>>> or failure?
>>> 
>>> Thanks,
>>> Tracy
>>> 
>>> 
>>> Tracy Wang
>>> Research Assistant
>>> Cognitive Neuroscience Laboratory
>>> 
>>> Washington University
>>> Department of Psychology, Campus Box 1125
>>> One Brookings Drive
>>> St. Louis MO 63130-4899
>>> 314-935-5019
>>> [EMAIL PROTECTED]
>>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
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>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422




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RE: [Freesurfer] intensity normalization failure

[Doug Greve]

You should be able to use mri_segstats somehow. You'll need a
segmentation, though. You could tell it to report
on the aseg wm values. You could also use the fill volume (127 and
255?). Check out the --help

doug


On Wed, 14 Sep 2005, Bruce Fischl wrote:

should be easy enough to do in matlab. Just load the wm volume, then find all 
the T1 voxels that are nonzero in it.


Bruce
On Thu, 15 Sep 2005, Fornito, Alexander wrote:


Is it possible to obtain and intensity histogram of the wm voxels, or
descriptive stats (eg., Mean, SD) as a quick check?

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, September 15, 2005 3:33 AM
To: Tracy Wang
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] intensity normalization failure

if it succeeds then the intensity in the wm should be exactly 110 over
much of the brain, and 90
Hi

What is a typical example of when the intensity normalization process

fails?

Does the over-all image seem brighter?  What is a good indicator of

success

or failure?

Thanks,
Tracy


Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
[EMAIL PROTECTED]


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

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RE: [Freesurfer] intensity normalization failure

[Bruce Fischl]

should be easy enough to do in matlab. Just load the wm volume, then find 
all the T1 voxels that are nonzero in it.


Bruce
On Thu, 15 Sep 2005, Fornito, 
Alexander wrote:



Is it possible to obtain and intensity histogram of the wm voxels, or
descriptive stats (eg., Mean, SD) as a quick check?

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, September 15, 2005 3:33 AM
To: Tracy Wang
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] intensity normalization failure

if it succeeds then the intensity in the wm should be exactly 110 over
much of the brain, and 90
Hi

What is a typical example of when the intensity normalization process

fails?

Does the over-all image seem brighter?  What is a good indicator of

success

or failure?

Thanks,
Tracy


Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
[EMAIL PROTECTED]


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RE: [Freesurfer] intensity normalization failure

[Fornito, Alexander]

Is it possible to obtain and intensity histogram of the wm voxels, or
descriptive stats (eg., Mean, SD) as a quick check? 

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Thursday, September 15, 2005 3:33 AM
To: Tracy Wang
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] intensity normalization failure

if it succeeds then the intensity in the wm should be exactly 110 over 
much of the brain, and 90 Hi
>
> What is a typical example of when the intensity normalization process
fails? 
> Does the over-all image seem brighter?  What is a good indicator of
success 
> or failure?
>
> Thanks,
> Tracy
>
>
> Tracy Wang
> Research Assistant
> Cognitive Neuroscience Laboratory
>
> Washington University
> Department of Psychology, Campus Box 1125
> One Brookings Drive
> St. Louis MO 63130-4899
> 314-935-5019
> [EMAIL PROTECTED]
>
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Re: [Freesurfer] intensity normalization failure

[Tracy Wang]

I'm using 1.5T MPRAGEs.  and the skull stripped T1 overall looks very bright.  However the intensity for WM is between 90 and 120. 

Tracy

On Sep 14, 2005, at 12:40 PM, Bagnato, Francesca (NIH/NINDS) wrote:

Just a cuoriosity:
which kind of volumes are you using?
I had lots of troubles with 3T SPGRs and saw the center of the images just
brighter.
francesca

_  

From: Tracy Wang [mailto:[EMAIL PROTECTED]
Sent: Wed 9/14/2005 1:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] intensity normalization failure



Hi 


What is a typical example of when the intensity normalization process fails?
Does the over-all image seem brighter? What is a good indicator of success
or failure? 


Thanks, 

Tracy 



Tracy Wang 

Research Assistant 

Cognitive Neuroscience Laboratory 


Washington University 

Department of Psychology, Campus Box 1125 

One Brookings Drive 

St. Louis MO 63130-4899 

314-935-5019 

[EMAIL PROTECTED] 


Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University 
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
[EMAIL PROTECTED]

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RE: [Freesurfer] intensity normalization failure

[Bagnato, Francesca (NIH/NINDS)]

Just a cuoriosity:
which kind of volumes are you using?
I had lots of troubles with 3T SPGRs and saw the center of the images just
brighter.
francesca

  _  

From: Tracy Wang [mailto:[EMAIL PROTECTED]
Sent: Wed 9/14/2005 1:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] intensity normalization failure



Hi 


What is a typical example of when the intensity normalization process fails?
Does the over-all image seem brighter? What is a good indicator of success
or failure? 


Thanks, 

Tracy 



Tracy Wang 

Research Assistant 

Cognitive Neuroscience Laboratory 


Washington University 

Department of Psychology, Campus Box 1125 

One Brookings Drive 

St. Louis MO 63130-4899 

314-935-5019 

[EMAIL PROTECTED] 

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Re: [Freesurfer] intensity normalization failure

[Bruce Fischl]

if it succeeds then the intensity in the wm should be exactly 110 over 
much of the brain, and 90

Bruce

On Wed, 14 Sep 
2005, Tracy Wang wrote:



Hi

What is a typical example of when the intensity normalization process fails? 
Does the over-all image seem brighter?  What is a good indicator of success 
or failure?


Thanks,
Tracy


Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
[EMAIL PROTECTED]


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