[Freesurfer] WM for ROIs

[Gabriel Go.Es.]

Dear freesurfers
 
im trying to obtain the wm volume for some ROIs created by myself, ando that 
not fit with the parcellation of FS, i'm using mri_segstats but i can't make it 
work, can any of you help me?
i always recibe a message that says:
 
"in Get MAC Adress (internal) : There was a configuration problem (or no cable 
!) on your platform: Success
ERROR: Option X unknown
 
the X is the name of the --sum, --i, --in or --seg that i write each time i've 
tried
 
Regards
Gabriel
 







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[Freesurfer] Problem changing the colourmap properties of the overlay ...

[Lloyd Elliott]

Hi,

  I am trying to modify the colour map of an overlay in tksurfer.   
Unfortunately, the changes I make to the View -> Configure -> Overlay  
tcl/tk control are either ignored, or end in errors.


  For example, if I left click on the histogram to set the lower  
thresh hold, and then click 'coppy settings to layer', then the thresh  
hold resets to the original value.


  If I change the X Axis Range manually, for example by entering '6'  
in the Max edit box, then I get something like this error whenever I  
try to change something:


ERROR updating histo: impossible limits (min 6.73089 >= max 6.73089)  
for axis "x"


I'm guessing that this is a bug --- that is, it's not that I am  
misusing these controls.


  I just want the brain to be coloured according to the whole range  
of values in my w file --- ie, for the heat map, the  minimum should  
be the darkest blue and the maximum should be the brightest red (no  
gray where I guess freesurfer assumes p>whatever --- this overlay is  
not a statistical test). Any suggestions?


lloyd$ tksurfer --version
stable4
lloyd$ uname -a
Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel Version  
9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386  
i386



surfer: current subjects dir: /Users/lloyd/work/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/lloyd
surfer: Reading header info from /Users/mathpunk/work/subjects/AAA03/ 
mri/T1.mgz

surfer: vertices=123084, faces=246164

Thanks!
L

PS --- a screenshot of these errors: 
http://mathpunk.churchturing.org/overlay-problems.png

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Re: [Freesurfer] Problem changing the colourmap properties of the overlay ...

[Bruce Fischl]

did you try right-clicking to set the upper threshold?
On Mon, 6 Apr 2009, 
Lloyd Elliott wrote:



Hi,

 I am trying to modify the colour map of an overlay in tksurfer. 
Unfortunately, the changes I make to the View -> Configure -> Overlay tcl/tk 
control are either ignored, or end in errors.


 For example, if I left click on the histogram to set the lower thresh hold, 
and then click 'coppy settings to layer', then the thresh hold resets to the 
original value.


 If I change the X Axis Range manually, for example by entering '6' in the 
Max edit box, then I get something like this error whenever I try to change 
something:


ERROR updating histo: impossible limits (min 6.73089 >= max 6.73089) for axis 
"x"


I'm guessing that this is a bug --- that is, it's not that I am misusing 
these controls.


 I just want the brain to be coloured according to the whole range of values 
in my w file --- ie, for the heat map, the  minimum should be the darkest 
blue and the maximum should be the brightest red (no gray where I guess 
freesurfer assumes p>whatever --- this overlay is not a statistical test). 
Any suggestions?


lloyd$ tksurfer --version
stable4
lloyd$ uname -a
Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel Version 9.6.0: 
Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386



surfer: current subjects dir: /Users/lloyd/work/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/lloyd
surfer: Reading header info from /Users/mathpunk/work/subjects/AAA03/ 
mri/T1.mgz

surfer: vertices=123084, faces=246164

Thanks!
L

PS --- a screenshot of these errors: 
http://mathpunk.churchturing.org/overlay-problems.png


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RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Nick,

I tried using your modified recon-all today but as soon as I try to process any 
data I receive following error message:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].

Also it doesn't matter at all which flags I add to recon-all or if I don't use 
any flags at all, the error is the same. The unmodified recon-all performs well.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

There are no plans in the near future, but in the long term we'd like to remove 
the dependence on conforming the data.

It just occurred to me that you could have the best of both worlds:
first run your data through the normal stream (conforming) up through 
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same 
resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask, 
which would save hours of work.  If i get few minutes i will try this.

You can copy that recon-all over top your existing v4.x freesurfer installation 
(attached again for the list).

