Re: thickness analysis display

2002-11-10 Thread Darren Weber

Hi Bruce,

thanks for the explanation of the p value display. I understand now and can
see what is happening using the matlab commands:

t = linspace(-4,4,1000); % t-test values
p = tpdf(t,20);   % corresponding p values with df=20 (requires stats
toolbox)
plot(t,p); hold on
plot(t,-log10(p),'r')

This works for the p values.

What do you use to display the t values output using the --t option of
mri_surfglm?  I'm trying to use these to determine whether the p values
indicate greater or lesser thickness between groups.  In my case, the
2-tailed t-critical values for df=15 can be obtained with the matlab stats
toolbox:

alpha = [.05 .01 .001]
 -tinv(alpha/2,15)

ans =

   2.1314   2.9467   4.0728

So might this give the following values, given that fslope = (2.9467 + 1) /
4.0728:

fthresh = 2.1314
fmid= 2.9467
fslope  = 0.9690

I'm using the heat scale (stat positive) to display this and it has both
blue and red regions.  Does tksurfer automatically assume a 2-tailed
distribution and when entering the values above, display for +/-
fthresh/fmid?

When displaying the results of a thickness analysis, what do you do to
correct for multiple comparisons?  Is there a sound argument for resel
correction?

Thanks in advance, Darren




- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, October 31, 2002 2:52 AM
Subject: Re: thickness analysis display


 Hi Darren,

 the -log10(p) transform simply means you're looking at the exponent, with
 increasing values meaning more significant. For example, if your threshold
 were set to:

 fthresh = 1
 fmid = 2
 fslope = 1

 nothing with p1e-1 would be colored, the mid point of the color scale
 would be p=1e-2 and the full saturation would be fmid+1/fslope=1e-3.
 If fslope is too confusing (which it is to most people) you can set fmax
 instead.


 Note that in your example you should be using log10 not log:

 -log10(0.05)

 ans =

 1.3010

 so setting fthresh = 1.3 would give you an effective threshold of .05
 (instead of .1 in the example above).

 cheers,
 Bruce

 
 Bruce Fischl   email: [EMAIL PROTECTED]
 Mass. General Hosp. NMR Center.tel:(617)-726-4897
 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
 Charlestown, MA 02129 USA


 On Wed, 30 Oct 2002, Darren Weber wrote:

 
  Dear Doug et al,
 
  I've completed mris_surfglm on the cortical thickness, comparing two
groups.
  For a linear regression, I would normally check the assumptions of
  linearity, homoscedasticity and normality in the residuals, but for
250,000
  analyses, it's a daunting, if not impossible, task!  So, lets assume the
  linear model applies.
 
  I need to confirm and clarify a few points on how to display/threshold
the
  stats.
 
  Firstly, I followed the --help option examples and saved the output
stats
  using:
 
  --sigt ./glm/group-sigt-rh.w paint
 
  I can now load these values as an overlay on the target subject surface
of
  choice, great.  Now the questions arise as to what quantity this is and
how
  to use the overlay threshold GUI.
 
  Firstly, what quantity is it?  According to the --help option:
 
  #Save the signficance (p-value) of the t-ratio of the contrast. The
  #value is actually the -log10 of the significance with the same
  #sign as the t-ratio from which it was computed. The significance
  #is computed from a double-sided t-test and is NOT corrected for
  #multiple comparisons across space. fmt is the format (see OUTPUT
  #FORMATS).
 
  So, the output values are not t or p, but -log10(p).  Why is this so?  I
  don't understand the advantage of doing this transform on the p-values.
 
  If so, and this should be simple, do we calculate a threshold of p = .05
as:
 
   p = .05;
   thresh = -log(p)
 
  thresh =2.9957
 
  This would be a 2-tail threshold for any value of p.  How would you
obtain a
  1-tailed threshold?  Perhaps multiply p by 2, ie:
 
   thresh = -log(p*2)
 
  thresh =2.3026
 
 
  OK, so we get a threshold value somehow.  I'm not sure how to use the
  overlay threshold GUI, which has three slides and a slope value.  The
  tksurfer manual does not describe the threshold controls, it only
contains
  the following description:
 
