[Freesurfer] 64 bits Mac

[Ed Gronenschild]

Hi,

The Mac OSX 10.6 version offers the possibility to
run in 64 bits mode (by pressing simultaneously
the 6 and 4 keys during startup).
I was wondering if Freesurfer can be used in 64 bits
mode? In other words: does it use the 64 bits or
does it run only in compatibility mode and in fact
in 32 bits mode?

Ed

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[Freesurfer] Group analysis, contrasts

[Per Selnes]

I'm trying to set ut a freesurfer group analysis. In my fsgd file there are 
four groups/classes and 2 variables, like so:

GroupDescriptorFile 1
  Title 
  Class Class1 
  Class Class2
  Class Class3 
  Class Class4
  SomeTag

Variables Variable1 Variable2
Input subj1 Class1 49 1 
Input subj2 Class2 50 2
Input subj3 Class3 51 3
Input subj3 Class4 52 4
Input...

I'm a bit puzzled as to how I should set up the contrasts. With DODS, there 
should be a matrix of 12 regressors, and
I want to model how thickness varies with Variable2, ignoring the effects of 
Variable1 and Class. Should my contrast be

0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25
or
0 0 0 0 0 0 0 0 1 1 1 1

or something completely different?

I have tried both contrasts, and they yield identical (and plausible) results.

Kind Regards,
Per Selnes
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Re: [Freesurfer] Group analysis, contrasts

[Douglas N Greve]

Both of those contrasts will give you the same p-value. The difference 
is if you look at the contrast values themselves (gamma.nii). The first 
contrast will give you values in units of mm. The second will give you 
values in units of 4*mm.

doug

Per Selnes wrote:
> I'm trying to set ut a freesurfer group analysis. In my fsgd file there are 
> four groups/classes and 2 variables, like so:
>
> GroupDescriptorFile 1
>   Title 
>   Class Class1 
>   Class Class2
>   Class Class3 
>   Class Class4
>   SomeTag
>
> Variables Variable1 Variable2
> Input subj1 Class1 49 1 
> Input subj2 Class2 50 2
> Input subj3 Class3 51 3
> Input subj3 Class4 52 4
> Input...
>
> I'm a bit puzzled as to how I should set up the contrasts. With DODS, there 
> should be a matrix of 12 regressors, and
> I want to model how thickness varies with Variable2, ignoring the effects of 
> Variable1 and Class. Should my contrast be
>
> 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25
> or
> 0 0 0 0 0 0 0 0 1 1 1 1
>
> or something completely different?
>
> I have tried both contrasts, and they yield identical (and plausible) results.
>
> Kind Regards,
> Per Selnes
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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

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Re: [Freesurfer] 64 bits Mac

[Nick Schmansky]

currently it runs in 32b mode.  we've had quite a bit of trouble trying
to get the 3rd party libs (tcl/tk/tix/blt and mni) to build as 64b on
the mac (but no problems on linux), which has prevented getting a true
64b mac build going.  still working on it

n.

On Mon, 2011-01-10 at 09:01 +0100, Ed Gronenschild wrote:
> Hi,
> 
> The Mac OSX 10.6 version offers the possibility to
> run in 64 bits mode (by pressing simultaneously
> the 6 and 4 keys during startup).
> I was wondering if Freesurfer can be used in 64 bits
> mode? In other words: does it use the 64 bits or
> does it run only in compatibility mode and in fact
> in 32 bits mode?
> 
> Ed
> 
> ___
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> 
> 

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 13

[Bevil R. Conway]

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not
have access to email.  For issues concerning my laboratory, please contact
my lab manager, Rosa Lafer-Sousa (rlafe...@wellesley.edu). 

Thank-you and I'll be in touch when I get back.  

Bevil

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[Freesurfer] Error FsFast Tutorial

[Fernanda Palhano]

Hi,

I am trying to run the FsFast tutorial, but I am getting the following
error:


Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study]
fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0
-aparc+aseg
tmp: Subscript out of range.
tmp: Subscript out of range.
tmp: Subscript out of range.
tmp: Subscript out of range.
ERROR: cannot find
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat
[Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study]
fernandapalhano% tksurfer-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0
-hemi lh -aparc
tmp: Subscript out of range.
tmp: Subscript out of range.
tmp: Subscript out of range.
tmp: Subscript out of range.
$Id: tksurfer-sess,v 1.15.2.1 2010/07/14 16:08:04 greve Exp $
Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0:
Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386
Mon Jan 10 15:08:15 BRT 2011
/Applications/freesurfer/bin/tksurfer

list odd-v-0
con/map odd-v-0
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
maplist
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
mri_concat
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
--o
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Writing to
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii
ERROR: cannot find
/Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat

I checked all the mgh files in fb1-analysis-study and any of them have
register.dof6.dat, there is only register.dat.
Where can I obtain these file?