Nick


On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
> Hi Nick,
> 
> Thank you very much. I'll have to look into that and try to process some 
> other volumes which might work a bit better, with less manual intervention.
> 
> Are there any plans to improve Freesurfer in the (near) future so that hires 
> data can be processed within the currently available stream?
> 
> Regards,
> Falk
> 
> -Original Message-
> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 01, 2009 7:53 PM
> To: Falk Lüsebrink
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] Measuring cortical thickness with high 
> resolution data
> 
> Falk,
> 
> Attached is a modified recon-all script where I've added a -hires switch to 
> force the stream to not conform the data to 1mm^3, and to not use the atlases.
> 
> Note that you should add the -clean flag to delete any work that had been 
> done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
> 
> However, in working with the .8mm data that you sent me, working with hires 
> data will require quite a bit of manual intervention due to the fact that the 
> atlases normally used cannot be used.  The first problem occurs in 
> skull-stripping, where quite a bit of dura and skull remains, and seems to 
> have intensity values close to gray matter.  This would have to be manually 
> erased on each of the slices.  If it is not erased (I did not do this because 
> of the amount of time required), then the wm.mgz file, which is what is 
> tessellated to create the initial surface, will be very wrong (it tessellates 
> the garbage surrounding the gray matter).
> 
> See also Bruce's prior posting on the problems of working with hires data in 
> freesurfer.
> 
> Nick
> 
> 
> On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
> > Hi Freesurfers,
> > 
> >  
> > 
> > I’m trying to evaluate the usefulness of high resolution scans 
> > acquired at 7T with an isometric voxel size of .6mm for the 
> > measurement of cortical thickness. The inhomogeneities are taken 
> > care of by dividing the scans with another scan of another sequence, 
> > so they are not an issue anymore.
> > 
> >  
> > 
> > My problem is that Freesurfer usually conforms the voxel size to 1mm 
> > which is not desirable. I tried using the –cm and –noaseg flags for 
> > the recon-all process to avoid the conformation and to skip the 
> > subcortical segmentation, but another problem arises while using 
> > these flags.
> > 
> >  
> > 
> > The error I receive is occurring after the WM Segmentation and 
> > states as follows:
> > 
> >  
> > 
> > #
> > 
> > #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
> > 
> >  
> > 
> >  cp wm.mgz wm.seg.mgz
> > 
> >  
> > 
> >  
> > 
> >  mri_segment -keep brain.mgz wm.seg.mgz
> > 
> >  
> > 
> > preserving editing changes in output volume...
> > 
> > doing initial intensity segmentation...
> > 
> > using local statistics to label ambiguous voxels...
> > 
> > computing class statistics for intensity windows...
> > 
> > WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
> > 
> > GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
> > 
> > setting bottom of white matter range to 77.9
> > 
> > setting top of gray matter range to 89.4
> > 
> > doing initial intensity segmentation...
> > 
> > using local statistics to label ambiguous voxels...
> > 
> > using local geometry to label remaining ambiguous voxels...
> > 
> >  
> > 
> > reclassifying voxels using Gaussian border classifier...
> > 
> >  
> > 
> > removing voxels with positive offset direction...
> > 
> >

Re: [Freesurfer] Problem changing the colourmap properties of the overlay ...

[Lloyd Elliott]

 Yes, I did try right clicking to set the upper threshold.  When I  
left click, or right click, the respective bar moves, but the colour  
map remains unchanged.  When I click "copy settings to layer" the bars  
almost always reset.  I've managed to make them not reset at least  
once, but the colour map still remained unchanged and I've been unable  
to reliably reproduce this non-resetting behaviour.


Thanks!
L

On 6-Apr-09, at 2:42 PM, Bruce Fischl wrote:


did you try right-clicking to set the upper threshold?
On Mon, 6 Apr 2009, Lloyd Elliott wrote:


Hi,

I am trying to modify the colour map of an overlay in tksurfer.  
Unfortunately, the changes I make to the View -> Configure ->  
Overlay tcl/tk control are either ignored, or end in errors.


For example, if I left click on the histogram to set the lower  
thresh hold, and then click 'coppy settings to layer', then the  
thresh hold resets to the original value.


