Re: [Freesurfer] vtkMultiThreader error

[Martin Kavec]

Hi Don,

I am in a similar situation. I am on a IBM BladeCenter cluster (though with 
one blade only) with 2 Quad core Intels, and I experience intermittent 
crashes of mri_volmask as well. Similarly as you, when I run the mri_volmask 
on the crashed subject on a desktop, this passes perfectly fine and sometimes 
also on the cluster as well.

I am wonder whether how do you obtain the debug information about the cause of 
the crash (being in the vtkMultiThreader)?

I also wonder, whether the crashes could be due to different compilation 
environments of the VTK libraries used in teh FS distribution (centos) and 
your redhat. I went on the bug-report site of VTK and there really isn't 
anythink major reported on this class. 

In my experience the mri_volmask runs fine for quite a while and then crashes. 
>From the debug messages you show it would thus could be that the process may 
hit some limit of the threads which could be allocated to a process.

What do you think?

Martin  

On Saturday 06 June 2009 04:19:51 Don Hagler wrote:
> When we run v430 on our cluster, running rocks redhat 4.3, we get the error
> message below when mris_volmask is run.  From a google search, I see that
> someone had the same error message back in Oct 2007.  Was a solution found
> for this?  It runs fine on our desktop machines as well as when we log in
> directly to a node and run the job interactively.
>
>
>
>  mris_volmask --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1
>
> SUBJECTS_DIR is /home/dhagler/data_test
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> pthread_create() returned 12
>
> Segmentation fault
> Linux compute-0-12.local 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT
> 2007 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Fri Jun  5 18:58:09 PDT 2009
>
>
>
>
>
> _
> Hotmail® has ever-growing storage! Don’t worry about storage limits.
> http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori
>al_Storage_062009


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[Freesurfer] extracting bval and bvecs from Siemens trio DWI

[raka maitra]

Hello Doug
The Siemen's Trio gives us Diffusion weighted images in the form 
of MR.10284.746.There are no extensions such as .dcm or .ima
I can convert the dicom to nifti .nii format using SPM or FSL.But neither 
program extracts the bval or bvec information.
I am working on Mac OsX 10.5 and am using FS v4.3.1
I tried using 
mri_convert subject/MR* dwi.nii -it siemens_dicom
I am trying to ckeck the quality of the DWI and hence would like to perform 
eddy current correction and preprocess the images to generate FA maps.

Thanks in advanceRaka







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[Freesurfer] Temporal lobe segmentation

[Seyed Shahab Sharifi]

Subject: Temporal lobe segmentation
Date: Tue, 2 Jun 2009 17:40:21 +0100








Hi all, 

I am interested in automated segmentation of temporal lobe using freesurfer. I 
understand that it is possible to add up the individual regions of a specific 
lobe, create one massive label for that lobe, and get statistics on those. But  
I am not sure about the practicality of this approach for two reasons; first if 
all the regions of a temporal lobe can be labeled by Free Surfer, second 
because I am thinking that the most medial border of the superior temporal lobe 
could be my arbitrary cut off point of segmenting the temporal lobe,  what 
anatomical/imaging feature has been defined for Free Surfer that distinguishes 
the white matter of the superior temporal lobe from the stem of temporal lobe 
(or say putamen) . I would appreciate it if one can guide me through this 
process if possible.

cheers

Shahab

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Re: [Freesurfer] Temporal lobe segmentation

[Bruce Fischl]

Hi Seyed,

I don't think there's any easy adding up of labels that gives you the 
temporal lobe, but Rahul and/or Christophe can correct me if I'm wrong. The 
easiest thing to do would be just draw the boundaries on fsaverage and map 
it to your subjects using mri_label2label. We should probably provide this 
at some point. Maybe Christophe or Rahul would be interested in doing in in 
a free moment.


cheers,
Bruce


On Mon, 8 Jun 2009, Seyed Shahab Sharifi wrote:






Subject: Temporal lobe segmentation
Date: Tue, 2 Jun 2009 17:40:21 +0100








Hi all,

I am interested in automated segmentation of temporal lobe using freesurfer. I 
understand that it is possible to add up the individual regions of a specific 
lobe, create one massive label for that lobe, and get statistics on those. But  
I am not sure about the practicality of this approach for two reasons; first if 
all the regions of a temporal lobe can be labeled by Free Surfer, second 
because I am thinking that the most medial border of the superior temporal lobe 
could be my arbitrary cut off point of segmenting the temporal lobe,  what 
anatomical/imaging feature has been defined for Free Surfer that distinguishes 
the white matter of the superior temporal lobe from the stem of temporal lobe 
(or say putamen) . I would appreciate it if one can guide me through this 
process if possible.

cheers

Shahab

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[Freesurfer] Color scale for the probability maps

[Eylem Kirlangic]

Hi,

When I plot the probability maps, the color scale bar takes negative 
values too (e.g., setting  the threshold min 0 max 0.5, you get a scale 
bar between -0.5 and +0.5). How can I change the color scale bar so that 
it shows percentages? 


Thanks!
Eylem





---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
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Re: [Freesurfer] Color scale for the probability maps

[Bruce Fischl]

Hi Eylem,

are you configuring it with the configure overlay window? If so, you 
should be able to enter 0 for the thresh and 1 for the max, and click 
"linear" to generate the same maps as the ones we published. You need to 
copy the label stats to an overlay first though (tools->label->copy label 
stats to overlay)

 cheers
Bruce

On Mon, 8 Jun 
2009, Eylem Kirlangic wrote:



Hi,

When I plot the probability maps, the color scale bar takes negative values 
too (e.g., setting  the threshold min 0 max 0.5, you get a scale bar between 
-0.5 and +0.5). How can I change the color scale bar so that it shows 
percentages? 
Thanks!

Eylem





---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
---
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Re: [Freesurfer] Color scale for the probability maps

[Eylem Kirlangic]

Hi Bruce,

That's exactly what I do. The maps do look nice, but the color scale bar 
does not. It is not a percentage scale, rather it takes a scale of -/+ 
max value (of course, a negative value does not exist on the probability 
map!!!).  I think it is just about the options of the color scale bar. 
But I could not figure out how to change it to a percentage scale.


