[Freesurfer] cortical parcellation in anterior cingulate region

[Marie Schaer]

Hello everybody,

Regarding the troubles raised in the mailing list and on the release  
notes about the anterior cingulate being misclassified with  
curvature.buckner40.filled.desikan_killiany, I would like to know if  
you have any updated version of the atlas available?
In my subjects, most of the anterior cingulate cortex is found in the  
frontal superior parcell. Alternatively, do I need to create my own  
atlas?


Many thanks for your response,

Marie

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[Freesurfer] (no subject)

[duhanjian]

hi, when I run the qdec & command, the error show as below:[EMAIL 
PROTECTED]:~> qdec &[1] 10941[EMAIL PROTECTED]:~> 
qdec.bin: error while loading shared libraries: libexpat.so.0: cannot 
open shared object file: No such file or directory I do't 
know  how to deal with this problem. Could you tell me how to resolve 
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Re: [Freesurfer] cortical parcellation in anterior cingulate region

[Bruce Fischl]

Hi Marie,

not quite yet, but we're close. I thought the problem was with the 
callosum and the cingulate, no? Rahul: do you know?


cheers,
Bruce


On Mon, 25 Jun 2007, Marie Schaer wrote:



Hello everybody,

Regarding the troubles raised in the mailing list and on the release notes 
about the anterior cingulate being misclassified with 
curvature.buckner40.filled.desikan_killiany, I would like to know if you have 
any updated version of the atlas available?
In my subjects, most of the anterior cingulate cortex is found in the frontal 
superior parcell. Alternatively, do I need to create my own atlas?


Many thanks for your response,

Marie



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Re: [Freesurfer] cortical parcellation in anterior cingulate region

[Bruce Fischl]

wow, that's awful. I don't think we usually see it be this bad. If you post 
this subject on our website we'll take a look


On Mon, 25 
Jun 2007, Marie Schaer wrote:



Hello Bruce & Rahul,

Indeed in my sample of subjects it's more the corpus callosum directly with 
the frontal superior, and the rostral cingulate becomes lost under the corpus 
callosum. I attached the image of my average subject, but each single subject 
looks pretty similar in that region.


Many thanks,

Marie



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[Freesurfer] long delay before tksurfer launches

[Robert Levy]

Hello,

Apologies for cross-posting (this list and martinos-tech), but I think 
that by posting here I might be able to reach a few more people who may 
have had the problem before and solved it.


I have been experiencing very long load-up times, when running 
tksurfer.  It can take up to 6 or 7 minutes to load.  As far as I can 
tell, the application does not have any unusual or slow behaviors once 
it finally launches.  The problem was not present until Friday, but has 
persisted since, and I run it the same now as I did before. 

Paul Raines mentioned on martinos-tech that there used to be a problem 
where the SUBJECTS_DIR was searched recursively and it would slow down 
the loading times for a comparable length of time.  Can anyone confirm 
that this is still what tksurfer does?   When I run it, I source the 
latest development version.


If the problem is not the long search and file checks, then what could 
be the source of the delay?


The command is: tksurfer average7 lh inflated
The output is normal and I'm running it from 
/space/ventzl/1/users/SUBJECTS_DIR/

This is the tksurfer  /usr/local/freesurfer/dev/bin/tksurfer

The initial output is:
surfer: current subjects dir: /space/ventzl/1/users/SUBJECTS_DIR
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /autofs/space/ventzl_001/users/SUBJECTS_DIR

Then it hangs for 6 minutes or longer, and launches the tk gui.

When I strace it, there is trace information to show initially, and then 
there is the text output I mentioned above, but during the waiting 
period there is no output from strace at all. 


Thanks in advance,
Rob
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Re: [Freesurfer] long delay before tksurfer launches

[Kevin Teich]

strace shows you the system calls being made by the program. When it's
hanging for a long time, note the last few lines of output from strace
and let us know what those are. The last one will be the call that is
taking so long to finish.