Thanks in advance,
Fernanda Palhano
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Re: [Freesurfer] Error FsFast Tutorial

[Douglas N Greve]

The current fsfast tutorial does not work with the new version. I'm 
preparing a new tutorial. Sorry about that.

doug

Fernanda Palhano wrote:
> Hi,
>
> I am trying to run the FsFast tutorial, but I am getting the following 
> error:
>
>
> Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] 
> fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c 
> odd-v-0 -aparc+aseg
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> ERROR: cannot find 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat
> [Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] 
> fernandapalhano% tksurfer-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c 
> odd-v-0 -hemi lh -aparc
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> tmp: Subscript out of range.
> $Id: tksurfer-sess,v 1.15.2.1 2010/07/14 16:08:04 greve Exp $
> Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 
> 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 
> i386
> Mon Jan 10 15:08:15 BRT 2011
> /Applications/freesurfer/bin/tksurfer
>
> list odd-v-0
> con/map odd-v-0 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
> maplist 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
> mri_concat 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii
>  
> --o 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii
> ninputs = 1
> Checking inputs
> nframestot = 1
> Allocing output
> Done allocing
> nframes = 1
> Writing to 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii
> ERROR: cannot find 
> /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat
>
> I checked all the mgh files in fb1-analysis-study and any of them have 
> register.dof6.dat, there is only register.dat.
> Where can I obtain these file?
>
> Thanks in advance,
> Fernanda Palhano
> 
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] redraw failed: no gl window open error

[juli]

Hello,

I am working in freesurfer-Linux-centos4_x86_64-stable-v4.0.5-20081003.

The issue I am having started several days ago when I was trying to create
overlap of thresholded stats maps using mri_binarize and mri_concat (from
sig.mgh files). When I was attempting to load the concatenated file I was
getting an error "surfer: ### redraw failed: no gl window open" and in the
tk window I am getting just an average recon without any overlay map.
Also, now I am unable to load any of the GLMs I have ran previously.

Going by the previous posts as well as
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems, I have
tried the following:
- setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride prior
to running freesurfer
- NVidia driver update
- setenv doublebufferflag 1
- I have also checked my xorg.conf file (attached) Depth is set to 24.

If you could point me in any other direction to fix/undo this issue I
would greatly appreciate it.

Thank you in advance,
Juli

xorg.conf
Description: Binary data
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[Freesurfer] (no subject)

[Eisenstein, Sarah]

Hello,

What goes into the calculation of subcortical volume?  We have tried adding 
volumes of individual subcortical areas but the total does not equal the 
subcortical volume provided by aseg.  Is the subcortical volume calculation 
accurate?

Thanks,

Sarah Eisenstein

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Re: [Freesurfer] (no subject)

[Douglas N Greve]

The aseg.stats file takes into account partial voluming which is not 
taken into account when you simply sum up the subcortical structures 
because some of those structures will be partially volumed with white 
matter.

doug

Eisenstein, Sarah wrote:
>
> Hello,
>
>  
>
> What goes into the calculation of subcortical volume?  We have tried 
> adding volumes of individual subcortical areas but the total does not 
> equal the subcortical volume provided by aseg.  Is the subcortical 
> volume calculation accurate?
>
>  
>
> Thanks,
>
>  
>
> Sarah Eisenstein
>
>  
>
> 
>
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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
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Re: [Freesurfer] what is subcortical volume?

[Douglas N Greve]

Yes, it is accurate. Why do you think it's not? There's lots of 
validation stuff on the wiki. The subcortical gray matter structures are 
given below.
Left_Thalamus)
Right_Thalamus)
Left_Thalamus_Proper)
Right_Thalamus_Proper)
Left_Caudate)
Right_Caudate)
Left_Putamen
Right_Putamen
Left_Pallidum)
Right_Pallidum)
Brain_Stem)
Left_Hippocampus)
Right_Hippocampus)
Left_Amygdala)
Right_Amygdala)
Left_Accumbens_area)
Right_Accumbens_area)
Left_VentralDC)
Right_VentralDC)
Left_Substancia_Nigra)
Right_Substancia_Nigra)
Left_Cerebellum_Cortex)
Right_Cerebellum_Cortex)



Eisenstein, Sarah wrote:
> Thank you for your response.  However, is this considered an accurate 
> estimation of subcortical volume?  As far as I know, Freesurfer is unable to 
> estimate some deep subcortical structure volumes.  So what is subcortical 
> volume (as given by Freesurfer aseg.stats) composed of?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, January 10, 2011 4:39 PM
> To: Eisenstein, Sarah
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> The aseg.stats file takes into account partial voluming which is not 
> taken into account when you simply sum up the subcortical structures 
> because some of those structures will be partially volumed with white 
> matter.
>
> doug
>
> Eisenstein, Sarah wrote:
>   
>> Hello,
>>
>>  
>>
>> What goes into the calculation of subcortical volume?  We have tried 
>> adding volumes of individual subcortical areas but the total does not 
>> equal the subcortical volume provided by aseg.  Is the subcortical 
>> volume calculation accurate?
>>
>>  
>>
>> Thanks,
>>
>>  
>>
>> Sarah Eisenstein
>>
>>  
>>
>> 
>>
>> ___
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>> 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
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Re: [Freesurfer] which volume to edit?

[Khoa Nguyen]

Hi Yang,

To edit the pial surface, you want to use brainmask.mgz.

As for the wm.mgz, you're right in that control points isn't the solution. 
Control points are to fix intensity problem, but you can also add wm 
voxels manually to fix any wm defects. In this case, adding that many control 
points 
would probably make the situation worse because the entire area will 
brighten and that would potentially extend the surfaces to include grey 
matter.

Is the area you pointed out by any chance the ventricle? If it is, then it 
doesn't matter that the white surface includes it. It's hard 
to tell with just this image. Do you mind sending a snapshot of the 
brainmask.mgz for this slice?