  Overlay File Display Options
  To select which overlay to show, use the View-Overlay Layer submenu.
The
  field names are automatically set to the file name loaded. You can
change
  this name by typing a new one into the information area in the Tool
window.
  The display for the current overlay can be configured in the
  View-Configure-Configure Overlay
  Display dialog. You can select the color scale to use with the radio
buttons
  in the top area of the dialog. The Truncate option can be checked to
turn
  off the display of negative values. Check the Reverse option to reverse
the
  sign of the values as they are drawn in the color scale. View- Inverse
and
  Complex are reserved for future

Re: mris_convert

2002-10-28 Thread Darren Weber

Hi Bruce,

thankyou, I had some minor bugs in the output asc file.  It was in meters,
but more importantly the vertices started at one, where FS vertices start at
zero.

Cheers, Darren


- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Monday, October 21, 2002 11:42 PM
Subject: Re: mris_convert


 Hi Darren,

 I think tkmedit/tksurfer can read .asc files natively, but if not
 mris_convert should be able to convert them to binary.

 cheers,
 Bruce

 
 Bruce Fischl   email: [EMAIL PROTECTED]
 Mass. General Hosp. NMR Center.tel:(617)-726-4897
 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
 Charlestown, MA 02129 USA


 On Mon, 21 Oct 2002,
 Darren Weber wrote:

 
  Dear Bruce et al,
 
  I wonder if we can convert ascii to binary surf files?
 
  I have some scalp and skull surfaces that can be saved into an ascii
file,
  is it possible to convert this to the freesurfer surf file format?  I
would
  like to display these surfaces using tkmedit to check their locations in
the
  MRI volume, given that they are generated from a volume with the
orientation
  and dims of the freesurfer volume.
 
  Take care, Darren
 
 
  --
  Darren Weber, PhD Student
  Cognitive Neuroscience, School of Psychology
  Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
  Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
  http://203.3.164.46/~dlw/homepages/index.html
 
 







Re: mris_make_template etc.

2002-10-18 Thread Darren Weber

G'day Bruce et al,

the template is uploading to
ftp://floyd.psy.flinders.edu.au/pub/weber/rh.wholebrain.tif (~5Mb, the
permissions should allow anonymous ftp access).  Could you take a look at
it?  I guess it's OK but I have no idea what it should look like, maybe it
makes sense in the light of your experience and insight?  If you notice any
problems, please let me know.  I have been able to view it with
http://www.irfanview.com/

Thanks, Darren


- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Saturday, October 19, 2002 1:18 AM
Subject: Re: mris_make_template etc.


 Hi Darren,

 yes, I think what youu are doing is essentially correct. Don't worry
 about the .gcs or tissue_params files, they have nothing to do with the
 spherical morphing. The .tif file you create should be a normal
multi-frame
 tif, with 9 frames in it, made up of 3 sets of 3 (mean,stderror,dof).
 These are statistics on the geometric properties of the group of subjects
 you gave to mris_make_template in a spherical parameterization (longitude
 and lattitude). You should be able to view them in anything that knows how
 to read multi-frame tif files I would think.

 cheers,
 Bruce

 p.s. Note that the dof frame has only 1 nonzero element (the 1st), which
 should be the # of subjects that make up the template.

 
 Bruce Fischl   email: [EMAIL PROTECTED]
 Mass. General Hosp. NMR Center.tel:(617)-726-4897
 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
 Charlestown, MA 02129 USA



 On Fri, 18 Oct 2002, Darren Weber wrote:

 
  Dear Bruce et al,
 
  could you please confirm the following is reasonable?
 
  I am trying to register whole brain surfaces across subjects, hence
  creating a study specific template (if anyone is interested in the
template,
  let me know).
 
  First, run the following to create an individual subject (C01) template:
 
  mris_make_template rh sphere c01
  /usr/local/freesurfer/average/rh.wholebrain.tif
 
  Are any other arguments required?  This command, as above, creates the
  output file only, no other files like those in the
  /usr/local/freesurfer/average/ area are created.  What are the *.gcs or
  tissue_parms.txt files?  The .tif is not a graphics file - what does tif
  stand for?  The rh.wholebrain.tif is the same size as other template
files,
  so that should be a good sign that it contains the required data.
 