On Mon, Jun 25, 2007 at 11:56:00AM -0400, Robert Levy wrote:
> Hello,
> 
> Apologies for cross-posting (this list and martinos-tech), but I think 
> that by posting here I might be able to reach a few more people who may 
> have had the problem before and solved it.
> 
> I have been experiencing very long load-up times, when running 
> tksurfer.  It can take up to 6 or 7 minutes to load.  As far as I can 
> tell, the application does not have any unusual or slow behaviors once 
> it finally launches.  The problem was not present until Friday, but has 
> persisted since, and I run it the same now as I did before. 
> 
> Paul Raines mentioned on martinos-tech that there used to be a problem 
> where the SUBJECTS_DIR was searched recursively and it would slow down 
> the loading times for a comparable length of time.  Can anyone confirm 
> that this is still what tksurfer does?   When I run it, I source the 
> latest development version.
> 
> If the problem is not the long search and file checks, then what could 
> be the source of the delay?
> 
> The command is: tksurfer average7 lh inflated
> The output is normal and I'm running it from 
> /space/ventzl/1/users/SUBJECTS_DIR/
> This is the tksurfer  /usr/local/freesurfer/dev/bin/tksurfer
> 
> The initial output is:
> surfer: current subjects dir: /space/ventzl/1/users/SUBJECTS_DIR
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /autofs/space/ventzl_001/users/SUBJECTS_DIR
> 
> Then it hangs for 6 minutes or longer, and launches the tk gui.
> 
> When I strace it, there is trace information to show initially, and then 
> there is the text output I mentioned above, but during the waiting 
> period there is no output from strace at all. 
> 
> Thanks in advance,
> Rob

-- 
Kevin Teich
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[Freesurfer] Re: long delay before tksurfer launches

[Help Desk -- Paul Raines]

Try again with 'strace -f -F tksurfer ...' to make sure forks are
followed.

--
---
Paul Rainesemail: raines at nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street Charlestown, MA 02129USA


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[Freesurfer] FS-FAST: missing time frame & time labeling of FIR analyses

[raij]

Hi,

I have done a FIR analysis of event-related data where my time window is
16 TR:s long, consisting of 2 pre-stimulus time frames plus 14
post-stimulus time frames. I view the results with tksurfer.

If I load the results from the h-lh.bhdr file, I have all 16 time frames
(0-15) which is as it should be.

However, if I load one of the contrast stat maps (e.g., cespct-lh.bhdr) I
only have 13 time frames (0-12). I should expect 14 time frames (as the
two pre-stimulus time frames are not supposed to show up). I therefore
have one time frame missing, and I do not know if my time scale is off by
one frame or if the last frame is missing.

So, which time frame is it that the cepct-lh.bhdr is missing - the 3rd or
the 16th?

Thanks,

Tommi

---
Tommi Raij, M.D., Ph.D.
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.
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Re: [Freesurfer] Segmentation

[Bruce Fischl]

Hi Antonio,

I wouldn't use the wm.mgz for much of anything. It's really just an 
intermediate step in the creation of the surfaces. In general we trust the 
?h.white and ?h.pial surfaces first, then the aseg.mgz for things like 
hippocampus, ventricles, etc...


Bruce


On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:


Hi All,

Upon reviewing subortical segmentations I see that often a mismatch
exists between what appears on the wm.mgz and the color-coded segmented
maps.

Precisely - as an example - in the attached figure you can see that in
the case of left insula WM, part of the tissue was classified as GM (in
brown) in the color-coded segmented map and as WM in the wm.mgz.
Contrariwise, the right temporal-parietal GM cortex part of the tissue
is classified as WM (in green) the color-coded segmented map and as
non-WM in the wm.mgz. The latter occurs in many regions of the brain
without a clear anatomical pattern.



I was wondering if this is just a display issue or it rather reflects
some mismatch in actual tissue classification with consequential errors
in the generated values of thickness and volumes as well?

If so, is there any way I can correct for this?



Thank you in advance,



Antonio





Antonio Gallo, MD

NIB-NINDS-NIH

10 Center Drive

Building 10, Room 5B16

Bethesda, MD, 20892 - USA

ph #: 001-301-402.6391

fax #: 001-301-402.0373

***





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Re: [Freesurfer] (no subject)

[Doug Greve]

QDEC has not been officially released yet -- soon!

[EMAIL PROTECTED] wrote:

> hi, when I run the qdec & command, the error show as below:
>
> [EMAIL PROTECTED]:~> qdec &
> [1] 10941
> [EMAIL PROTECTED]:~> qdec.bin: error while loading shared libraries:
> libexpat.so.0:
> cannot open shared object file: No such file or directory
>
> I do't know how to deal with this problem. Could you tell me how to
> resolve this, Thank you!!!
>
>
>
> 
> 我积分，我得奖，天天乐透！
> 
> *用搜狗拼音写邮件，体验更流畅的中文输入>>
> 
>
>
>
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>

-- 
Douglas N. Greve, Ph.D.
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:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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RE: [Freesurfer] Segmentation

[Gallo, Antonio (NIH/NINDS) [F]]

Hi Bruce,
Thank you for your quick response.

