Re: [Freesurfer] CSF calculation

[Bruce Fischl]

Hi Anthony,

we compute ventricular CSF but not sulcal CSF (which you can't really see 
in a T1-weighted image).


cheers,
Bruce
On Tue, 2 Dec 2008, Anthony wrote:


Dear all,

Is there anyway to calculate CSF volume using freesurfer? I only know 
freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats .

Thanks,
Anthony



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[Freesurfer] CSF calculation

[Anthony]

Dear all, 

Is there anyway to calculate CSF volume using freesurfer? I only know 
freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats . 

Thanks,
Anthony



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[Freesurfer] comparing hemispheres

[CARL]

Hi Frederic,

To amplify, are you are talking about vertex by vertex analyses in the
context of between group comparisons?  As Doug says, the optimal tools are
not there yet.

As you know, you can always drop the threshold on the other side and see
if activations/thickness blobs emerge in the same areas on the
contralateral side though this is not a formal statistical test of
laterality.

Of course there are the other simpler  approaches if you are not talking
vertex by vertex.  — If you have a result based on an mean thickness or
fMRI activation in an aprior cortical parcellation (say, parsorbitalis) or
an amalgam of such parcellations, then you are free to compare this with
mean value from the same area in contralateral hemisphere, and formally
test for a laterality interaction using a repeated measures GLM.

But depending on what you want to do, even with vertex by vertex data
there are some ways to interrogate your data more formally for laterality
effects.  Suppose you have a label/subregion/blub in one hemisphere (could
be functional or structural) and you want to test formally for laterality
( formal two way interaction with side).  You could draw by hand the
mirror image of the blob in the other hemisphere either by anatomical
landmarks or perhaps better, by recording the min and max tal coordinates
in x,y,z (and some additional control points) for the hemisphere where you
have your activation, flipping the sign of the x coordinate, and then
marking the vertex in the other hemisphere that corresponds to the flipped
tal coordinate.  Then make a label of the mirror image blob, extract mean
signal for each subject within boundries of said blob, AND run a glm  on
this with dx, gender or whatever else you are interested in.  Notice if
you do this, you are not biased in the same way you would be if you ran
your test statistics based on individual subjects values extracted form
the original hemisphere blob which would be circular. And I don’t think,
but you can check with Doug, that you are biased if you included a term
for side and compare the original label with the mirror label as a
repeated within subject factor, as long as you are not using the outcome
of the  analysis to test for the significance of the between group
difference in the original hemisphere (which you KNOW HAS to be
significant because that’s how you defined the original label).  But that
bias would seem to be absent for the contralateral label.

Carl


-- 
Carl E. Schwartz, M.D.
Harvard Medical School
Director, Developmental Neuroimaging & Psychopathology Laboratory
Psychiatric Neuroscience Program
Massachusetts General Hospital
tel 617-726-8965
fax 617-726-4078


On 12/2/08 11:19 AM, "Doug Greve" <[EMAIL PROTECTED]> wrote:

We don't have a good way to do this yet. I've have been working on one
but have dropped the ball. Some people will analyzed both the
correctly-oriented data and left-right reversed for each subject, but
this is not the best way to do it.

doug

Fr?ede?ric Andersson wrote:

> Hi,
>
> Is there any way to compare left vs right hemisphere (surface morpho.
> and functional data). I mean, is there any function to flip one
> hemisphere in order to compare it with the other one?
>
> Thanks,
>
> Frederic Andersson
>
>
> ___
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>

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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422

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RE: [Freesurfer] Possible to constrain FDR to a label in the volume?

[Dan Dillon]

Hi Doug. Yup, the FDR button is working for me in tkmedit. I see the mask to
brain, but as you can probably guess I'm interested in masking to the basal
ganglia.

 

DD

 

From: Doug Greve [mailto:[EMAIL PROTECTED] 
Sent: Tuesday, December 02, 2008 12:04 PM
To: Dan Dillon
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Possible to constrain FDR to a label in the
volume?

 

Yea, there's not a mask to label. There is a mask to brain, but I'm not sure
if you can substitute your own mask for it. I just tried to run it, and
could not get FDR to work at all in tkmedit. Is it working for you at all?

doug

Dan Dillon wrote: 

Dear FreeSurfers,

 

I've created a basal ganglia label and am wondering if it's possible to
constrain the FDR calculation to that label? Based on earlier messages it
seems like tksurfer has a "marked label only" option for FDR, but I haven't
been able to find something similar in tkmedit. Any help greatly
appreciated.

 

Thanks!

 

Dan Dillon, Ph.D.

Post-doctoral Fellow

Affective Neuroscience Lab

Dept. of Psychology, Harvard University

Phone: (617) 495-1889

E-mail: [EMAIL PROTECTED]

 



  _  



 
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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422
 
In order to help us help you, please follow the steps in:
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Re: [Freesurfer] Possible to constrain FDR to a label in the volume?