On Mon, 10 Jan 2011, Yang Liu wrote:

> Hi Freesurferers,
>
> I am correcting some defects in the white matter surface (yellow) and the
> pial surfaces (red). But I am not very sure of which volume I should work
> on.
> I did several experiments on editing one volume at a time.
>
> For pial (the red) surface, I edited brain.mgz first. I found it corrected
> some pial defects.
> However, I found one previous post here said the volume that should be
> edited is brainmask.mgz.
> So the second time I only changed brainmask.mgz. It also works.
>
> So, which one should I work on?
>
> brian.mgz or brainmask.mgz?
>
> Also, for defects on the white matter surface (the yellow one),  I found the
> surface doesn't follow the white matter segmentation closely, although I
> have a good wm.mgz. (see attached image).
> At the location pointed by the red arrow in the attached image, both the
> green and yellow sufaces includes a lot of gray matter at the location. It
> is strange that the wm.mgz has a very well defined slice in that
> neighborhood.
> I am familiar with situations where the surfaces miss a few white matter
> pixels, for which I can add a few control points to improve it.
>
> How shall I edit wm.mgz to correct this?  Adding more control points is not
> a solution, apparently.
>
> Thank you.
>
> Yang
>
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Re: [Freesurfer] which volume to edit?

[Bruce Fischl]

Does the aseg label that as ventricle?



On Jan 10, 2011, at 9:34 PM, Yang Liu  wrote:

> Hi Khoa,
> 
> Thanks for your reply. 
> I attached the snapshot of the same slice with brainmask.mgz. You can see 
> clearly that the green and yellow surface at the wrong regions. They doesn't 
> look like  ventricles to me.  
> It is strange that even the green surface doesn't follow the original wm.mgz, 
> though the wm.mgz as attached in the previous email 
> has very well defined boundaries near the wrong regions.
> Any idea to correct this?
> 
> 
> Yang
> 
> 
> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen  wrote:
> Hi Yang,
> 
> To edit the pial surface, you want to use brainmask.mgz.
> 
> As for the wm.mgz, you're right in that control points isn't the solution. 
> Control points are to fix intensity problem, but you can also add wm voxels 
> manually to fix any wm defects. In this case, adding that many control points 
> would probably make the situation worse because the entire area will brighten 
> and that would potentially extend the surfaces to include grey matter.
> 
> Is the area you pointed out by any chance the ventricle? If it is, then it 
> doesn't matter that the white surface includes it. It's hard to tell with 
> just this image. Do you mind sending a snapshot of the brainmask.mgz for this 
> slice?
> 
> 
> On Mon, 10 Jan 2011, Yang Liu wrote:
> 
> Hi Freesurferers,
> 
> I am correcting some defects in the white matter surface (yellow) and the
> pial surfaces (red). But I am not very sure of which volume I should work
> on.
> I did several experiments on editing one volume at a time.
> 
> For pial (the red) surface, I edited brain.mgz first. I found it corrected
> some pial defects.
> However, I found one previous post here said the volume that should be
> edited is brainmask.mgz.
> So the second time I only changed brainmask.mgz. It also works.
> 
> So, which one should I work on?
> 
> brian.mgz or brainmask.mgz?
> 
> Also, for defects on the white matter surface (the yellow one),  I found the
> surface doesn't follow the white matter segmentation closely, although I
> have a good wm.mgz. (see attached image).
> At the location pointed by the red arrow in the attached image, both the
> green and yellow sufaces includes a lot of gray matter at the location. It
> is strange that the wm.mgz has a very well defined slice in that
> neighborhood.
> I am familiar with situations where the surfaces miss a few white matter
> pixels, for which I can add a few control points to improve it.
> 
> How shall I edit wm.mgz to correct this?  Adding more control points is not
> a solution, apparently.
> 
> Thank you.
> 
> Yang
> 
> 
> 
> 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.
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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] which volume to edit?

[Sebastian Moeller]

Hi All,


On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:

> Does the aseg label that as ventricle?

This pretty much looks like macaque data, so I think there is no aseg 
for that. I would love to be corrected on that point though.

Best
Sebastian

> 
> 
> 
> On Jan 10, 2011, at 9:34 PM, Yang Liu  wrote:
> 
>> Hi Khoa,
>> 
>> Thanks for your reply. 
>> I attached the snapshot of the same slice with brainmask.mgz. You can see 
>> clearly that the green and yellow surface at the wrong regions. They doesn't 
>> look like  ventricles to me.  
>> It is strange that even the green surface doesn't follow the original 
>> wm.mgz, though the wm.mgz as attached in the previous email 
>> has very well defined boundaries near the wrong regions.
>> Any idea to correct this?
>> 
>> 
>> Yang
>> 
>> 
>> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen  
>> wrote:
>> Hi Yang,
>> 
>> To edit the pial surface, you want to use brainmask.mgz.
>> 
>> As for the wm.mgz, you're right in that control points isn't the solution. 
>> Control points are to fix intensity problem, but you can also add wm voxels 
>> manually to fix any wm defects. In this case, adding that many control 
>> points would probably make the situation worse because the entire area will 
>> brighten and that would potentially extend the surfaces to include grey 
>> matter.
>> 
>> Is the area you pointed out by any chance the ventricle? If it is, then it 
>> doesn't matter that the white surface includes it. It's hard to tell with 
>> just this image. Do you mind sending a snapshot of the brainmask.mgz for 
>> this slice?
>> 
>> 
>> On Mon, 10 Jan 2011, Yang Liu wrote:
>> 
>> Hi Freesurferers,
>> 
>> I am correcting some defects in the white matter surface (yellow) and the
>> pial surfaces (red). But I am not very sure of which volume I should work
>> on.
>> I did several experiments on editing one volume at a time.
>> 
>> For pial (the red) surface, I edited brain.mgz first. I found it corrected
>> some pial defects.
>> However, I found one previous post here said the volume that should be
>> edited is brainmask.mgz.
>> So the second time I only changed brainmask.mgz. It also works.
>> 
>> So, which one should I work on?
>> 
>> brian.mgz or brainmask.mgz?
>> 
>> Also, for defects on the white matter surface (the yellow one),  I found the
>> surface doesn't follow the white matter segmentation closely, although I
>> have a good wm.mgz. (see attached image).
>> At the location pointed by the red arrow in the attached image, both the
>> green and yellow sufaces includes a lot of gray matter at the location. It
>> is strange that the wm.mgz has a very well defined slice in that
>> neighborhood.
>> I am familiar with situations where the surfaces miss a few white matter
>> pixels, for which I can add a few control points to improve it.
>> 
>> How shall I edit wm.mgz to correct this?  Adding more control points is not
>> a solution, apparently.
>> 
>> Thank you.
>> 
>> Yang
>> 
>> 
>> 
>> 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.
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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.