Cheers
Eylem


Bruce Fischl wrote:

Hi Eylem,

are you configuring it with the configure overlay window? If so, you 
should be able to enter 0 for the thresh and 1 for the max, and click 
"linear" to generate the same maps as the ones we published. You need 
to copy the label stats to an overlay first though (tools->label->copy 
label stats to overlay)

 cheers
Bruce

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi,

When I plot the probability maps, the color scale bar takes negative 
values too (e.g., setting  the threshold min 0 max 0.5, you get a 
scale bar between -0.5 and +0.5). How can I change the color scale 
bar so that it shows percentages? Thanks!

Eylem








---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
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Re: [Freesurfer] Color scale for the probability maps

[Bruce Fischl]

did you hit return when you typed in the 0/1 values? This is a tk thing - 
it won't take the values until you hit return. Then click apply and it 
should redraw with the new values

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi Bruce,

That's exactly what I do. The maps do look nice, but the color scale bar does 
not. It is not a percentage scale, rather it takes a scale of -/+ max value 
(of course, a negative value does not exist on the probability map!!!).  I 
think it is just about the options of the color scale bar. But I could not 
figure out how to change it to a percentage scale.


Cheers
Eylem


Bruce Fischl wrote:

Hi Eylem,

are you configuring it with the configure overlay window? If so, you should 
be able to enter 0 for the thresh and 1 for the max, and click "linear" to 
generate the same maps as the ones we published. You need to copy the label 
stats to an overlay first though (tools->label->copy label stats to 
overlay)

 cheers
Bruce

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi,

When I plot the probability maps, the color scale bar takes negative 
values too (e.g., setting  the threshold min 0 max 0.5, you get a scale 
bar between -0.5 and +0.5). How can I change the color scale bar so that 
it shows percentages? Thanks!

Eylem








---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
---


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Re: [Freesurfer] Temporal lobe segmentation

[rahul]

Hi Seyed,

As Bruce mentions, currently the best way to get a complete temporal lobe
segmentation might be to add each of the invidual temporal lobe labels
(using either of the two parcellation systems). With regards to your
specific questions, 1) both of the parcellation atlases do a fairly good
job of subdividing the temporal lobe into anatomic units -- mine uses a
gyral based approach whereas Christophe's uses a more detailed sulcal and
gyral approach, 2) within my parcellation atlas, for the superior temporal
gyrus, the anterior boundary is the limen insulae and the medial border is
the insular cortex -- for more details on how the wm and gm are segmented,
please see Fischl et al., 1999, 2002.

Hope that helps,

rahul

> Hi Seyed,
>
> I don't think there's any easy adding up of labels that gives you the
> temporal lobe, but Rahul and/or Christophe can correct me if I'm wrong.
> The
> easiest thing to do would be just draw the boundaries on fsaverage and map
> it to your subjects using mri_label2label. We should probably provide this
> at some point. Maybe Christophe or Rahul would be interested in doing in
> in
> a free moment.
>
> cheers,
> Bruce
>
>
> On Mon, 8 Jun 2009, Seyed Shahab Sharifi wrote:
>
>>
>>
>>
>>
>> Subject: Temporal lobe segmentation
>> Date: Tue, 2 Jun 2009 17:40:21 +0100
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi all,
>>
>> I am interested in automated segmentation of temporal lobe using
>> freesurfer. I understand that it is possible to add up the individual
>> regions of a specific lobe, create one massive label for that lobe, and
>> get statistics on those. But  I am not sure about the practicality of
>> this approach for two reasons; first if all the regions of a temporal
>> lobe can be labeled by Free Surfer, second because I am thinking that
>> the most medial border of the superior temporal lobe could be my
>> arbitrary cut off point of segmenting the temporal lobe,  what
>> anatomical/imaging feature has been defined for Free Surfer that
>> distinguishes the white matter of the superior temporal lobe from the
>> stem of temporal lobe (or say putamen) . I would appreciate it if one
>> can guide me through this process if possible.
>>
>> cheers
>>
>> Shahab
>>
>> View your Twitter and Flickr updates from one place - Learn more!
>> _
>> Share your photos with Windows Live Photos ? Free.
>> http://clk.atdmt.com/UKM/go/134665338/direct/01/
>
>
>

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Re: [Freesurfer] Color scale for the probability maps

[Eylem Kirlangic]

I can change the values min and max in the configuration window, this 
changes the threshold and apllies to the map. I can observe these 
changes on the map, the scale bar changes accordingly, too. But, as I 
said, it is not a percental (%) scale bar, rather takes -/+ max value 
(which is input in the configuration window) for its range, and I am 
trying to have it like in the  publication (0% - 100%) range.


Bruce Fischl wrote:
did you hit return when you typed in the 0/1 values? This is a tk 
thing - it won't take the values until you hit return. Then click 
apply and it should redraw with the new values

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi Bruce,

That's exactly what I do. The maps do look nice, but the color scale 
bar does not. It is not a percentage scale, rather it takes a scale 
of -/+ max value (of course, a negative value does not exist on the 
probability map!!!).  I think it is just about the options of the 
color scale bar. But I could not figure out how to change it to a 
percentage scale.


Cheers
Eylem


Bruce Fischl wrote:

Hi Eylem,

are you configuring it with the configure overlay window? If so, you 
should be able to enter 0 for the thresh and 1 for the max, and 
click "linear" to generate the same maps as the ones we published. 
You need to copy the label stats to an overlay first though 
(tools->label->copy label stats to overlay)

 cheers
Bruce

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi,

When I plot the probability maps, the color scale bar takes 
negative values too (e.g., setting  the threshold min 0 max 0.5, 
you get a scale bar between -0.5 and +0.5). How can I change the 
color scale bar so that it shows percentages? Thanks!

Eylem










---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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Re: [Freesurfer] Color scale for the probability maps

[Bruce Fischl]

I think for the pub it was 0-1, not 0-100. Can you generate that?
On Mon, 8 
Jun 2009, Eylem Kirlangic wrote:


I can change the values min and max in the configuration window, this changes 
the threshold and apllies to the map. I can observe these changes on the map, 
the scale bar changes accordingly, too. But, as I said, it is not a percental 
(%) scale bar, rather takes -/+ max value (which is input in the 
configuration window) for its range, and I am trying to have it like in the 
publication (0% - 100%) range.


Bruce Fischl wrote:
did you hit return when you typed in the 0/1 values? This is a tk thing - 
it won't take the values until you hit return. Then click apply and it 
should redraw with the new values

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi Bruce,

That's exactly what I do. The maps do look nice, but the color scale bar 
does not. It is not a percentage scale, rather it takes a scale of -/+ max 
value (of course, a negative value does not exist on the probability 
map!!!).  I think it is just about the options of the color scale bar. But 
I could not figure out how to change it to a percentage scale.