[Doug Greve]

Yea, there's not a mask to label. There is a mask to brain, but I'm not 
sure if you can substitute your own mask for it. I just tried to run it, 
and could not get FDR to work at all in tkmedit. Is it working for you 
at all?


doug

Dan Dillon wrote:


Dear FreeSurfers,

 

I've created a basal ganglia label and am wondering if it's possible 
to constrain the FDR calculation to that label? Based on earlier 
messages it seems like tksurfer has a "marked label only" option for 
FDR, but I haven't been able to find something similar in tkmedit. Any 
help greatly appreciated.


 


Thanks!

 


Dan Dillon, Ph.D.

Post-doctoral Fellow

Affective Neuroscience Lab

Dept. of Psychology, Harvard University

Phone: (617) 495-1889

E-mail: [EMAIL PROTECTED] 



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


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Re: [Freesurfer] Error with motion-correction session(ms-sess)

[Doug Greve]

Looks like matlab is having trouble running from the shell. I have no 
idea what causes this, you may have to ask your system administrator for 
help.


doug

 wrote:


Hi, Mr or Ms

My name is Kenta in Japan. I'm undergraduate student.
Please help me!
I've tried some things to solve the error with mc-sess.
But I could not solve this error.

The mc-sess processing didn't completely run and  following message 
showed up.


I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5.
If you want some information about this error or another things, let 
me know.


==
->> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2008-12-02 
20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- 
can't fully enable headless mode.

==

Yours sincerely.

Kenta



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


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Re: [Freesurfer] Using qdec to compare groups of twins?

[Doug Greve]

Do you just want to do a paired analysis? Do you want to include other 
covariates?


Burmicz, Ryzarda wrote:



Hello,

Could you please advise as to whether or not the following analysis is 
suitable?


I would like to compare groups of monozygotic twins (MZ concordant vs. 
MZ control ; MZ discordant affected twin vs. unaffected twin) using 
qdec. This is not as straightforward as group comparisons usually are 
because I cannot make the assumption of all data being independent as 
twin pairs are, obviously, related to one another.


To get around this issue I have started a qdec analysis and added a 
category 'pair' in which twin pairs share a category as follows 
(qdec.table.dat), in order to indicate that they have shared genetic 
and environmental influence:


subject no
subjid  pairdiagnosis   age gender
1   a   MZ_Discord_Well ... ...
2   a   MZ_Discord_Ill 
3   b   MZ_Discord_Ill 
4   b   MZ_Discord_Well
5   c   MZ_Discord_Well
6   c   MZ_Discord_Ill 
7   h   MZ_Discord_Well
8   h   MZ_Discord_Ill 
9   l   MZ_Discord_Well
10  l   MZ_Discord_Ill 
11  m   MZ_Discord_Well
12  m   MZ_Discord_Ill 
13  n   MZ_Discord_Well
14  n   MZ_Discord_Ill 
15  p   MZ_Discord_Well
16  p   MZ_Discord_Ill 
17  s   MZ_Discord_Well
18  s   MZ_Discord_Ill 
19  t   MZ_Discord_Well
20  t   MZ_Discord_Ill 


I would appreciate if you could suggest a more robust way around this.

Many thanks,

Rysia



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


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Re: [Freesurfer] How to compare left vs right hemi (flip RL)

[Doug Greve]

We don't have a good way to do this yet. I've have been working on one 
but have dropped the ball. Some people will analyzed both the 
correctly-oriented data and left-right reversed for each subject, but 
this is not the best way to do it.


doug

FrŽedeŽric Andersson wrote:


Hi,

Is there any way to compare left vs right hemisphere (surface morpho. 
and functional data). I mean, is there any function to flip one 
hemisphere in order to compare it with the other one?


Thanks,

Frederic Andersson


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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


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surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] question on tksurfer tcl

[Doug Greve]

try just running tksurfer with the -label-outline option.

j janssen wrote:


Hi,

using version 4.0.5

my goal: to display in tksurfer an inflated brain with curvature and 
an *outlined* label, using a tcl-script.


there are probably numerous ways, i did:

 tksurfer "subject" rh inflated -gray -tcl tksurf.tcl

where tksurf.tcl contains:

make_lateral_view
rotate_brain_x -90
redraw
labl_load "label-file"
set gaLinkedVars(redrawlockflag) 0
SendLinkedVarGroup redrawlock
set gaLinkedVars(labelstyle) 1
SendLinkedVarGroup view
save_tiff "tiff_file.tiff"

all works except for the label to be outlined. any suggestions?

thanks!
-joost



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
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Re: [Freesurfer] Rerunning previously edited subjects on 4.10, no fill.

[Bruce Fischl]

Hi Inge,

what does the aseg look like? Are the ventricles and caudate properly 
labeled in both versions?


Bruce


On Tue, 2 Dec 
2008, Inge K. Amlien wrote:



Hi list!
I am experiencing a problem when reprocessing 70-something previously
edited (FS 4.05) subjects on FS version 4.10. It seems fill fails, but no
errors are returned. I cannot find anything in the logs either.
The problem is not present when starting over fresh and processing from
dicoms, at least for the one subject I tried.