  Then, after spherical transforms for all subjects, the rh.sphere
surfaces
  are registered to this individual subject template, using a csh script
  containing:
 
  set avg=/usr/local/freesurfer/average/rh.wholebrain.tif
  mris_register -curv -w 0 ${sub}/surf/rh.sphere $avg
  ${sub}/surf/rh.sphere.reg
 
  What are the -curv and -w options and how do they affect the
registration?
 
  That completes the first pass of the registration process.  Then create
a
  new wholebrain template, using all subjects' sphere.reg files:
 
  set sub=c01 c02 c03 c04 c05 c06 c07 c08 c09 c10 p02 p04 p05 p06 p07 p08
  p09
  mris_make_template rh sphere.reg $sub
  /usr/local/freesurfer/average/rh.wholebrain.tif
 
  This should create a template that is the average of all these subjects.
  Then the registration process is repeated to overwrite the sphere.reg
files
  for each subject, using the new averaged template.
 
  Is this reasonable?  If it has worked correctly, it should now be
possible
  to use mris_surfglm on the rh.sphere.reg files.
 
  Thanks, Darren
 
 
 
 
  --
  Darren Weber, PhD Student
  Cognitive Neuroscience, School of Psychology
  Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
  Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
  http://203.3.164.46/~dlw/homepages/index.html
 
 







Re: skull stripping

2002-10-17 Thread Darren Weber

Hi Bob et al,

I prefer mri_strip_skull to mri_watershed.  I think the former was a
previous method that has now been replaced by the latter.  Please find
attached a small csh script (process_anatomy.csh) that I find useful for
doing the skull strip and segmentation (note that mri_watershed is hashed
out).  I use another script to loop over subjects (process_allanatomy.bash).

Kind regards, Darren


- Original Message -
From: Bob Thoma [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, October 17, 2002 3:58 AM
Subject: skull stripping


 All,

 I've been having some difficulty with skull stripping, it doesn't appear
to
 be removing enough.  I have tried changing the remove skull settings under
 expert preferences, but have had no luck.  I found a previous email with a
 similar problem. Bruce, I believe you replied as such:

 are you using a talairaching procedure? If so, please check that it worked
 properly. If it fails, everything after it fails as well. Please also
check
 your T1 volume by bringing it up in tkmedit. The vast majority of the
white
 matter should have an intensity of exactly 110. If this is not the
case,then
 the intensity normalization didn't work properly, possibly because of a
 talairach failure, or for some other reason. The segmentation itself
usually
 works pretty well, so I suspect that it is one of the previous steps that
is
 causing you problems.

 cheers,
 Bruce

 I have two questions, one, how can i check to see if the talairaching
 procedure worked properly or how to not run the talairaching procedure.
 Second, where do I locate the white matter intensity that you stated to be
 110.

 Or if anyone has any other suggestions, I would be grateful.

 Thanks
 Natalie







 _
 Protect your PC - get McAfee.com VirusScan Online
 http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963





process_anatomy.csh
Description: Binary data


process_allanatomy.bash
Description: Binary data


registration of whole cortical sheet

2002-10-10 Thread Darren Weber


Dear Bruce et al,

my query is about how to register cortical surfaces across X subjects, given
that we have modified the usual left/right surface separation.

Some time ago we discussed how to extract a complete cortical surface,
rather than the left/right hemi surfaces.  The purpose of this being to use
a complete cortical surface for ERP/MEG source modelling methods.  This
involves a couple of modifications to the wm volume and the usual inputs to
the fill white matter process (see attached shell script for details).  In
my case, the resulting surfaces are called rh.*, although they actually
contain both left and right hemispheres, joined by the corpus callosum (not
strictly cortex, but unavoidable in this approach).  For source modelling,
these surfaces are nice.

Having obtained these surfaces for nearly 20 subjects, we've raised the
possibility of doing a cortical thickness analysis for two groups, controls
and PTSD patients.  This requires that any vertex A is located in the same
coordinate system and location for all subjects, so they must be
coregistered (Fischl et al, 1999, Human Brain Mapping 8:272-284;
http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=67501785).