-- 
Sebastian Moeller

telephone: 626-807-5242 / 626-395-6523 / 626-395-6616
fax: 626-395-8826
German GSM:  0 15 77 - 1 90 31 41
US CDMA: + 1 - 626 - 807 - 5242
moel...@caltech.edu

Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA

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Re: [Freesurfer] which volume to edit?

[Yang Liu]

Hi Sebastian,

Yes. It is Macaque. There is no aseg.

Yang


On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <
sebastian.moell...@rwth-aachen.de> wrote:

> Hi All,
>
>
> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>
> > Does the aseg label that as ventricle?
>
> This pretty much looks like macaque data, so I think there is no
> aseg for that. I would love to be corrected on that point though.
>
> Best
>Sebastian
>
> >
> >
> >
> > On Jan 10, 2011, at 9:34 PM, Yang Liu  wrote:
> >
> >> Hi Khoa,
> >>
> >> Thanks for your reply.
> >> I attached the snapshot of the same slice with brainmask.mgz. You can
> see clearly that the green and yellow surface at the wrong regions. They
> doesn't look like  ventricles to me.
> >> It is strange that even the green surface doesn't follow the original
> wm.mgz, though the wm.mgz as attached in the previous email
> >> has very well defined boundaries near the wrong regions.
> >> Any idea to correct this?
> >>
> >>
> >> Yang
> >>
> >>
> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen 
> wrote:
> >> Hi Yang,
> >>
> >> To edit the pial surface, you want to use brainmask.mgz.
> >>
> >> As for the wm.mgz, you're right in that control points isn't the
> solution. Control points are to fix intensity problem, but you can also add
> wm voxels manually to fix any wm defects. In this case, adding that many
> control points would probably make the situation worse because the entire
> area will brighten and that would potentially extend the surfaces to include
> grey matter.
> >>
> >> Is the area you pointed out by any chance the ventricle? If it is, then
> it doesn't matter that the white surface includes it. It's hard to tell with
> just this image. Do you mind sending a snapshot of the brainmask.mgz for
> this slice?
> >>
> >>
> >> On Mon, 10 Jan 2011, Yang Liu wrote:
> >>
> >> Hi Freesurferers,
> >>
> >> I am correcting some defects in the white matter surface (yellow) and
> the
> >> pial surfaces (red). But I am not very sure of which volume I should
> work
> >> on.
> >> I did several experiments on editing one volume at a time.
> >>
> >> For pial (the red) surface, I edited brain.mgz first. I found it
> corrected
> >> some pial defects.
> >> However, I found one previous post here said the volume that should be
> >> edited is brainmask.mgz.
> >> So the second time I only changed brainmask.mgz. It also works.
> >>
> >> So, which one should I work on?
> >>
> >> brian.mgz or brainmask.mgz?
> >>
> >> Also, for defects on the white matter surface (the yellow one),  I found
> the
> >> surface doesn't follow the white matter segmentation closely, although I
> >> have a good wm.mgz. (see attached image).
> >> At the location pointed by the red arrow in the attached image, both the
> >> green and yellow sufaces includes a lot of gray matter at the location.
> It
> >> is strange that the wm.mgz has a very well defined slice in that
> >> neighborhood.
> >> I am familiar with situations where the surfaces miss a few white matter
> >> pixels, for which I can add a few control points to improve it.
> >>
> >> How shall I edit wm.mgz to correct this?  Adding more control points is
> not
> >> a solution, apparently.
> >>
> >> Thank you.
> >>
> >> Yang
> >>
> >>
> >>
> >> 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.
> >>
> >>
> >> 
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
>
>
> --
> Sebastian Moeller
>
> telephone: 626-807-5242 / 626-395-6523 / 626-395-6616
> fax: 626-395-8826
> German GSM:  0 15 77 - 1 90 31 41
> US CDMA: + 1 - 626 - 807 - 5242
> moel...@caltech.edu
>
> Division of Biology
> MC 114-96
> California Institute of Technology
> 1200 East California Boulevard
> CA 91125, Pasadena
> USA
>
>
___
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h

Re: [Freesurfer] which volume to edit?