Cheers
Eylem


Bruce Fischl wrote:

Hi Eylem,

are you configuring it with the configure overlay window? If so, you 
should be able to enter 0 for the thresh and 1 for the max, and click 
"linear" to generate the same maps as the ones we published. You need to 
copy the label stats to an overlay first though (tools->label->copy label 
stats to overlay)

 cheers
Bruce

On Mon, 8 Jun 2009, Eylem Kirlangic wrote:


Hi,

When I plot the probability maps, the color scale bar takes negative 
values too (e.g., setting  the threshold min 0 max 0.5, you get a scale 
bar between -0.5 and +0.5). How can I change the color scale bar so that 
it shows percentages? Thanks!

Eylem










---
---
Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
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Re: [Freesurfer] vtkMultiThreader error

[Nick Schmansky]

Don and Martin,

I dont have a good solution for you to this problem.  The error code
indicates an 'out-of-memory' error returned by pthread_create, and I do
know the mris_vol_mask uses a lot of memory (at least 1GB).

I have not been able to find any clues to the source of this problem on
the web either.  The only curious thing to it is that in the source
code, that section is conditionally compiled to ignore the return code
if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior
on some special HP platform build.

mris_vol_mask has been a real thorn in the side of the recon-all stream,
but its not easy to replace because it does a subjectively better job of
finding the voxels which intersect the pial and white surfaces.  For
comparison, or even to solve your problem, you can use
mris_vol_mask_novtk to create the ribbon.mgz files.  The output is not
the same as that produced by mris_vol_mask though.  Perhaps you can run
it, and compare the results side-by-side and give us your opinion on
which is the better ribbon (as there is no objective measure on what a
'correct' ribbon.mgz should like like, ie, should it include voxels that
intersect more than half way through a surface, or not at all?).

Nick


On Mon, 2009-06-08 at 09:16 +0200, Martin Kavec wrote:
> Hi Don,
> 
> I am in a similar situation. I am on a IBM BladeCenter cluster (though with 
> one blade only) with 2 Quad core Intels, and I experience intermittent 
> crashes of mri_volmask as well. Similarly as you, when I run the mri_volmask 
> on the crashed subject on a desktop, this passes perfectly fine and sometimes 
> also on the cluster as well.
> 
> I am wonder whether how do you obtain the debug information about the cause 
> of 
> the crash (being in the vtkMultiThreader)?
> 
> I also wonder, whether the crashes could be due to different compilation 
> environments of the VTK libraries used in teh FS distribution (centos) and 
> your redhat. I went on the bug-report site of VTK and there really isn't 
> anythink major reported on this class. 
> 
> In my experience the mri_volmask runs fine for quite a while and then 
> crashes. 
> >From the debug messages you show it would thus could be that the process may 
> hit some limit of the threads which could be allocated to a process.
> 
> What do you think?
> 
> Martin  
> 
> On Saturday 06 June 2009 04:19:51 Don Hagler wrote:
> > When we run v430 on our cluster, running rocks redhat 4.3, we get the error
> > message below when mris_volmask is run.  From a google search, I see that
> > someone had the same error message back in Oct 2007.  Was a solution found
> > for this?  It runs fine on our desktop machines as well as when we log in
> > directly to a node and run the job interactively.
> >
> >
> >
> >  mris_volmask --label_left_white 2 --label_left_ribbon 3
> > --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> > --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1
> >
> > SUBJECTS_DIR is /home/dhagler/data_test
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > pthread_create() returned 12
> >
> > Segmentation fault
> > Linux compute-0-12.local 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT
> > 2007 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all exited with ERRORS at Fri Jun  5 18:58:09 PDT 2009
> >
> >
> >
> >
> >
> > _
> > Hotmail® has ever-growing storage! Don’t worry about storage limits.
> > http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori
> >al_Storage_062009
> 
> 
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> 

Re: [Freesurfer] Disentangling age effects

[Douglas N Greve]

mmoay...@uhnres.utoronto.ca wrote:

Hi,

I am studying two groups and have found that age is a confound (or is a covariate with an interaction between the two groups).  Simply, when I correlate age between the two groups, there is an interaction (i.e., the slopes are different).  

My questions are: 


1) is it appropriate to proceed with a map-wise t-test (with or without age as 
a nuisance covariate)?
  
If there is an age effect in the data, then you should include it in 
your model.

2) is there a way to pull out age effects on each group specifically, i.e., use 
age as a covariate of interest?
  
I'm not sure what you mean. It sounds like that is what you've already 
done. You can create a contrasts to test the age effect in each group 
separately.

If neither of these methods is statistically sound, is there a method that can 
be used to describe age effects in each group, or characterize the findings?

Thanks,

Massih Moayedi


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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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[Freesurfer] Re: extracting bval and bvecs from Siemens trio DWI

[Douglas N Greve]

Just give it one file from the series you want to convert.

doug

ps Please consult surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for 
suggestions on how to make bug reports. Thanks!


raka maitra wrote:


Hello Doug

The Siemen's Trio gives us Diffusion weighted images in the form
of MR.10284.746.
There are no extensions such as .dcm or .ima

I can convert the dicom to nifti .nii format using SPM or FSL.
But neither program extracts the bval or bvec information.

I am working on Mac OsX 10.5 and am using FS v4.3.1

I tried using 


mri_convert subject/MR* dwi.nii -it siemens_dicom


I am trying to ckeck the quality of the DWI and hence would like
to perform eddy current correction and preprocess the images to
generate FA maps.


Thanks in advance

Raka









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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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[Freesurfer] about ROI

[Gabriel Go.Es.]

hello freesurfers

 

i have a doubt:

i have convert a subject brainmask from freesurfer to nii and then

i've convert a label that i create on freesurfer to *.nii using for 
registration the brainmask.mgz, i've made that for working in SPM, but when i 
open the ROI just not match with my subject...

 

Regards

Gabriel

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[Freesurfer] Talairach coordinates

[Rafa x]

Dear Freesurfer team,
I used the lh.inflated file in an average subject to obtain its
vertex’s coordinates. My question is: What anatomical space or
reference system was use in this file? or instead, How I could obtain
the Talairach coordinates of each vertex?
Thank you in advance,
Rafa.