Normally, I assume the registration process morphs each left/right hemi
cortex into two unit spheres (rather than morphing each hemi cortex onto the
left/right hemisphere of one unit sphere).  So, many of the examples in
Fischl et al (1999) illustrate one hemisphere or another.  Thus, we normally
have lh.sphere and rh.sphere, two unit spheres, one for each hemi cortex
surface.  Further, the spherical sulcal patterns of each lh.sphere and
rh.sphere are then further morphed (non-linear) to match the patterns of
some average template.  Obviously the whole cortical surfaces we have are
not separated into lh/rh, rather the rh contains both.

My concern here is with this template - I don't know much about it.  I
assume the template (average7) is specific for each left/right hemi-cortex.
It might not be a good template for our data, which contains the whole
cortex, including the sagittal fissure and corpus callosum.

Can you recommend a template for registration of these subjects' surfaces?
Is it reasonable to use one subject surface as a template for all others?
If so, what do you think of a two stage process, first registering all
subjects to subject X, then averaging across all subjects to create a study
specific average, then reregister all subjects to this average?

Many thanks for your consideration, Darren


--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html



process_fillwm.csh
Description: Binary data


Re: registration of whole cortical sheet

2002-10-10 Thread Darren Weber


Thanks, Bruce.

mris_make_template --help stops at 'valid options are:'  :-(

One of the input parameters is a surface name - I suppose 'orig', 'white',
'pial' etc are valid.  I'm not sure what surface to specify; is it 'sphere'
or 'inflated' or something else?

Cheers, Darren

- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Friday, October 11, 2002 12:12 PM
Subject: Re: registration of whole cortical sheet


 Hi Darren,

 that's pretty much the way I generated the lh and rh templates we use.
 There's a binary named mris_make_template,which you probably have, that
 will take a bunch of surface models and construct a template (.tif) from
 them. You'll have to name the individual surface lh or rh, since it's
 expecting a hemisphere. The mris_register binary is actually smart enough
 to change it's default parameters if the target is from a single surface
 (it uses a more rigid morph).

 Good luck,
 Bruce





 On
 Fri, 11 Oct 2002, Darren Weber wrote:

 
  Dear Bruce et al,
 
  my query is about how to register cortical surfaces across X subjects,
given
  that we have modified the usual left/right surface separation.
 
  Some time ago we discussed how to extract a complete cortical surface,
  rather than the left/right hemi surfaces.  The purpose of this being to
use
  a complete cortical surface for ERP/MEG source modelling methods.  This
  involves a couple of modifications to the wm volume and the usual inputs
to
  the fill white matter process (see attached shell script for details).
In
  my case, the resulting surfaces are called rh.*, although they actually
  contain both left and right hemispheres, joined by the corpus callosum
(not
  strictly cortex, but unavoidable in this approach).  For source
modelling,
  these surfaces are nice.
 
  Having obtained these surfaces for nearly 20 subjects, we've raised the

  possibility of doing a cortical thickness analysis for two groups,
controls
  and PTSD patients.  This requires that any vertex A is located in the
same
  coordinate system and location for all subjects, so they must be
  coregistered (Fischl et al, 1999, Human Brain Mapping 8:272-284;
  http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=67501785).
 
  Normally, I assume the registration process morphs each left/right hemi
  cortex into two unit spheres (rather than morphing each hemi cortex onto
the
  left/right hemisphere of one unit sphere).  So, many of the examples in
  Fischl et al (1999) illustrate one hemisphere or another.  Thus, we
normally
  have lh.sphere and rh.sphere, two unit spheres, one for each hemi cortex
  surface.  Further, the spherical sulcal patterns of each lh.sphere and
  rh.sphere are then further morphed (non-linear) to match the patterns of
  some average template.  Obviously the whole cortical surfaces we have
are
  not separated into lh/rh, rather the rh contains both.
 
  My concern here is with this template - I don't know much about it.  I
  assume the template (average7) is specific for each left/right
hemi-cortex.
  It might not be a good template for our data, which contains the whole
  cortex, including the sagittal fissure and corpus callosum.
 
  Can you recommend a template for registration of these subjects'
surfaces?
  Is it reasonable to use one subject surface as a template for all
others?
  If so, what do you think of a two stage process, first registering all
  subjects to subject X, then averaging across all subjects to create a
study
  specific average, then reregister all subjects to this average?
 