Our problem, actually, is that when we visualize the aseg.mgz volume
(with color-coded subcortical structures) we see that WM is classified
as GM (left circle around insula in the figure) and GM is classified as
WM (right lower circle in the figure).
So, even if the surfaces look good, we are worried about the effects of
this misclassification on volume measurements in aseg.mgz.

Thanks,

Antonio



>-Original Message-
>From: Bruce Fischl [mailto:[EMAIL PROTECTED]
>Sent: Monday, June 25, 2007 4:10 PM
>To: Gallo, Antonio (NIH/NINDS) [F]
>Cc: freesurfer@nmr.mgh.harvard.edu
>Subject: Re: [Freesurfer] Segmentation
>
>Hi Antonio,
>
>I wouldn't use the wm.mgz for much of anything. It's really just an
>intermediate step in the creation of the surfaces. In general we trust
the
>?h.white and ?h.pial surfaces first, then the aseg.mgz for things like
>hippocampus, ventricles, etc...
>
>Bruce
>
>
>On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
>
>> Hi All,
>>
>> Upon reviewing subortical segmentations I see that often a mismatch
>> exists between what appears on the wm.mgz and the color-coded
segmented
>> maps.
>>
>> Precisely - as an example - in the attached figure you can see that
in
>> the case of left insula WM, part of the tissue was classified as GM
(in
>> brown) in the color-coded segmented map and as WM in the wm.mgz.
>> Contrariwise, the right temporal-parietal GM cortex part of the
tissue
>> is classified as WM (in green) the color-coded segmented map and as
>> non-WM in the wm.mgz. The latter occurs in many regions of the brain
>> without a clear anatomical pattern.
>>
>>
>>
>> I was wondering if this is just a display issue or it rather reflects
>> some mismatch in actual tissue classification with consequential
errors
>> in the generated values of thickness and volumes as well?
>>
>> If so, is there any way I can correct for this?
>>
>>
>>
>> Thank you in advance,
>>
>>
>>
>> Antonio
>>
>>
>>
>>
>>
>> Antonio Gallo, MD
>>
>> NIB-NINDS-NIH
>>
>> 10 Center Drive
>>
>> Building 10, Room 5B16
>>
>> Bethesda, MD, 20892 - USA
>>
>> ph #: 001-301-402.6391
>>
>> fax #: 001-301-402.0373
>>
>> ***
>>
>>
>>
>>

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RE: [Freesurfer] Segmentation

[Bruce Fischl]

Hi Antonio,

that's why we we use the surfaces for white matter and cortical gray 
matter volume.


cheers,
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:


Hi Bruce,
Thank you for your quick response.

Our problem, actually, is that when we visualize the aseg.mgz volume
(with color-coded subcortical structures) we see that WM is classified
as GM (left circle around insula in the figure) and GM is classified as
WM (right lower circle in the figure).
So, even if the surfaces look good, we are worried about the effects of
this misclassification on volume measurements in aseg.mgz.

Thanks,

Antonio




-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Monday, June 25, 2007 4:10 PM
To: Gallo, Antonio (NIH/NINDS) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation

Hi Antonio,

I wouldn't use the wm.mgz for much of anything. It's really just an
intermediate step in the creation of the surfaces. In general we trust

the

?h.white and ?h.pial surfaces first, then the aseg.mgz for things like
hippocampus, ventricles, etc...

Bruce


On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:


Hi All,

Upon reviewing subortical segmentations I see that often a mismatch
exists between what appears on the wm.mgz and the color-coded

segmented

maps.

Precisely - as an example - in the attached figure you can see that

in

the case of left insula WM, part of the tissue was classified as GM

(in

brown) in the color-coded segmented map and as WM in the wm.mgz.
Contrariwise, the right temporal-parietal GM cortex part of the

tissue

is classified as WM (in green) the color-coded segmented map and as
non-WM in the wm.mgz. The latter occurs in many regions of the brain
without a clear anatomical pattern.



I was wondering if this is just a display issue or it rather reflects
some mismatch in actual tissue classification with consequential

errors

in the generated values of thickness and volumes as well?