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Re: [Freesurfer] Talairach coordinates

[Douglas N Greve]

The coordinates are in mni305 space. If you load it into tksurfer, you 
can see both MNI305 and Talairach coords. The Talairach coords are based 
on a transform from MNI305 from Mathew Brett.


doug

Rafa x wrote:

Dear Freesurfer team,
I used the lh.inflated file in an average subject to obtain its
vertex’s coordinates. My question is: What anatomical space or
reference system was use in this file? or instead, How I could obtain
the Talairach coordinates of each vertex?
Thank you in advance,
Rafa.

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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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[Freesurfer] using cortical thickness values

[Kai Lutz]

Dear List,

in an attempt to divide grey matter segments into an outer and inner 
layer, I am currently using the vertex coordinates for pial surface (in 
Matlab>> read_surf('lh.pial') ) and vertex coordinates for white matter 
surface (MATLAB>>read_surf('lh.white') ). Perhaps naively, I assume, 
that the order of the two coordinate matrices is identical and calculate 
the wanted coordinates of a point on a line (say half way) in between 
the corresponding pial and white matter vertices.


What puzzles me is that the distances between corresponding (?) white 
matter and pial surface vertices are not equal to the cortical thickness 
values given by >>read_curv('lh.thickness')
(GM-WM distances up to 9.3 mm are found, whereas cortical thickness 
values vary between -0.24 and 5 mm in the data set I am working on)


--> To determine a layer, separating outer from inner half of the 
cortex, would it be a more valid to
A: determine vertex normals of pial surface and travel along them by a 
distance 1/2 the cortical thickness? (Q: which thickness value belongs 
to which vertex? where do the negative thickness values come from?)

or
B: determine points half way in between vertex coordinates of 
corresponding pial and WM vertices? (Q: how can I assure their 
correspondence?)


Is anyone working on / has solved a related problem? Any hint would be 
greatly appreciated!


Cheers,
Kai

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Neuropsychology
Institute for Psychology
University of Zurich
Binzmühlestrasse 14 /Box 25
CH-8050 Zürich
Switzerland


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RE: [Freesurfer] vtkMultiThreader error

[Don Hagler]

Hi Nick,

Thanks for the reply.  I will look into the memory limit issue some more (we 
recently instituted per job memory limits), but I have done a test run with a 
16GB memory limit (running one job per node).

Meanwhile, thanks for the novtk suggestion.  Our fallback option is to just 
disable the ribbon generation.  I don't think we ever use them for anything.

Don


> Subject: Re: [Freesurfer] vtkMultiThreader error
> From: ni...@nmr.mgh.harvard.edu
> To: martin.ka...@gmail.com; dhagle...@hotmail.com
> Date: Mon, 8 Jun 2009 11:15:51 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> Don and Martin,
> 
> I dont have a good solution for you to this problem.  The error code
> indicates an 'out-of-memory' error returned by pthread_create, and I do
> know the mris_vol_mask uses a lot of memory (at least 1GB).
> 
> I have not been able to find any clues to the source of this problem on
> the web either.  The only curious thing to it is that in the source
> code, that section is conditionally compiled to ignore the return code
> if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior
> on some special HP platform build.
> 
> mris_vol_mask has been a real thorn in the side of the recon-all stream,
> but its not easy to replace because it does a subjectively better job of
> finding the voxels which intersect the pial and white surfaces.  For
> comparison, or even to solve your problem, you can use
> mris_vol_mask_novtk to create the ribbon.mgz files.  The output is not
> the same as that produced by mris_vol_mask though.  Perhaps you can run
> it, and compare the results side-by-side and give us your opinion on
> which is the better ribbon (as there is no objective measure on what a
> 'correct' ribbon.mgz should like like, ie, should it include voxels that
> intersect more than half way through a surface, or not at all?).
> 
> Nick
> 
> 
> On Mon, 2009-06-08 at 09:16 +0200, Martin Kavec wrote:
> > Hi Don,
> > 
> > I am in a similar situation. I am on a IBM BladeCenter cluster (though with 
> > one blade only) with 2 Quad core Intels, and I experience intermittent 
> > crashes of mri_volmask as well. Similarly as you, when I run the 
> > mri_volmask 
> > on the crashed subject on a desktop, this passes perfectly fine and 
> > sometimes 
> > also on the cluster as well.
> > 
> > I am wonder whether how do you obtain the debug information about the cause 
> > of 
> > the crash (being in the vtkMultiThreader)?
> > 
> > I also wonder, whether the crashes could be due to different compilation 
> > environments of the VTK libraries used in teh FS distribution (centos) and 
> > your redhat. I went on the bug-report site of VTK and there really isn't 
> > anythink major reported on this class. 
> > 
> > In my experience the mri_volmask runs fine for quite a while and then 
> > crashes. 
> > >From the debug messages you show it would thus could be that the process 
> > >may 
> > hit some limit of the threads which could be allocated to a process.
> > 
> > What do you think?
> > 
> > Martin  
> > 
> > On Saturday 06 June 2009 04:19:51 Don Hagler wrote:
> > > When we run v430 on our cluster, running rocks redhat 4.3, we get the 
> > > error
> > > message below when mris_volmask is run.  From a google search, I see that
> > > someone had the same error message back in Oct 2007.  Was a solution found
> > > for this?  It runs fine on our desktop machines as well as when we log in
> > > directly to a node and run the job interactively.
> > >
> > >
> > >
> > >  mris_volmask --label_left_white 2 --label_left_ribbon 3
> > > --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> > > --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1
> > >
> > > SUBJECTS_DIR is /home/dhagler/data_test
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkM

[Freesurfer] TAL QA check failed

[Barnali Basu]

Experts,

I got the following error while running a subject with recon-all autorecon1


ERROR: Talairach QA check failed!
   z-score = -8 <= -4 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 2008 i686
GNU/Linux

recon-all exited with ERRORS at Fri Jun  5 22:35:17 PDT 2009


I gathered from other posts on this error that the fix depends upon the z
-score.  In this case the z-score is -8, what is the best way to get it
fixed. Previously i had fixed similar error and i had fixed it with
tkregister2, but z-score was different

Thanks and Regards
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[Freesurfer] mris_anatomical_stats

[Kevin Scheibel]

I am running mris_anatomical_stats and keep getting the same error.  Here's
the entire log file.looks like the big error happens at 'glibc detected'

 

computing statistics for each annotation in
/ifs/woods/scott_temp/kevin_work/freeseg/subj/078/label/rh.aparc.annot.

outputting results to
/ifs/tmp/pipeline-4.2/pipelnvr/2009June08_15h03m16s361ms/MRISAnatomicalStats
.StatsFile_0-077.stats...

reading volume
/ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/mri/wm.mgz...