[Bruce Fischl]

Then I must be a topologica defect 



On Jan 10, 2011, at 10:37 PM, Yang Liu  wrote:

> Hi Sebastian,
> 
> Yes. It is Macaque. There is no aseg.
> 
> Yang
> 
> 
> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller 
>  wrote:
> Hi All,
> 
> 
> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
> 
> > Does the aseg label that as ventricle?
> 
>This pretty much looks like macaque data, so I think there is no aseg 
> for that. I would love to be corrected on that point though.
> 
> Best
>Sebastian
> 
> >
> >
> >
> > On Jan 10, 2011, at 9:34 PM, Yang Liu  wrote:
> >
> >> Hi Khoa,
> >>
> >> Thanks for your reply.
> >> I attached the snapshot of the same slice with brainmask.mgz. You can see 
> >> clearly that the green and yellow surface at the wrong regions. They 
> >> doesn't look like  ventricles to me.
> >> It is strange that even the green surface doesn't follow the original 
> >> wm.mgz, though the wm.mgz as attached in the previous email
> >> has very well defined boundaries near the wrong regions.
> >> Any idea to correct this?
> >>
> >>
> >> Yang
> >>
> >>
> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen  
> >> wrote:
> >> Hi Yang,
> >>
> >> To edit the pial surface, you want to use brainmask.mgz.
> >>
> >> As for the wm.mgz, you're right in that control points isn't the solution. 
> >> Control points are to fix intensity problem, but you can also add wm 
> >> voxels manually to fix any wm defects. In this case, adding that many 
> >> control points would probably make the situation worse because the entire 
> >> area will brighten and that would potentially extend the surfaces to 
> >> include grey matter.
> >>
> >> Is the area you pointed out by any chance the ventricle? If it is, then it 
> >> doesn't matter that the white surface includes it. It's hard to tell with 
> >> just this image. Do you mind sending a snapshot of the brainmask.mgz for 
> >> this slice?
> >>
> >>
> >> On Mon, 10 Jan 2011, Yang Liu wrote:
> >>
> >> Hi Freesurferers,
> >>
> >> I am correcting some defects in the white matter surface (yellow) and the
> >> pial surfaces (red). But I am not very sure of which volume I should work
> >> on.
> >> I did several experiments on editing one volume at a time.
> >>
> >> For pial (the red) surface, I edited brain.mgz first. I found it corrected
> >> some pial defects.
> >> However, I found one previous post here said the volume that should be
> >> edited is brainmask.mgz.
> >> So the second time I only changed brainmask.mgz. It also works.
> >>
> >> So, which one should I work on?
> >>
> >> brian.mgz or brainmask.mgz?
> >>
> >> Also, for defects on the white matter surface (the yellow one),  I found 
> >> the
> >> surface doesn't follow the white matter segmentation closely, although I
> >> have a good wm.mgz. (see attached image).
> >> At the location pointed by the red arrow in the attached image, both the
> >> green and yellow sufaces includes a lot of gray matter at the location. It
> >> is strange that the wm.mgz has a very well defined slice in that
> >> neighborhood.
> >> I am familiar with situations where the surfaces miss a few white matter
> >> pixels, for which I can add a few control points to improve it.
> >>
> >> How shall I edit wm.mgz to correct this?  Adding more control points is not
> >> a solution, apparently.
> >>
> >> Thank you.
> >>
> >> Yang
> >>
> >>
> >>
> >> 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.
> >>
> >>
> >> 
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> 
> 
> --
> Sebastian Moeller
> 
> telephone: 626-807-5242 / 626-395-6523 / 626-395-6616
> fax: 626-395-8826
> German GSM:  0 15 77 - 1 90 31 41
> US CDMA: + 1 - 626 - 807 - 5242
> moel...@caltech.edu
> 
> Division of Biology
> MC 114-96
> California Institute of Technology
> 1200 East Calif

Re: [Freesurfer] which volume to edit?

[Yang Liu]

Hi Bruce,

Do you know how to fix it?

Yang

On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
wrote:

> Then I must be a topologica defect
>
>
>
> On Jan 10, 2011, at 10:37 PM, Yang Liu  wrote:
>
> Hi Sebastian,
>
> Yes. It is Macaque. There is no aseg.
>
> Yang
>
>
> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller 
> <
> sebastian.moell...@rwth-aachen.de> wrote:
>
>> Hi All,
>>
>>
>> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>>
>> > Does the aseg label that as ventricle?
>>
>> This pretty much looks like macaque data, so I think there is no
>> aseg for that. I would love to be corrected on that point though.
>>
>> Best
>>Sebastian
>>
>> >
>> >
>> >
>> > On Jan 10, 2011, at 9:34 PM, Yang Liu < 
>> liu.yan...@gmail.com> wrote:
>> >
>> >> Hi Khoa,
>> >>
>> >> Thanks for your reply.
>> >> I attached the snapshot of the same slice with brainmask.mgz. You can
>> see clearly that the green and yellow surface at the wrong regions. They
>> doesn't look like  ventricles to me.
>> >> It is strange that even the green surface doesn't follow the original
>> wm.mgz, though the wm.mgz as attached in the previous email
>> >> has very well defined boundaries near the wrong regions.
>> >> Any idea to correct this?
>> >>
>> >>
>> >> Yang
>> >>
>> >>
>> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <
>> k...@nmr.mgh.harvard.edu> wrote:
>> >> Hi Yang,
>> >>
>> >> To edit the pial surface, you want to use brainmask.mgz.
>> >>
>> >> As for the wm.mgz, you're right in that control points isn't the
>> solution. Control points are to fix intensity problem, but you can also add
>> wm voxels manually to fix any wm defects. In this case, adding that many
>> control points would probably make the situation worse because the entire
>> area will brighten and that would potentially extend the surfaces to include
>> grey matter.
>> >>
>> >> Is the area you pointed out by any chance the ventricle? If it is, then
>> it doesn't matter that the white surface includes it. It's hard to tell with
>> just this image. Do you mind sending a snapshot of the brainmask.mgz for
>> this slice?
>> >>
>> >>
>> >> On Mon, 10 Jan 2011, Yang Liu wrote:
>> >>
>> >> Hi Freesurferers,
>> >>
>> >> I am correcting some defects in the white matter surface (yellow) and
>> the
>> >> pial surfaces (red). But I am not very sure of which volume I should
>> work
>> >> on.
>> >> I did several experiments on editing one volume at a time.
>> >>
>> >> For pial (the red) surface, I edited brain.mgz first. I found it
>> corrected
>> >> some pial defects.
>> >> However, I found one previous post here said the volume that should be
>> >> edited is brainmask.mgz.
>> >> So the second time I only changed brainmask.mgz. It also works.
>> >>
>> >> So, which one should I work on?
>> >>
>> >> brian.mgz or brainmask.mgz?
>> >>
>> >> Also, for defects on the white matter surface (the yellow one),  I
>> found the
>> >> surface doesn't follow the white matter segmentation closely, although
>> I
>> >> have a good wm.mgz. (see attached image).
>> >> At the location pointed by the red arrow in the attached image, both
>> the
>> >> green and yellow sufaces includes a lot of gray matter at the location.
>> It
>> >> is strange that the wm.mgz has a very well defined slice in that
>> >> neighborhood.
>> >> I am familiar with situations where the surfaces miss a few white
>> matter
>> >> pixels, for which I can add a few control points to improve it.
>> >>
>> >> How shall I edit wm.mgz to correct this?  Adding more control points is
>> not
>> >> a solution, apparently.
>> >>
>> >> Thank you.
>> >>
>> >> Yang
>> >>
>> >>
>> >>
>> >> 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.
>> >>
>> >>
>> >> 
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > 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.par

Re: [Freesurfer] which volume to edit?

[Bruce Fischl]

Not without scrolling through the wm volume. You will need to edit it. Have you 
done the troubleshooting tutorial?



On Jan 10, 2011, at 10:48 PM, Yang Liu  wrote:

> Hi Bruce,
> 
> Do you know how to fix it?
> 
> Yang
> 
> On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl  
> wrote:
> Then I must be a topologica defect 
> 
> 
> 
> On Jan 10, 2011, at 10:37 PM, Yang Liu  wrote:
> 
>> Hi Sebastian,
>> 
>> Yes. It is Macaque. There is no aseg.
>> 
>> Yang
>> 
>> 
>> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller 
>>  wrote:
>> Hi All,
>> 
>> 
>> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>> 
>> > Does the aseg label that as ventricle?
>> 
>>This pretty much looks like macaque data, so I think there is no aseg 
>> for that. I would love to be corrected on that point though.
>> 
>> Best
>>Sebastian
>> 
>> >
>> >
>> >
>> > On Jan 10, 2011, at 9:34 PM, Yang Liu  wrote:
>> >
>> >> Hi Khoa,
>> >>
>> >> Thanks for your reply.
>> >> I attached the snapshot of the same slice with brainmask.mgz. You can see 
>> >> clearly that the green and yellow surface at the wrong regions. They 
>> >> doesn't look like  ventricles to me.
>> >> It is strange that even the green surface doesn't follow the original 
>> >> wm.mgz, though the wm.mgz as attached in the previous email
>> >> has very well defined boundaries near the wrong regions.
>> >> Any idea to correct this?
>> >>
>> >>
>> >> Yang
>> >>
>> >>
>> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen  
>> >> wrote:
>> >> Hi Yang,
>> >>
>> >> To edit the pial surface, you want to use brainmask.mgz.
>> >>
>> >> As for the wm.mgz, you're right in that control points isn't the 
>> >> solution. Control points are to fix intensity problem, but you can also 
>> >> add wm voxels manually to fix any wm defects. In this case, adding that 
>> >> many control points would probably make the situation worse because the 
>> >> entire area will brighten and that would potentially extend the surfaces 
>> >> to include grey matter.
>> >>
>> >> Is the area you pointed out by any chance the ventricle? If it is, then 
>> >> it doesn't matter that the white surface includes it. It's hard to tell 
>> >> with just this image. Do you mind sending a snapshot of the brainmask.mgz 
>> >> for this slice?
>> >>
>> >>
>> >> On Mon, 10 Jan 2011, Yang Liu wrote:
>> >>
>> >> Hi Freesurferers,
>> >>
>> >> I am correcting some defects in the white matter surface (yellow) and the
>> >> pial surfaces (red). But I am not very sure of which volume I should work
>> >> on.
>> >> I did several experiments on editing one volume at a time.
>> >>
>> >> For pial (the red) surface, I edited brain.mgz first. I found it corrected
>> >> some pial defects.
>> >> However, I found one previous post here said the volume that should be
>> >> edited is brainmask.mgz.
>> >> So the second time I only changed brainmask.mgz. It also works.
>> >>
>> >> So, which one should I work on?
>> >>
>> >> brian.mgz or brainmask.mgz?
>> >>
>> >> Also, for defects on the white matter surface (the yellow one),  I found 
>> >> the
>> >> surface doesn't follow the white matter segmentation closely, although I
>> >> have a good wm.mgz. (see attached image).
>> >> At the location pointed by the red arrow in the attached image, both the
>> >> green and yellow sufaces includes a lot of gray matter at the location. It
>> >> is strange that the wm.mgz has a very well defined slice in that
>> >> neighborhood.
>> >> I am familiar with situations where the surfaces miss a few white matter
>> >> pixels, for which I can add a few control points to improve it.
>> >>
>> >> How shall I edit wm.mgz to correct this?  Adding more control points is 
>> >> not
>> >> a solution, apparently.
>> >>
>> >> Thank you.
>> >>
>> >> Yang
>> >>
>> >>
>> >>
>> >> 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.
>> >>
>> >>
>> >> 
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > 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 w