If so, is there any way I can correct for this?



Thank you in advance,



Antonio





Antonio Gallo, MD

NIB-NINDS-NIH

10 Center Drive

Building 10, Room 5B16

Bethesda, MD, 20892 - USA

ph #: 001-301-402.6391

fax #: 001-301-402.0373

***






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[Freesurfer] problems with -clean-bm flag

[Gallo, Antonio (NIH/NINDS) [F]]

Hi All,

 

I'm trying to see how much my thickness measures are affected by my
manual edits.

When I tried to use the -clean-bm flag with autorecon2 I always got this
message:

 

-1): read error

mri_em_register: could not open mask volume brainmask.mgz.

 

It seems to me that this flag delete the brainmask.mgz file but doesn't
generate a new copy of this file from the brainmask.auto.mgz file.

Could you help me with that?

 

Thank you in advance,

 

Antonio

 

 

 

 

Antonio Gallo, MD

NIB-NINDS-NIH

10 Center Drive

Building 10, Room 5B16

Bethesda, MD, 20892 - USA

ph #: 001-301-402.6391

fax #: 001-301-402.0373

***

 

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[Freesurfer] Cortical surface tessellation and smoothing

[Kai Li]

Dear list,
   Is there a paper or any documentation describing how freesurfer 
tessellate and smooth cortical surfaces? In particular, does freesurfer 
use any specific variety of marching cube isosurface algorithm? Regular 
surface smoothing (like the Laplacian smoothing) may cause undesired 
surface shrinking. It looks that freesurfer does a good job on surface 
smothing. So I'm wondering what smoothing algorithm freesurfer employ.


Thanks,
Kai
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Re: [Freesurfer] Cortical surface tessellation and smoothing

[Bruce Fischl]

Hi Kai,

it was described in the Dale, et al. 1999 paper in NeuroImage, or maybe 
part in 
that and part in the 2nd part of it (Fischl et al., 1999 also NeuroImage). 
They are both on our wiki (surfer.nmr.mgh.harvard.edu/fswiki). We don't use 
marching cubes, but a custom tesselation algorithm. The surface smoothing 
is like a Laplacian, but the surface area of the inflated surface is 
constrained to be the same as the original surface.



cheers,
Bruce


On Mon, 25 Jun 2007, Kai Li wrote:


Dear list,
  Is there a paper or any documentation describing how freesurfer tessellate 
and smooth cortical surfaces? In particular, does freesurfer use any specific 
variety of marching cube isosurface algorithm? Regular surface smoothing 
(like the Laplacian smoothing) may cause undesired surface shrinking. It 
looks that freesurfer does a good job on surface smothing. So I'm wondering 
what smoothing algorithm freesurfer employ.


Thanks,
Kai
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Re: [Freesurfer] edit brain lesion?

[Bruce Fischl]

yes, usually you can just fill these in on the wm.mgz volume, then run 
autorecon2-wm.


cheers,
Bruce
On Mon, 25 Jun 2007, Lusineh Gharapetian wrote:


Hello,

One of our subjects has a left temporal lobe lesion (which appears on the
MRI). But FS does not recognize the lesion. Is there any way to edit this to
create better wm and pial surfaces? Attached is an image of the
brainmask.mgz view as well as an image of the wm.mgz view.

Thanks for you help!

-Lusineh


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RE: [Freesurfer] problems with -clean-bm flag

[Jenni Pacheco]

Hi Antonio,

 

What is the complete command you are using the -clean-bm flag with?

 

Jenni

  _  

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Gallo, Antonio
(NIH/NINDS) [F]
Sent: Monday, June 25, 2007 7:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] problems with -clean-bm flag

 

Hi All,

 

I'm trying to see how much my thickness measures are affected by my manual
edits.

When I tried to use the -clean-bm flag with autorecon2 I always got this
message:

 

-1): read error

mri_em_register: could not open mask volume brainmask.mgz.

 

It seems to me that this flag delete the brainmask.mgz file but doesn't
generate a new copy of this file from the brainmask.auto.mgz file.

Could you help me with that?

 

Thank you in advance,

 

Antonio

 

 

 

 

Antonio Gallo, MD

NIB-NINDS-NIH

10 Center Drive

Building 10, Room 5B16

Bethesda, MD, 20892 - USA

ph #: 001-301-402.6391

fax #: 001-301-402.0373

***

 

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