reading input surface
/ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.pial...

reading input pial surface
/ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.pial...

reading input white surface
/ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin
al.txt)

*** glibc detected ***
/usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats: free(): invalid
pointer: 0x2af35c93d000 ***

=== Backtrace: =

/lib64/libc.so.6[0x35c4671684]

/lib64/libc.so.6(cfree+0x8c)[0x35c4674ccc]

/lib64/libc.so.6(_IO_free_backup_area+0x18)[0x35c466dd68]

/lib64/libc.so.6(_IO_file_overflow+0x1d2)[0x35c466bd62]

/lib64/libc.so.6(_IO_vfprintf+0x4a7e)[0x35c4646d4e]

/lib64/libc.so.6(_IO_fprintf+0x88)[0x35c464cf68]

/usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats(vfprintf+0x338d)
[0x40898d]

/lib64/libc.so.6(__libc_start_main+0xf4)[0x35c461d8b4]

/usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats(__gxx_personalit
y_v0+0xfa)[0x40626a]

=== Memory map: 

0040-00786000 r-xp  00:16 238900739
/usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats

00886000-008e rw-p 00386000 00:16 238900739
/usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats

008e-0209f000 rw-p 008e 00:00 0 

04da5000-0b132000 rw-p 04da5000 00:00 0 

35c420-35c421a000 r-xp  08:01 4321433
/lib64/ld-2.5.so

35c441a000-35c441b000 r--p 0001a000 08:01 4321433
/lib64/ld-2.5.so

35c441b000-35c441c000 rw-p 0001b000 08:01 4321433
/lib64/ld-2.5.so

35c460-35c474a000 r-xp  08:01 4321434
/lib64/libc-2.5.so

35c474a000-35c4949000 ---p 0014a000 08:01 4321434
/lib64/libc-2.5.so

35c4949000-35c494d000 r--p 00149000 08:01 4321434
/lib64/libc-2.5.so

35c494d000-35c494e000 rw-p 0014d000 08:01 4321434
/lib64/libc-2.5.so

35c494e000-35c4953000 rw-p 35c494e000 00:00 0 

35c4a0-35c4a21000 r-xp  08:01 12354411
/usr/lib64/libjpeg.so.62.0.0

35c4a21000-35c4c2 ---p 00021000 08:01 12354411
/usr/lib64/libjpeg.so.62.0.0

35c4c2-35c4c21000 rw-p 0002 08:01 12354411
/usr/lib64/libjpeg.so.62.0.0

35c4e0-35c4e57000 r-xp  08:01 12354412
/usr/lib64/libtiff.so.3.8.2

35c4e57000-35c5056000 ---p 00057000 08:01 12354412
/usr/lib64/libtiff.so.3.8.2

35c5056000-35c5059000 rw-p 00056000 08:01 12354412
/usr/lib64/libtiff.so.3.8.2

35c520-35c5282000 r-xp  08:01 4321204
/lib64/libm-2.5.so

35c5282000-35c5481000 ---p 00082000 08:01 4321204
/lib64/libm-2.5.so

35c5481000-35c5482000 r--p 00081000 08:01 4321204
/lib64/libm-2.5.so

35c5482000-35c5483000 rw-p 00082000 08:01 4321204
/lib64/libm-2.5.so

35c620-35c6214000 r-xp  08:01 12346484
/usr/lib64/libz.so.1.2.3

35c6214000-35c6413000 ---p 00014000 08:01 12346484
/usr/lib64/libz.so.1.2.3

35c6413000-35c6414000 rw-p 00013000 08:01 12346484
/usr/lib64/libz.so.1.2.3

35c660-35c6609000 r-xp  08:01 4321447
/lib64/libcrypt-2.5.so

35c6609000-35c6808000 ---p 9000 08:01 4321447
/lib64/libcrypt-2.5.so

35c6808000-35c6809000 r--p 8000 08:01 4321447
/lib64/libcrypt-2.5.so

35c6809000-35c680a000 rw-p 9000 08:01 4321447
/lib64/libcrypt-2.5.so

35c680a000-35c6838000 rw-p 35c680a000 00:00 0 

35c6a0-35c6ae6000 r-xp  08:01 12346051
/usr/lib64/libstdc++.so.6.0.8

35c6ae6000-35c6ce5000 ---p 000e6000 08:01 12346051
/usr/lib64/libstdc++.so.6.0.8

35c6ce5000-35c6ceb000 r--p 000e5000 08:01 12346051
/usr/lib64/libstdc++.so.6.0.8

35c6ceb000-35c6cee000 rw-p 000eb000 08:01 12346051
/usr/lib64/libstdc++.so.6.0.8

35c6cee000-35c6d0 rw-p 35c6cee000 00:00 0 

35c720-35c720d000 r-xp  08:01 4321444
/lib64/libgcc_s-4.1.2-20080102.so.1

35c720d000-35c740d000 ---p d000 08:01 4321444
/lib64/libgcc_s-4.1.2-20080102.so.1

35c740d000-35c740e000 rw-p d000 08:01 4321444
/lib64/libgcc_s-4.1.2-20080102.so.1

2af35799b000-2af35799e000 rw-p 2af35799b000 00:00 0 

2af3579a7000-2af3579a8000 rw-p 2af3579a7000 00:00 0 

2af3579a8000-2af3579aa000 r-xp  08:01 4321435
/lib64/libdl-2.5.so

2af3579aa000-2af357baa000 ---p 2000 08:01 4321435
/lib64/libdl-2.5.so

2af357baa000-2af357bab000 r--p 2000 08:01 4321435
/lib64/libdl-2.5.so

2af357bab000-2af357bac000 rw-p 3000 08:01 4321435
/lib64/libdl-2.5.so

2af357bac000-2af357bc1000 r-xp  08:01 4321439
/lib64/libpthread-2.5.so

2af357bc1000-2af357dc

[Freesurfer] mri_glmfit significiance verification outside freesurfer

[Jeff Sadino]

Hello Surfers,

I am trying to verify the p-value sig.mgh maps outputted from the mri_glmfit 
command as the first part of a more advanced analysis.  We have been extracting 
the thickness data for a single vertex from each of our 58 subjects in two 
control groups and then running a significiance analysis is SAS.  We thought 
that the output from SAS should match the p-value in the sig.mgh file, but the 
p-values do not match at all.  We have tested multiple data points.  Does 
freesurfer do some sort of a more advanced significance analysis that is not in 
the standard documentation?