If I change the X Axis Range manually, for example by entering '6'  
in the Max edit box, then I get something like this error whenever  
I try to change something:


ERROR updating histo: impossible limits (min 6.73089 >= max  
6.73089) for axis "x"


I'm guessing that this is a bug --- that is, it's not that I am  
misusing these controls.


I just want the brain to be coloured according to the whole range  
of values in my w file --- ie, for the heat map, the  minimum  
should be the darkest blue and the maximum should be the brightest  
red (no gray where I guess freesurfer assumes p>whatever --- this  
overlay is not a statistical test). Any suggestions?


lloyd$ tksurfer --version
stable4
lloyd$ uname -a
Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel  
Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/ 
RELEASE_I386 i386



surfer: current subjects dir: /Users/lloyd/work/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/lloyd
surfer: Reading header info from /Users/mathpunk/work/subjects/ 
AAA03/ mri/T1.mgz

surfer: vertices=123084, faces=246164

Thanks!
L

PS --- a screenshot of these errors: 
http://mathpunk.churchturing.org/overlay-problems.png

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Re: [Freesurfer] Problem changing the colourmap properties of the overlay ...

[Lloyd Elliott]

  The problem is that the Apply Close and Help button controls don't  
appear on the mac because the window is too long (MacBook laptops have  
a maximum resolution of 1280x800) (I didn't realise there was such a  
button because the beveling behind the rest of the controls makes it  
look like the window ends before the apply ---).  I actually thought  
that this might be the case after I first posted, so I searched mac  
forums for a way to move windows without having to drag the title bar  
but I could only find other people with the same problem.  I suppose I  
will hack the tcl to make it display in columns or add a scrollbar or  
something.


Rather embarrassed,
L

On 6-Apr-09, at 5:07 PM, Bruce Fischl wrote:


did you try clickin "apply"?
On Mon, 6 Apr 2009, Lloyd Elliott wrote:

Yes, I did try right clicking to set the upper threshold.  When I  
left click, or right click, the respective bar moves, but the  
colour map remains unchanged.  When I click "copy settings to  
layer" the bars almost always reset.  I've managed to make them not  
reset at least once, but the colour map still remained unchanged  
and I've been unable to reliably reproduce this non-resetting  
behaviour.


Thanks!
L

On 6-Apr-09, at 2:42 PM, Bruce Fischl wrote:


did you try right-clicking to set the upper threshold?
On Mon, 6 Apr 2009, Lloyd Elliott wrote:

Hi,
I am trying to modify the colour map of an overlay in tksurfer.  
Unfortunately, the changes I make to the View -> Configure ->  
Overlay tcl/tk control are either ignored, or end in errors.
For example, if I left click on the histogram to set the lower  
thresh hold, and then click 'coppy settings to layer', then the  
thresh hold resets to the original value.
If I change the X Axis Range manually, for example by entering  
'6' in the Max edit box, then I get something like this error  
whenever I try to change something:
ERROR updating histo: impossible limits (min 6.73089 >= max  
6.73089) for axis "x"
I'm guessing that this is a bug --- that is, it's not that I am  
misusing these controls.
I just want the brain to be coloured according to the whole range  
of values in my w file --- ie, for the heat map, the  minimum  
should be the darkest blue and the maximum should be the  
brightest red (no gray where I guess freesurfer assumes  
p>whatever --- this overlay is not a statistical test). Any  
suggestions?

lloyd$ tksurfer --version
stable4
lloyd$ uname -a
Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel  
Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/ 
RELEASE_I386 i386

surfer: current subjects dir: /Users/lloyd/work/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/lloyd
surfer: Reading header info from /Users/mathpunk/work/subjects/ 
AAA03/ mri/T1.mgz

surfer: vertices=123084, faces=246164
Thanks!
L
PS --- a screenshot of these errors: 
http://mathpunk.churchturing.org/overlay-problems.png
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Re: [Freesurfer] Problem changing the colourmap properties of the overlay ...

[Bruce Fischl]

no problem. The space bar is bound to the "apply" button, which should do 
the trick for you

On Mon, 6 Apr 2009, Lloyd Elliott wrote:

 The problem is that the Apply Close and Help button controls don't appear 
on the mac because the window is too long (MacBook laptops have a maximum 
resolution of 1280x800) (I didn't realise there was such a button because the 
beveling behind the rest of the controls makes it look like the window ends 
before the apply ---).  I actually thought that this might be the case after 
I first posted, so I searched mac forums for a way to move windows without 
having to drag the title bar but I could only find other people with the same 
problem.  I suppose I will hack the tcl to make it display in columns or add 
a scrollbar or something.