Re: [Freesurfer] which volume to edit?

[khoa]

Hi Yang,

Are the slices before and after this slice the same as this one?

> Hi Bruce,
>
> Do you know how to fix it?
>
> Yang
>
> On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
> wrote:
>
>> Then I must be a topologica defect
>>
>>
>>
>> On Jan 10, 2011, at 10:37 PM, Yang Liu  wrote:
>>
>> Hi Sebastian,
>>
>> Yes. It is Macaque. There is no aseg.
>>
>> Yang
>>
>>
>> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller
>> <
>> sebastian.moell...@rwth-aachen.de> wrote:
>>
>>> Hi All,
>>>
>>>
>>> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>>>
>>> > Does the aseg label that as ventricle?
>>>
>>> This pretty much looks like macaque data, so I think there is
>>> no
>>> aseg for that. I would love to be corrected on that point though.
>>>
>>> Best
>>>Sebastian
>>>
>>> >
>>> >
>>> >
>>> > On Jan 10, 2011, at 9:34 PM, Yang Liu < 
>>> liu.yan...@gmail.com> wrote:
>>> >
>>> >> Hi Khoa,
>>> >>
>>> >> Thanks for your reply.
>>> >> I attached the snapshot of the same slice with brainmask.mgz. You
>>> can
>>> see clearly that the green and yellow surface at the wrong regions.
>>> They
>>> doesn't look like  ventricles to me.
>>> >> It is strange that even the green surface doesn't follow the
>>> original
>>> wm.mgz, though the wm.mgz as attached in the previous email
>>> >> has very well defined boundaries near the wrong regions.
>>> >> Any idea to correct this?
>>> >>
>>> >>
>>> >> Yang
>>> >>
>>> >>
>>> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen
>>> <
>>> k...@nmr.mgh.harvard.edu> wrote:
>>> >> Hi Yang,
>>> >>
>>> >> To edit the pial surface, you want to use brainmask.mgz.
>>> >>
>>> >> As for the wm.mgz, you're right in that control points isn't the
>>> solution. Control points are to fix intensity problem, but you can also
>>> add
>>> wm voxels manually to fix any wm defects. In this case, adding that
>>> many
>>> control points would probably make the situation worse because the
>>> entire
>>> area will brighten and that would potentially extend the surfaces to
>>> include
>>> grey matter.
>>> >>
>>> >> Is the area you pointed out by any chance the ventricle? If it is,
>>> then
>>> it doesn't matter that the white surface includes it. It's hard to tell
>>> with
>>> just this image. Do you mind sending a snapshot of the brainmask.mgz
>>> for
>>> this slice?
>>> >>
>>> >>
>>> >> On Mon, 10 Jan 2011, Yang Liu wrote:
>>> >>
>>> >> Hi Freesurferers,
>>> >>
>>> >> I am correcting some defects in the white matter surface (yellow)
>>> and
>>> the
>>> >> pial surfaces (red). But I am not very sure of which volume I should
>>> work
>>> >> on.
>>> >> I did several experiments on editing one volume at a time.
>>> >>
>>> >> For pial (the red) surface, I edited brain.mgz first. I found it
>>> corrected
>>> >> some pial defects.
>>> >> However, I found one previous post here said the volume that should
>>> be
>>> >> edited is brainmask.mgz.
>>> >> So the second time I only changed brainmask.mgz. It also works.
>>> >>
>>> >> So, which one should I work on?
>>> >>
>>> >> brian.mgz or brainmask.mgz?
>>> >>
>>> >> Also, for defects on the white matter surface (the yellow one),  I
>>> found the
>>> >> surface doesn't follow the white matter segmentation closely,
>>> although
>>> I
>>> >> have a good wm.mgz. (see attached image).
>>> >> At the location pointed by the red arrow in the attached image, both
>>> the
>>> >> green and yellow sufaces includes a lot of gray matter at the
>>> location.
>>> It
>>> >> is strange that the wm.mgz has a very well defined slice in that
>>> >> neighborhood.
>>> >> I am familiar with situations where the surfaces miss a few white
>>> matter
>>> >> pixels, for which I can add a few control points to improve it.
>>> >>
>>> >> How shall I edit wm.mgz to correct this?  Adding more control points
>>> is
>>> not
>>> >> a solution, apparently.
>>> >>
>>> >> Thank you.
>>> >>
>>> >> Yang
>>> >>
>>> >>
>>> >>
>>> >> 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.
>>> >>
>>> >>
>>> >> 
>>> >> ___
>>> >> Freesurfer mailing list
>>> >> Freesurfer@nmr.mgh.harvard.edu
>>> >> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> > 

Re: [Freesurfer] which volume to edit?