Thank you very much,
Jeff Sadino

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Re: [Freesurfer] mri_glmfit significiance verification outside freesurfer

[Nick Schmansky]

Jeff,

sig.mgh actually stores the -log10(p), not p, so to get the true p-value
of say, -2 (in the sig.mgh), take 10^-2  (giving you the true p-value of
0.01).

Nick


On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
> Hello Surfers,
> 
> I am trying to verify the p-value sig.mgh maps outputted from the
> mri_glmfit command as the first part of a more advanced analysis.  We
> have been extracting the thickness data for a single vertex from each
> of our 58 subjects in two control groups and then running a
> significiance analysis is SAS.  We thought that the output from SAS
> should match the p-value in the sig.mgh file, but the p-values do not
> match at all.  We have tested multiple data points.  Does freesurfer
> do some sort of a more advanced significance analysis that is not in
> the standard documentation?
> 
> Thank you very much,
> Jeff Sadino
> 
> 
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Re: [Freesurfer] mri_glmfit significiance verification outside freesurfer

[Douglas N Greve]

Also, p-values for t-tests are two-sided.

Nick Schmansky wrote:

Jeff,

sig.mgh actually stores the -log10(p), not p, so to get the true p-value
of say, -2 (in the sig.mgh), take 10^-2  (giving you the true p-value of
0.01).

Nick


On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
  

Hello Surfers,

I am trying to verify the p-value sig.mgh maps outputted from the
mri_glmfit command as the first part of a more advanced analysis.  We
have been extracting the thickness data for a single vertex from each
of our 58 subjects in two control groups and then running a
significiance analysis is SAS.  We thought that the output from SAS
should match the p-value in the sig.mgh file, but the p-values do not
match at all.  We have tested multiple data points.  Does freesurfer
do some sort of a more advanced significance analysis that is not in
the standard documentation?

Thank you very much,
Jeff Sadino


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[Freesurfer] Brain cortical structures segmentation - comparison of hippocampal volumes

[Flavio Seixas]

My name is Flavio, student at Universidade Federal Fluminense. I research
image segmentation methods applied to brain cortical structures
segmentation.

 

I've compared against the hippocampal region got from FIRST-FSL to
Freesurfer, using the same magnetic resonance (MR) image.

 

The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford.
I found out a great volume difference between segmentations. Despite
different automated image analysis tool,  I was expecting a higher volume
overlap index when comparing the same brain structure from the same MR
image. I got about 25% volume overlap.

 

Is there any "recon-all" flag that I can use in conjunction with entire
process so as to get better volume overlap? I would appreciate any
suggestion.

 

Thank you in advance,

Flavio.

 

 

 

 

 

 

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Re: [Freesurfer] mris_anatomical_stats

[Nick Schmansky]

Kevin,

I've tracked down some memory trampling going on in
mris_anatomical_stats, and posted a fixed version for linux x86_64 here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/linux-
centos4_x86_64

Nick

On Mon, 2009-06-08 at 15:10 -0700, Kevin Scheibel wrote:
> I am running mris_anatomical_stats and keep getting the same error.
> Here’s the entire log file…looks like the big error happens at ‘glibc
> detected’
> 
>  
> 
> computing statistics for each annotation
> in /ifs/woods/scott_temp/kevin_work/freeseg/subj/078/label/rh.aparc.annot.
> 
> outputting results
> to 
> /ifs/tmp/pipeline-4.2/pipelnvr/2009June08_15h03m16s361ms/MRISAnatomicalStats.StatsFile_0-077.stats...
> 
> reading
> volume /ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/mri/wm.mgz...
> 
> reading input
> surface /ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.pial...
> 
> reading input pial
> surface /ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.pial...
> 
> reading input white
> surface /ifs/woods/scott_temp/kevin_work/freeseg/subj_xfm/078/surf/lh.white...
> 
> reading colortable from annotation file...
> 
> colortable with 36 entries read
> (originally 
> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
> 
> *** glibc detected
> *** /usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats: free
> (): invalid pointer: 0x2af35c93d000 ***
> 
> === Backtrace: =
> 
> /lib64/libc.so.6[0x35c4671684]
> 
> /lib64/libc.so.6(cfree+0x8c)[0x35c4674ccc]
> 
> /lib64/libc.so.6(_IO_free_backup_area+0x18)[0x35c466dd68]
> 
> /lib64/libc.so.6(_IO_file_overflow+0x1d2)[0x35c466bd62]
> 
> /lib64/libc.so.6(_IO_vfprintf+0x4a7e)[0x35c4646d4e]
> 
> /lib64/libc.so.6(_IO_fprintf+0x88)[0x35c464cf68]
> 
> /usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats(vfprintf
> +0x338d)[0x40898d]
> 
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x35c461d8b4]
> 
> /usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats
> (__gxx_personality_v0+0xfa)[0x40626a]
> 
> === Memory map: 
> 
> 0040-00786000 r-xp  00:16
> 238900739  
> /usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats
> 
> 00886000-008e rw-p 00386000 00:16
> 238900739  
> /usr/local/freesurfer-4.3.0_64bit/bin/mris_anatomical_stats
> 
> 008e-0209f000 rw-p 008e 00:00 0 
> 
> 04da5000-0b132000 rw-p 04da5000 00:00 0 
> 
> 35c420-35c421a000 r-xp  08:01
> 4321433/lib64/ld-2.5.so
> 
> 35c441a000-35c441b000 r--p 0001a000 08:01
> 4321433/lib64/ld-2.5.so
> 
> 35c441b000-35c441c000 rw-p 0001b000 08:01
> 4321433/lib64/ld-2.5.so
> 
> 35c460-35c474a000 r-xp  08:01
> 4321434/lib64/libc-2.5.so
> 
> 35c474a000-35c4949000 ---p 0014a000 08:01
> 4321434/lib64/libc-2.5.so
> 
> 35c4949000-35c494d000 r--p 00149000 08:01
> 4321434/lib64/libc-2.5.so
> 
> 35c494d000-35c494e000 rw-p 0014d000 08:01
> 4321434/lib64/libc-2.5.so
> 
> 35c494e000-35c4953000 rw-p 35c494e000 00:00 0 
> 
> 35c4a0-35c4a21000 r-xp  08:01
> 12354411   /usr/lib64/libjpeg.so.62.0.0
> 
> 35c4a21000-35c4c2 ---p 00021000 08:01
> 12354411   /usr/lib64/libjpeg.so.62.0.0
> 
> 35c4c2-35c4c21000 rw-p 0002 08:01
> 12354411   /usr/lib64/libjpeg.so.62.0.0
> 
> 35c4e0-35c4e57000 r-xp  08:01
> 12354412   /usr/lib64/libtiff.so.3.8.2
> 
> 35c4e57000-35c5056000 ---p 00057000 08:01
> 12354412   /usr/lib64/libtiff.so.3.8.2
> 
> 35c5056000-35c5059000 rw-p 00056000 08:01
> 12354412   /usr/lib64/libtiff.so.3.8.2
> 
> 35c520-35c5282000 r-xp  08:01
> 4321204/lib64/libm-2.5.so
> 
> 35c5282000-35c5481000 ---p 00082000 08:01
> 4321204/lib64/libm-2.5.so
> 
> 35c5481000-35c5482000 r--p 00081000 08:01
> 4321204/lib64/libm-2.5.so
> 
> 35c5482000-35c5483000 rw-p 00082000 08:01
> 4321204/lib64/libm-2.5.so
> 
> 35c620-35c6214000 r-xp  08:01
> 12346484   /usr/lib64/libz.so.1.2.3
> 
> 35c6214000-35c6413000 ---p 00014000 08:01
> 12346484   /usr/lib64/libz.so.1.2.3
> 
> 35c6413000-35c6414000 rw-p 00013000 08:01 12346484
>  /usr/lib64/libz.so.1.2.3
> 
> 35c660-35c6609000 r-xp  08:01
> 4321447/lib64/libcrypt-2.5.so
> 
> 35c6609000-35c6808000 ---p 9000 08:01
> 4321447/lib64/libcrypt-2.5.so
> 
> 35c6808000-35c6809000 r--p 8000 08:01
> 4321447/lib64/libcrypt-2.5.so
> 
> 35c6809000-35c680a000 rw-p 9000 08:01
> 4321447/lib64/libcrypt-2.5.so
> 
> 35c680a000-35c6838000 rw-p 35c680a000 00:

Re: [Freesurfer] TAL QA check failed

[Douglas N Greve]

did the you look at the registration?

Barnali Basu wrote:

Experts,

I got the following error while running a subject with recon-all 
autorecon1



ERROR: Talairach QA check failed!
   z-score = -8 <= -4 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 
2008 i686 GNU/Linux


recon-all exited with ERRORS at Fri Jun  5 22:35:17 PDT 2009


I gathered from other posts on this error that the fix depends upon 
the z -score.  In this case the z-score is -8, what is the best way to 
get it fixed. Previously i had fixed similar error and i had fixed it 
with tkregister2, but z-score was different


Thanks and Regards
--
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Cell   : 425 638 2936
Home: 206 257 0174


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Re: [Freesurfer] Brain cortical structures segmentation - comparison of hippocampal volumes

[Bruce Fischl]

Hi Flavio,

25% is pretty low. Can you send us an example image of our segmentation?

cheers,
Bruce
On 
Mon, 8 Jun 2009, Flavio Seixas wrote:



My name is Flavio, student at Universidade Federal Fluminense. I research
image segmentation methods applied to brain cortical structures
segmentation.



I've compared against the hippocampal region got from FIRST-FSL to
Freesurfer, using the same magnetic resonance (MR) image.



The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford.
I found out a great volume difference between segmentations. Despite
different automated image analysis tool,  I was expecting a higher volume
overlap index when comparing the same brain structure from the same MR
image. I got about 25% volume overlap.



Is there any "recon-all" flag that I can use in conjunction with entire
process so as to get better volume overlap? I would appreciate any
suggestion.



Thank you in advance,

Flavio.















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Re: [Freesurfer] TAL QA check failed

[Barnali Basu]

No. Do I need to look at it with tkregister?

On Mon, Jun 8, 2009 at 5:05 PM, Douglas N Greve
wrote:

> did the you look at the registration?
>
> Barnali Basu wrote:
>
>> Experts,
>>
>> I got the following error while running a subject with recon-all
>> autorecon1
>>
>>
>> ERROR: Talairach QA check failed!
>>   z-score = -8 <= -4 = threshold
>> Manual Talairach alignment may be necessary, or
>> include the -notal-check flag to skip this test.
>> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
>> Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 2008
>> i686 GNU/Linux
>>
>> recon-all exited with ERRORS at Fri Jun  5 22:35:17 PDT 2009
>>
>>
>> I gathered from other posts on this error that the fix depends upon the z
>> -score.  In this case the z-score is -8, what is the best way to get it
>> fixed. Previously i had fixed similar error and i had fixed it with
>> tkregister2, but z-score was different
>>
>> Thanks and Regards
>> --
>> Barnali Basu
>>
>> Cell   : 425 638 2936
>> Home: 206 257 0174
>> 
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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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:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>


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Cell   : 425 638 2936
Home: 206 257 0174
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Re: [Freesurfer] TAL QA check failed

[Douglas N Greve]

Yea, as the error message says, you should check out the web page, it 
will give you all the instructions you need.


doug

Barnali Basu wrote:

No. Do I need to look at it with tkregister?

On Mon, Jun 8, 2009 at 5:05 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


did the you look at the registration?

Barnali Basu wrote:

Experts,

I got the following error while running a subject with
recon-all autorecon1


ERROR: Talairach QA check failed!
  z-score = -8 <= -4 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00
UTC 2008 i686 GNU/Linux

recon-all exited with ERRORS at Fri Jun  5 22:35:17 PDT 2009


I gathered from other posts on this error that the fix depends
upon the z -score.  In this case the z-score is -8, what is
the best way to get it fixed. Previously i had fixed similar
error and i had fixed it with tkregister2, but z-score was
different

Thanks and Regards
-- 
Barnali Basu


Cell   : 425 638 2936
Home: 206 257 0174


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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






--
Barnali Basu

Cell   : 425 638 2936
Home: 206 257 0174


--
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] mri_glmfit significiance verification outside freesurfer

[Jeff Sadino]

Hello Everyone,
Thank you all for your replies.  We converted the values into -log10(p) and 
accounted for two-tailed, but the values were still off, and they are not even 
off in any consistent pattern.  For example:
FS:   .1541   .1109   .0749   .0641   .0514   .0281   .0182   .0141   .0132   
.0025   .0007   .0006
SAS: .3226   .0852   .2131   .0818   .0760   .2425   .6196   .0020   .0458   
.0039   .0003   .0020

Our SAS program only gives output to four digits.  Could the discrepencies be 
coming from rounding errors?