Rather embarrassed,
L

On 6-Apr-09, at 5:07 PM, Bruce Fischl wrote:


did you try clickin "apply"?
On Mon, 6 Apr 2009, Lloyd Elliott wrote:

Yes, I did try right clicking to set the upper threshold.  When I left 
click, or right click, the respective bar moves, but the colour map 
remains unchanged.  When I click "copy settings to layer" the bars almost 
always reset.  I've managed to make them not reset at least once, but the 
colour map still remained unchanged and I've been unable to reliably 
reproduce this non-resetting behaviour.


Thanks!
L

On 6-Apr-09, at 2:42 PM, Bruce Fischl wrote:


did you try right-clicking to set the upper threshold?
On Mon, 6 Apr 2009, Lloyd Elliott wrote:

Hi,
I am trying to modify the colour map of an overlay in tksurfer. 
Unfortunately, the changes I make to the View -> Configure -> Overlay 
tcl/tk control are either ignored, or end in errors.
For example, if I left click on the histogram to set the lower thresh 
hold, and then click 'coppy settings to layer', then the thresh hold 
resets to the original value.
If I change the X Axis Range manually, for example by entering '6' in 
the Max edit box, then I get something like this error whenever I try to 
change something:
ERROR updating histo: impossible limits (min 6.73089 >= max 6.73089) for 
axis "x"
I'm guessing that this is a bug --- that is, it's not that I am misusing 
these controls.
I just want the brain to be coloured according to the whole range of 
values in my w file --- ie, for the heat map, the  minimum should be the 
darkest blue and the maximum should be the brightest red (no gray where 
I guess freesurfer assumes p>whatever --- this overlay is not a 
statistical test). Any suggestions?

lloyd$ tksurfer --version
stable4
lloyd$ uname -a
Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel Version 
9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 
i386

surfer: current subjects dir: /Users/lloyd/work/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/lloyd
surfer: Reading header info from /Users/mathpunk/work/subjects/AAA03/ 
mri/T1.mgz

surfer: vertices=123084, faces=246164
Thanks!
L
PS --- a screenshot of these errors: 
http://mathpunk.churchturing.org/overlay-problems.png

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RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Doug Greve]

Falk,  it looks like that file was somehow converted to DOS. try:

dos2unix recon-all
chmod a+x recon-all

then re-run

doug


On Mon, 6 Apr 2009, Falk Lüsebrink wrote:


Hi Nick,

I tried using your modified recon-all today but as soon as I try to process any 
data I receive following error message:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].

Also it doesn't matter at all which flags I add to recon-all or if I don't use 
any flags at all, the error is the same. The unmodified recon-all performs well.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

There are no plans in the near future, but in the long term we'd like to remove 
the dependence on conforming the data.

It just occurred to me that you could have the best of both worlds:
first run your data through the normal stream (conforming) up through 
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same 
resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask, 
which would save hours of work.  If i get few minutes i will try this.

You can copy that recon-all over top your existing v4.x freesurfer installation 
(attached again for the list).

Nick


On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:

Hi Nick,

Thank you very much. I'll have to look into that and try to process some other 
volumes which might work a bit better, with less manual intervention.

Are there any plans to improve Freesurfer in the (near) future so that hires 
data can be processed within the currently available stream?

Regards,
Falk

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 01, 2009 7:53 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Measuring cortical thickness with high
resolution data

Falk,

Attached is a modified recon-all script where I've added a -hires switch to 
force the stream to not conform the data to 1mm^3, and to not use the atlases.

Note that you should add the -clean flag to delete any work that had been done 
prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).

However, in working with the .8mm data that you sent me, working with hires 
data will require quite a bit of manual intervention due to the fact that the 
atlases normally used cannot be used.  The first problem occurs in 
skull-stripping, where quite a bit of dura and skull remains, and seems to have 
intensity values close to gray matter.  This would have to be manually erased 
on each of the slices.  If it is not erased (I did not do this because of the 
amount of time required), then the wm.mgz file, which is what is tessellated to 
create the initial surface, will be very wrong (it tessellates the garbage 
surrounding the gray matter).