  Many thanks for your consideration, Darren
 
 
  --
  Darren Weber, PhD Student
  Cognitive Neuroscience, School of Psychology
  Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
  Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
  http://203.3.164.46/~dlw/homepages/index.html
 







Re: mris_surfglm

2002-10-10 Thread Darren Weber


Hi Doug et al,

from looking at the help on mris_surfglm it appears that vertices in the
analyses are not as dense as those from the subject surfaces.  I'm guessing
that using the ico surface with 7 iterations of refinement (lots of
vertices!), you then locate the nearest vertex in each subject for each ico
vertex.  So, the GLM analyses for any given ico vertex use data from
different vertex numbers across subjects - are these vertex indices and ico
vertex correspondence available as an output option or are they stored in a
temp file or something?  Say, for each vertex number of ico, a row vector of
subject vertex indices, in the order they are input to mris_surfglm.

Also, if the above assumption is correct, the implication may be that some
slight variations in registration (alignment accuracy might vary to within
1 - 10 vertices, perhaps) could have an impact on the results?  Is there any
local vertex neighbourhood averaging of thickness values when extracting the
individual subject values for the GLM?

Cheers, Darren


- Original Message -
From: Doug Greve [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Friday, October 11, 2002 2:13 AM
Subject: Re: mris_surfglm



 Hi Darren,

 the ico and average7 are about the same computationally. However, it is
 more convenient to use average7 it has a surface that you can directly
 render the results on. With ico, you'd still have to run mri_surf2surf
 to convert it to another surface.

 I'm not sure what you're trying to do in terms of the surface
 registration...

 doug


 Darren Weber wrote:
 
  Dear Doug et al,
 
  surfglm looks good.  I have processed 10 controls and 8 patients such
that
  each surface contains a whole cortical surface, without the usual split
  through the corpus callosum.  How would I use the surface registration
  process?  Should I use 'ico' as the average or can I use one of the
  subjects?
 
  Take care, Darren
 
  --
  Darren Weber, PhD Student
  Cognitive Neuroscience, School of Psychology
  Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
  Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
  http://203.3.164.46/~dlw/homepages/index.html

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






mris_surfglm

2002-10-09 Thread Darren Weber


Dear Doug et al,

surfglm looks good.  I have processed 10 controls and 8 patients such that
each surface contains a whole cortical surface, without the usual split
through the corpus callosum.  How would I use the surface registration
process?  Should I use 'ico' as the average or can I use one of the
subjects?

Take care, Darren


--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html





Re: RF bias correction with mri_convert

2002-08-29 Thread Darren Weber


I am referring to a command line option to mri_convert:

--unwarp-gradient-nonlinearity ...




- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, August 29, 2002 9:30 PM
Subject: Re: RF bias correction with mri_convert


 p.s. what we do is not really bias field estimation/correction, but
 something much more aggressive, really a pre-segmentation, which accounts
 for bias fields as well as tissue inhomogeneity. If what you want is
really
 the bias field for some other purpose, you're probably better of using the
 EM stuff from the FSL (unless you can measure it directly with your
 scanner, which is the best solution!).

 Bruce

 On Thu, 29 Aug 2002, Stephen Smith wrote:

 
  Hi - no, it doesn't - that is part of the initial freesurfer processing
  (which estimates white matter and then estimates bias field on the basis
  of white matter points), not the format conversion.
 
  ttfn, Steve.
 
  On Thu, 29 Aug 2002, Darren Weber wrote:
 
  
   Dear Bruce et al,
  
   does mri_convert automatically apply RF bias field
estimation/correction?
   If it can do the RF bias correction, what is the best command line
option
   for this?
  
   Take care, Darren
  
  
   --
   Darren Weber, PhD Student
   Cognitive Neuroscience, School of Psychology
   Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
   Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
   http://203.3.164.46/~dlw/homepages/index.html
  
  
  
 
   Stephen M. Smith
   Head of Image Analysis, FMRIB
 
   Oxford University Centre for Functional MRI of the Brain
   John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
   +44 (0) 1865 222726  (fax 222717)
 
   [EMAIL PROTECTED]  http://www.fmrib.ox.ac.uk/~steve
 







Re: RF bias correction with mri_convert

2002-08-29 Thread Darren Weber


Hi Bruce, et al,

The Markov random field approach with FSL FAST is intensive (~ 2000 sec on
Athlon 1700, 1Gb PC2700 on VIA KT333A) and the results appear to be good.
Of course, it could be better to measure the quantity on the scanner.  Would
this approach require access and modification of the kspace images before
reconstruction?  Naturally we could all rest easily if the scanner
engineering and signal processing took care of the problem ;-)  We don't
have a research scanner and any access to any of that :-(  It would be nice
to evaluate this latter physical solution with that from FAST.