[Yang Liu]

Hi Bruce,

I followed the tutorial at
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.

But I couldn't find similar examples as mine in the tutorial.
I don't really understand why don't the yellow and green surfaces follow the
boundary of wm.mgz, especially the boundary is well defined in the slices.


Yang


On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl
wrote:

> Not without scrolling through the wm volume. You will need to edit it. Have
> you done the troubleshooting tutorial?
>
>
>
> On Jan 10, 2011, at 10:48 PM, Yang Liu  wrote:
>
> Hi Bruce,
>
> Do you know how to fix it?
>
> Yang
>
> On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
>
>> Then I must be a topologica defect
>>
>>
>>
>> On Jan 10, 2011, at 10:37 PM, Yang Liu < 
>> liu.yan...@gmail.com> wrote:
>>
>> Hi Sebastian,
>>
>> Yes. It is Macaque. There is no aseg.
>>
>> Yang
>>
>>
>> On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller 
>> <
>> sebastian.moell...@rwth-aachen.de> wrote:
>>
>>> Hi All,
>>>
>>>
>>> On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
>>>
>>> > Does the aseg label that as ventricle?
>>>
>>> This pretty much looks like macaque data, so I think there is no
>>> aseg for that. I would love to be corrected on that point though.
>>>
>>> Best
>>>Sebastian
>>>
>>> >
>>> >
>>> >
>>> > On Jan 10, 2011, at 9:34 PM, Yang Liu < 
>>> > 
>>> liu.yan...@gmail.com> wrote:
>>> >
>>> >> Hi Khoa,
>>> >>
>>> >> Thanks for your reply.
>>> >> I attached the snapshot of the same slice with brainmask.mgz. You can
>>> see clearly that the green and yellow surface at the wrong regions. They
>>> doesn't look like  ventricles to me.
>>> >> It is strange that even the green surface doesn't follow the original
>>> wm.mgz, though the wm.mgz as attached in the previous email
>>> >> has very well defined boundaries near the wrong regions.
>>> >> Any idea to correct this?
>>> >>
>>> >>
>>> >> Yang
>>> >>
>>> >>
>>> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen 
>>> >> <
>>> k...@nmr.mgh.harvard.edu> wrote:
>>> >> Hi Yang,
>>> >>
>>> >> To edit the pial surface, you want to use brainmask.mgz.
>>> >>
>>> >> As for the wm.mgz, you're right in that control points isn't the
>>> solution. Control points are to fix intensity problem, but you can also add
>>> wm voxels manually to fix any wm defects. In this case, adding that many
>>> control points would probably make the situation worse because the entire
>>> area will brighten and that would potentially extend the surfaces to include
>>> grey matter.
>>> >>
>>> >> Is the area you pointed out by any chance the ventricle? If it is,
>>> then it doesn't matter that the white surface includes it. It's hard to tell
>>> with just this image. Do you mind sending a snapshot of the brainmask.mgz
>>> for this slice?
>>> >>
>>> >>
>>> >> On Mon, 10 Jan 2011, Yang Liu wrote:
>>> >>
>>> >> Hi Freesurferers,
>>> >>
>>> >> I am correcting some defects in the white matter surface (yellow) and
>>> the
>>> >> pial surfaces (red). But I am not very sure of which volume I should
>>> work
>>> >> on.
>>> >> I did several experiments on editing one volume at a time.
>>> >>
>>> >> For pial (the red) surface, I edited brain.mgz first. I found it
>>> corrected
>>> >> some pial defects.
>>> >> However, I found one previous post here said the volume that should be
>>> >> edited is brainmask.mgz.
>>> >> So the second time I only changed brainmask.mgz. It also works.
>>> >>
>>> >> So, which one should I work on?
>>> >>
>>> >> brian.mgz or brainmask.mgz?
>>> >>
>>> >> Also, for defects on the white matter surface (the yellow one),  I
>>> found the
>>> >> surface doesn't follow the white matter segmentation closely, although
>>> I
>>> >> have a good wm.mgz. (see attached image).
>>> >> At the location pointed by the red arrow in the attached image, both
>>> the
>>> >> green and yellow sufaces includes a lot of gray matter at the
>>> location. It
>>> >> is strange that the wm.mgz has a very well defined slice in that
>>> >> neighborhood.
>>> >> I am familiar with situations where the surfaces miss a few white
>>> matter
>>> >> pixels, for which I can add a few control points to improve it.
>>> >>
>>> >> How shall I edit wm.mgz to correct this?  Adding more control points
>>> is not
>>> >> a solution, apparently.
>>> >>
>>> >> Thank you.
>>> >>
>>> >> Yang
>>> >>
>>> >>
>>> >>
>>> >> 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] Freesurfer Digest, Vol 83, Issue 19

[Bevil R. Conway]

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not
have access to email.  For issues concerning my laboratory, please contact
my lab manager, Rosa Lafer-Sousa (rlafe...@wellesley.edu). 

Thank-you and I'll be in touch when I get back.  

Bevil

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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.