See also Bruce's prior posting on the problems of working with hires data in 
freesurfer.

Nick


On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:

Hi Freesurfers,



Iÿÿm trying to evaluate the usefulness of high resolution scans
acquired at 7T with an isometric voxel size of .6mm for the
measurement of cortical thickness. The inhomogeneities are taken
care of by dividing the scans with another scan of another sequence,
so they are not an issue anymore.



My problem is that Freesurfer usually conforms the voxel size to 1mm
which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for
the recon-all process to avoid the conformation and to skip the
subcortical segmentation, but another problem arises while using
these flags.



The error I receive is occurring after the WM Segmentation and
states as follows:



#

#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009



 cp wm.mgz wm.seg.mgz





 mri_segment -keep brain.mgz wm.seg.mgz



preserving editing changes in output volume...

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

computing class statistics for intensity windows...

WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]

GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]

setting bottom of white matter range to 77.9

setting top of gray matter range to 89.4

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

using local geometry to label remaining ambiguous voxels...



reclassifying voxels using Gaussian border classifier...



removing voxels with positive offset direction...

smoothing T1 volume with sigma = 0.250

removing 1-dimensional structures...

thickening thin strands

20 segments, 4813 filled

10270 bright non-wm voxels segmented.

5589 diagonally connected voxels added...

wh

Re: [Freesurfer] Masking brainmask based on surfaces

[Douglas N Greve]

This looks like a problem we had with an older version. What version of 
freesurfer are you running?


Martin Kavec wrote:

Hi,

I am trying to mask a non-brain tissue left by watershed based on the cortical 
surfaces. I found that all what I need to be left is in aparc+aseg.mgz, so I 
converted it to nifiti, along with brainmask.mgz and used FSL to binarize 
aparc+aseg and mask the brainmask. I found that at many places the results is 
too conservative and too much of the GM is missing, see the attached images, 
and particularly the temporal lobes.


Is there a better approach to what I am trying to do and what could be the 
explanation to the results I get.


Thanks,

Martin
  









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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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] WM for ROIs

[Douglas N Greve]

what's your command line?

Gabriel Go.Es. wrote:


Dear freesurfers
 
im trying to obtain the wm volume for some ROIs created by myself, 
ando that not fit with the parcellation of FS, i'm using mri_segstats 
but i can't make it work, can any of you help me?

i always recibe a message that says:
 
"in Get MAC Adress (internal) : There was a configuration problem (or 
no cable !) on your platform: Success

ERROR: Option X unknown
 
the X is the name of the --sum, --i, --in or --seg that i write each 
time i've tried
 
Regards

Gabriel
 







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Re: [Freesurfer] Masking brainmask based on surfaces

[Martin Kavec]

Hi Dough,

this data were analyzed using 4.0.4. So indeed it not the latest, which I am 
running normally. From which version has this been fixed, so I can check, 
before re-runing. From which point should I rerun the analysis.

Thanks,

Martin

On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:
> This looks like a problem we had with an older version. What version of
> freesurfer are you running?
>
> Martin Kavec wrote:
> > Hi,
> >
> > I am trying to mask a non-brain tissue left by watershed based on the
> > cortical surfaces. I found that all what I need to be left is in
> > aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and
> > used FSL to binarize aparc+aseg and mask the brainmask. I found that at
> > many places the results is too conservative and too much of the GM is
> > missing, see the attached images, and particularly the temporal lobes.
> >
> > Is there a better approach to what I am trying to do and what could be
> > the explanation to the results I get.
> >
> > Thanks,
> >
> > Martin
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[Freesurfer] Fwd: FW: XNAT update: Processing failed for PrenatalMA_13_MR_1

[Nurunisa Neyzi]

Hi, just a quick question...

We get this error:

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
GCAhistoScaleImageIntensities: could not find wm peak
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=6.0
using (99, 95, 113) as brain centroid...
mean wm in atlas = 126, using box (82,71,91) --> (116, 118,134) to find MRI wm
before smoothing, mri peak at 0
after smoothing, mri peak at 0, scaling input intensities by inf
Darwin mac124901.med.cornell.edu 8.11.1 Darwin Kernel Version 8.11.1:
Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386
i386

recon-all exited with ERRORS at Mon Apr  6 15:19:36 EDT 2009


How do we scale the nu.mgz images?
Our 001.mgz are looking fine...

thanks!