Thanks for clarifying the mri_normalize process.  It will be interesting,
although overkill, to see what happens when FreeSurfer is fed one of the
volumes after RF correction with FAST.  In particular, whether it will
improve the segmentation any.  Another interesting experiment might be to
segment the WM with freesurfer and use that volume as a prior input to FAST.
Again, overkill, but anything that could improve the automation of the first
segmentation stage might decrease the latter manual editing.  The cost is
the extra processing overheads.

Yes, there is some other work to be done on just the RF bias corrected
volume.

Cheers, Darren



- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, August 29, 2002 9:30 PM
Subject: Re: RF bias correction with mri_convert


 p.s. what we do is not really bias field estimation/correction, but
 something much more aggressive, really a pre-segmentation, which accounts
 for bias fields as well as tissue inhomogeneity. If what you want is
really
 the bias field for some other purpose, you're probably better of using the
 EM stuff from the FSL (unless you can measure it directly with your
 scanner, which is the best solution!).

 Bruce

 On Thu, 29 Aug 2002, Stephen Smith wrote:

 
  Hi - no, it doesn't - that is part of the initial freesurfer processing
  (which estimates white matter and then estimates bias field on the basis
  of white matter points), not the format conversion.
 
  ttfn, Steve.
 
  On Thu, 29 Aug 2002, Darren Weber wrote:
 
  
   Dear Bruce et al,
  
   does mri_convert automatically apply RF bias field
estimation/correction?
   If it can do the RF bias correction, what is the best command line
option
   for this?
  
   Take care, Darren
  
  
   --
   Darren Weber, PhD Student
   Cognitive Neuroscience, School of Psychology
   Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
   Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
   http://203.3.164.46/~dlw/homepages/index.html
  
  
  
 
   Stephen M. Smith
   Head of Image Analysis, FMRIB
 
   Oxford University Centre for Functional MRI of the Brain
   John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
   +44 (0) 1865 222726  (fax 222717)
 
   [EMAIL PROTECTED]  http://www.fmrib.ox.ac.uk/~steve
 







RF bias correction with mri_convert

2002-08-28 Thread Darren Weber


Dear Bruce et al,

does mri_convert automatically apply RF bias field estimation/correction?
If it can do the RF bias correction, what is the best command line option
for this?

Take care, Darren


--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html






eeg-toolbox release

2002-08-15 Thread Darren Weber


Hi,

there is a new release of the matlab eeg-toolbox/mri-toolbox available via
http://eeg.sourceforge.net/.

This release incorporates a new mesh_shrinkwrap function (alpha release) for
generating a surface from an Analyze MRI volume.  If given the Analyze
version of the original input to freesurfer (eg, mri_convert -oid 1 0 0 -ojd
0 1 0 -okd 0 0 1 orig orig.asc), it will output a scalp in the same space as
the freesurfer cortex asc file (created by freesurfer command,
mris_convert).  It is possible to use the FSL BET program to get a skull
from volume from this orig volume, which can be tesselated also.  Please see
the mesh_3shell_script for an example of this process.

This release also updates the mesh plot functions, to provide overlays and
transparency.

For recipients who would like to hear about or discuss releases of this
toolbox, please subscribe to the eeg-users email list.  This will be the
last announcement for this toolbox that will be sent to related email lists.
I sincerely apologise to regular users of these lists and their
administrators for this 'off-topic' announcement, but I hope the
distribution of these tools might benefit other users of scan, freesurfer,
spm, fsl, etc tools.  All communication related to this matlab toolbox will
hereafter be conducted in [EMAIL PROTECTED]

All the best with your work.

Kind regards, Darren


--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph:  (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html






test

2002-06-23 Thread Darren Weber




apologies for any inconvenience

some of my email to the list has not been working