Any tips on what to try appreciated!

See attached images, it is the same subject, the same slice, version 4.10
on the left, 4.05 on the right.

FREESURFER_HOME: /psyklab/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
RedHat release: CentOS release 5 (Final)
Kernel info: Linux 2.6.18-53.1.6.el5.centos.plus x86_64
recon-all -all -s $id

Have a nice day
Inge Amlien
Center for the Study of Human Cognition
University of Oslo
Norway

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Re: [Freesurfer] recon-all rerun

[Allison Stevens]

recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they 
should be the same.

Allison

On Tue, 2 Dec 2008, Barkay, Gavriel wrote:


Hi,
I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the 
analysis without -clean.
Is the new skull stripped volume stored in brainmask.auto.mgz instead of 
brainmask.mgz?
Thanks,
Gabi



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[Freesurfer] Error with motion-correction session(ms-sess)

[卯野賢太]

Hi, Mr or Ms

My name is Kenta in Japan. I'm undergraduate student.
Please help me!
I've tried some things to solve the error with mc-sess.
But I could not solve this error.

The mc-sess processing didn't completely run and  following message showed
up.

I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5.
If you want some information about this error or another things, let me
know.

==
->> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2008-12-02
20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- can't
fully enable headless mode.
==

Yours sincerely.

Kenta
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Re: [Freesurfer] question on tksurfer tcl

[Bruce Fischl]

try adding:

set labelstyle 1

On Tue, 2 Dec 2008, j janssen wrote:


Hi,

using version 4.0.5

my goal: to display in tksurfer an inflated brain with curvature and an
*outlined* label, using a tcl-script.

there are probably numerous ways, i did:

tksurfer "subject" rh inflated -gray -tcl tksurf.tcl

where tksurf.tcl contains:

make_lateral_view
rotate_brain_x -90
redraw
labl_load "label-file"
set gaLinkedVars(redrawlockflag) 0
SendLinkedVarGroup redrawlock
set gaLinkedVars(labelstyle) 1
SendLinkedVarGroup view
save_tiff "tiff_file.tiff"

all works except for the label to be outlined. any suggestions?

thanks!
-joost


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[Freesurfer] question on tksurfer tcl

[j janssen]

Hi,

using version 4.0.5

my goal: to display in tksurfer an inflated brain with curvature and an
*outlined* label, using a tcl-script.

there are probably numerous ways, i did:

 tksurfer "subject" rh inflated -gray -tcl tksurf.tcl

where tksurf.tcl contains:

make_lateral_view
rotate_brain_x -90
redraw
labl_load "label-file"
set gaLinkedVars(redrawlockflag) 0
SendLinkedVarGroup redrawlock
set gaLinkedVars(labelstyle) 1
SendLinkedVarGroup view
save_tiff "tiff_file.tiff"

all works except for the label to be outlined. any suggestions?

thanks!
-joost
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[Freesurfer] Using qdec to compare groups of twins?

[Burmicz, Ryzarda]

Hello,

Could you please advise as to whether or not the following analysis is suitable?

I would like to compare groups of monozygotic twins (MZ concordant vs. MZ 
control ; MZ discordant affected twin vs. unaffected twin) using qdec. This is 
not as straightforward as group comparisons usually are because I cannot make 
the assumption of all data being independent as twin pairs are, obviously, 
related to one another. 

To get around this issue I have started a qdec analysis and added a category 
'pair' in which twin pairs share a category as follows (qdec.table.dat), in 
order to indicate that they have shared genetic and environmental influence:

subject no
subjid  pairdiagnosis   age gender
1   a   MZ_Discord_Well ... ...
2   a   MZ_Discord_Ill  
3   b   MZ_Discord_Ill  
4   b   MZ_Discord_Well 
5   c   MZ_Discord_Well 
6   c   MZ_Discord_Ill  
7   h   MZ_Discord_Well 
8   h   MZ_Discord_Ill  
9   l   MZ_Discord_Well 
10  l   MZ_Discord_Ill  
11  m   MZ_Discord_Well 
12  m   MZ_Discord_Ill  
13  n   MZ_Discord_Well 
14  n   MZ_Discord_Ill  
15  p   MZ_Discord_Well 
16  p   MZ_Discord_Ill  
17  s   MZ_Discord_Well 
18  s   MZ_Discord_Ill  
19  t   MZ_Discord_Well 
20  t   MZ_Discord_Ill  

I would appreciate if you could suggest a more robust way around this.

Many thanks,

Rysia
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[Freesurfer] How to compare left vs right hemi (flip RL)

[FrŽedeŽric Andersson]

Hi,

Is there any way to compare left vs right hemisphere (surface morpho. and 
functional data). I mean, is there any function to flip one hemisphere in order 
to compare it with the other one?

Thanks,

Frederic Andersson


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