-- Forwarded message --
From: Nurunisa Neyzi 
Date: Mon, Apr 6, 2009 at 3:31 PM
Subject: Re: FW: XNAT update: Processing failed for PrenatalMA_13_MR_1
To: Chris Derauf 


i think this is what's going on:

we get

"before smoothing, mri peak at 0
after smoothing, mri peak at 0, scaling input intensities by inf"
which is wrong.

this is happening because nu.mgz is very dark.

same problem they had here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007603.html

in our case though I think 001.mgz is looking fine, it is the nu.mgz
that's kind of dark.

let's see what's the easiest way fix it.




On Mon, Apr 6, 2009 at 3:25 PM, Nurunisa Neyzi  wrote:
> actually it goes wrong in the first step. even outside the pipeline.
> so it's not an XNAT issue.
>
> On Mon, Apr 6, 2009 at 3:23 PM, Chris Derauf  wrote:
>> Yes, I did specify the BK Pediatric atlas
>>
>>
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Re: [Freesurfer] Masking brainmask based on surfaces

[Doug Greve]

I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,

tkmedit subject orig.mgz -seg ribbon.mgz

aparc+aseg is suppossed to inherit the cortex from ribbon.mgz

doug




On Mon, 6 Apr 2009, Martin Kavec wrote:


Hi Dough,

this data were analyzed using 4.0.4. So indeed it not the latest, which I am
running normally. From which version has this been fixed, so I can check,
before re-runing. From which point should I rerun the analysis.

Thanks,

Martin

On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:

This looks like a problem we had with an older version. What version of
freesurfer are you running?

Martin Kavec wrote:

Hi,

I am trying to mask a non-brain tissue left by watershed based on the
cortical surfaces. I found that all what I need to be left is in
aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and
used FSL to binarize aparc+aseg and mask the brainmask. I found that at
many places the results is too conservative and too much of the GM is
missing, see the attached images, and particularly the temporal lobes.

Is there a better approach to what I am trying to do and what could be
the explanation to the results I get.

Thanks,

Martin






--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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] Masking brainmask based on surfaces

[Martin Kavec]

Doug,

ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces ?h.white.

Thanks,

Martin

On Monday 06 April 2009 22:17:18 Doug Greve wrote:
> I thought it was 4.0.3, so maybe that's not it. Can you look at the
> ribbon.mgz file? You can load it as a segmentation, ie,
>
> tkmedit subject orig.mgz -seg ribbon.mgz
>
> aparc+aseg is suppossed to inherit the cortex from ribbon.mgz
>
> doug
>
> On Mon, 6 Apr 2009, Martin Kavec wrote:
> > Hi Dough,
> >
> > this data were analyzed using 4.0.4. So indeed it not the latest, which I
> > am running normally. From which version has this been fixed, so I can
> > check, before re-runing. From which point should I rerun the analysis.
> >
> > Thanks,
> >
> > Martin
> >
> > On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:
> >> This looks like a problem we had with an older version. What version of
> >> freesurfer are you running?
> >>
> >> Martin Kavec wrote:
> >>> Hi,
> >>>
> >>> I am trying to mask a non-brain tissue left by watershed based on the
> >>> cortical surfaces. I found that all what I need to be left is in
> >>> aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz
> >>> and used FSL to binarize aparc+aseg and mask the brainmask. I found
> >>> that at many places the results is too conservative and too much of the
> >>> GM is missing, see the attached images, and particularly the temporal
> >>> lobes.
> >>>
> >>> Is there a better approach to what I am trying to do and what could be
> >>> the explanation to the results I get.
> >>>
> >>> Thanks,
> >>>
> >>> Martin
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Re: [Freesurfer] Masking brainmask based on surfaces

[Doug Greve]

but you are using aparc+aseg to generate the mask, so if aparc+aseg is
perfect, the mask should be as well. Do the mask and aparc+aseg match?



On Mon, 6 Apr 2009, Martin Kavec wrote:


Doug,

ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces ?h.white.

Thanks,

Martin

On Monday 06 April 2009 22:17:18 Doug Greve wrote:

I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,

tkmedit subject orig.mgz -seg ribbon.mgz

aparc+aseg is suppossed to inherit the cortex from ribbon.mgz

doug

On Mon, 6 Apr 2009, Martin Kavec wrote:

Hi Dough,

this data were analyzed using 4.0.4. So indeed it not the latest, which I
am running normally. From which version has this been fixed, so I can
check, before re-runing. From which point should I rerun the analysis.

Thanks,

Martin

On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:

This looks like a problem we had with an older version. What version of
freesurfer are you running?

Martin Kavec wrote:

Hi,

I am trying to mask a non-brain tissue left by watershed based on the
cortical surfaces. I found that all what I need to be left is in
aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz
and used FSL to binarize aparc+aseg and mask the brainmask. I found
that at many places the results is too conservative and too much of the
GM is missing, see the attached images, and particularly the temporal
lobes.

Is there a better approach to what I am trying to do and what could be
the explanation to the results I get.

Thanks,

Martin






--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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] tksurfer Load Group Descriptor File error

[Jeff Sadino]

Thank you for the advice Sid.  I added those lines, and now my errors 
disappear, but I still get a blank screen where there should be a scatterplot.  
Is this a graphics issue with my hardware, or do I need to do something 
differently?

This is my fsgd file:
GroupDescriptorFile 1
Title try1
MeasurementName thickness
Class nc circle red
Variables Age
Input 060017_HG01 nc .5 
Input 060023_F01 nc .8 
Input 060024_HG01 nc .1 
Input 060025_HG01 nc .5
...
...

The screen that pops up has thickness on the y-axis, but a range of only 0-1 
and Age on x-axis with range 0-1.  My ages were "real" (50.8, 40.8, 50.1, 
etc.), but I changed them to between 0 and 1 to see if that helped, but no good.

Thanks in advance for your help,
Jeff Sadino

Date: Thu, 12 Mar 2009 18:52:45 -0700
Subject: Re: [Freesurfer] tksurfer Load Group Descriptor File error
From: sid...@gmail.com
To: jsad...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

Class ctrl should be followed by marker and color specification (Class ctrl 
circle red, for e.g). ditto
for cd .

sid.

On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino  wrote:






Hello,

Can someone help me get scatterplots of my data?  I am using freesurfer 3.0.5.  
I have ran these commands:

mris_preproc  --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness 
--out lh.try1.mgh

mri_surf2surf  --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval 
lh.try1.fw.mgh
mri_glmfit  --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf 
fsaverage lh --glmdir lh.try1.dir
tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay 
lh.try1.dir/try1.mtx/sig.mgh


Then selected a vertex, then File->Load Group Descriptor File and selected 
try1.fsgd, but I get this error:

WARNING: Marker for class ctrl was invalid.
WARNING: Color for class ctrl was invalid.
WARNING: Marker for class cd was invalid.

WARNING: Color for class cd was invalid.

This is try1.fsgd:

GroupDescriptorFile 1
Title try1
MeasurementName thickness
Class ctrl
Class cd
Variables Age
Input 040004_P02 ctrl 55.18 
Input 050046_S02 ctrl 37.45 

...
...
Input 070073_S01 cd 20.54 
Input 070114_OGM01 cd 46.03



I also tried with lh.try1.dir/y.fsgd, but get a similar error:

INFO: ignoring tag Creator 
INFO: ignoring tag SUBJECTS_DIR 

INFO: ignoring tag SynthSeed 
INFO: gdfRead: reshaping
WARNING: Marker for class ctrl was invalid.
WARNING: Color for class ctrl was invalid.
WARNING: Marker for class cd was invalid.
WARNING: Color for class cd was invalid.


y.fsgd looks like this:

GroupDescriptorFile 1
Title try1
MeasurementName external
Tessellation surface
PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh
DesignMatFile fsgd.X.mat dods
ResidualFWHM 22.331472

Class ctrl
Class cd
Variables Age 
Input 040004_P02 ctrl 55.18 
Input 050046_S02 ctrl 37.45 
...
...
Input 070073_S01 cd 20.54 
Input 070114_OGM01 cd 46.03 
Creator  mri_glmfit
SUBJECTS_DIR /share/apps/freesurfer/subjects

SynthSeed1237057379

In both cases, a graph pops up, but it is blank.  Thank you in advance for your 
suggestions,
Jeff Sadino

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