Mahalo,
Jeff

> Date: Mon, 8 Jun 2009 19:21:53 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: ni...@nmr.mgh.harvard.edu
> CC: jsad...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit significiance verification outside   
> freesurfer
> 
> Also, p-values for t-tests are two-sided.
> 
> Nick Schmansky wrote:
> > Jeff,
> >
> > sig.mgh actually stores the -log10(p), not p, so to get the true p-value
> > of say, -2 (in the sig.mgh), take 10^-2  (giving you the true p-value of
> > 0.01).
> >
> > Nick
> >
> >
> > On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
> >   
> >> Hello Surfers,
> >>
> >> I am trying to verify the p-value sig.mgh maps outputted from the
> >> mri_glmfit command as the first part of a more advanced analysis.  We
> >> have been extracting the thickness data for a single vertex from each
> >> of our 58 subjects in two control groups and then running a
> >> significiance analysis is SAS.  We thought that the output from SAS
> >> should match the p-value in the sig.mgh file, but the p-values do not
> >> match at all.  We have tested multiple data points.  Does freesurfer
> >> do some sort of a more advanced significance analysis that is not in
> >> the standard documentation?
> >>
> >> Thank you very much,
> >> Jeff Sadino
> >>
> >>
> >> __
> >> Windows Live™ SkyDrive™: Get 25 GB of free online storage. Get it on
> >> your BlackBerry or iPhone.
> >> ___
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> >> 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
> >
> >
> >   
> 
> -- 
> 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] Brain cortical structures segmentation - comparison of hippocampal volumes

[Pedro Paulo de Magalhães Oliveira Junior]

I think FreeSurfer has more reliability. In houndreds of manually
segmented hippocampi we found FreeSurfer measures to be pretty stable.

the manually segmented hippocampi usually has 15% - 20% less volume.
However we still don't know which method is more accurate. There's a
study right now in USP to try to figure it out using the removed
hippocampi.

If you need a local help (I mean in Brazil) you can write to my e-mail

2009/6/8, Flavio Seixas :
> My name is Flavio, student at Universidade Federal Fluminense. I research
> image segmentation methods applied to brain cortical structures
> segmentation.
>
>
>
> I've compared against the hippocampal region got from FIRST-FSL to
> Freesurfer, using the same magnetic resonance (MR) image.
>
>
>
> The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford.
> I found out a great volume difference between segmentations. Despite
> different automated image analysis tool,  I was expecting a higher volume
> overlap index when comparing the same brain structure from the same MR
> image. I got about 25% volume overlap.
>
>
>
> Is there any "recon-all" flag that I can use in conjunction with entire
> process so as to get better volume overlap? I would appreciate any
> suggestion.
>
>
>
> Thank you in advance,
>
> Flavio.
>
>
>
>
>
>
>
>
>
>
>
>
>
>

-- 
Enviado do meu celular

---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br

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Re: [Freesurfer] Brain cortical structures segmentation - comparison of hippocampal volumes

[Bruce Fischl]

you also have to be careful of differences in definition (e.g. is the 
fimbria part of the hippocampus?)


cheers,
Bruce
On Mon, 8 Jun 2009, Pedro Paulo de 
Magalhães Oliveira Junior wrote:



I think FreeSurfer has more reliability. In houndreds of manually
segmented hippocampi we found FreeSurfer measures to be pretty stable.

the manually segmented hippocampi usually has 15% - 20% less volume.
However we still don't know which method is more accurate. There's a
study right now in USP to try to figure it out using the removed
hippocampi.

If you need a local help (I mean in Brazil) you can write to my e-mail

2009/6/8, Flavio Seixas :

My name is Flavio, student at Universidade Federal Fluminense. I research
image segmentation methods applied to brain cortical structures
segmentation.



I've compared against the hippocampal region got from FIRST-FSL to
Freesurfer, using the same magnetic resonance (MR) image.



The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford.
I found out a great volume difference between segmentations. Despite
different automated image analysis tool,  I was expecting a higher volume
overlap index when comparing the same brain structure from the same MR
image. I got about 25% volume overlap.



Is there any "recon-all" flag that I can use in conjunction with entire
process so as to get better volume overlap? I would appreciate any
suggestion.



Thank you in advance,

Flavio.
















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Re: [Freesurfer] Brain cortical structures segmentation - comparison of hippocampal volumes

[Jamie Hanson]

also of note, there are three recent papers comparing manual
hippocampal tracing to freesurfer automated segments...

Shen L, Firpi HA, Saykin AJ, West JD. (2009). Parametric surface
modeling and registration for comparison of manual and automated
segmentation of the hippocampus. Hippocampus. Jun;19(6):588-95.

Cherbuin N, Anstey KJ, Réglade-Meslin C, Sachdev PS. (2009). In vivo
hippocampal measurement and memory: a comparison of manual tracing and
automated segmentation in a large community-based sample. PLoS ONE.
4(4):e5265. Epub 2009 Apr 16.

Morey RA, Petty CM, Xu Y, Hayes JP, Wagner HR 2nd, Lewis DV, LaBar KS,
Styner M, McCarthy G. (2009). A comparison of automated segmentation
and manual tracing for quantifying hippocampal and amygdala volumes.
Neuroimage. 2009 Apr 15;45(3):855-66. Epub 2008 Dec 30.
***This paper looked at Freesurfer, FSL's FAST, and manual tracings...

Best,
jamie.




> I think FreeSurfer has more reliability. In houndreds of manually
> segmented hippocampi we found FreeSurfer measures to be pretty stable.
>
> the manually segmented hippocampi usually has 15% - 20% less volume.
> However we still don't know which method is more accurate. There's a
> study right now in USP to try to figure it out using the removed
> hippocampi.
>
> If you need a local help (I mean in Brazil) you can write to my e-mail
>
> 2009/6/8, Flavio Seixas :
>> My name is Flavio, student at Universidade Federal Fluminense. I research
>> image segmentation methods applied to brain cortical structures
>> segmentation.
>>
>>
>>
>> I've compared against the hippocampal region got from FIRST-FSL to
>> Freesurfer, using the same magnetic resonance (MR) image.
>>
>>
>>
>> The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford.
>> I found out a great volume difference between segmentations. Despite
>> different automated image analysis tool,  I was expecting a higher volume
>> overlap index when comparing the same brain structure from the same MR
>> image. I got about 25% volume overlap.
>>
>>
>>
>> Is there any "recon-all" flag that I can use in conjunction with entire
>> process so as to get better volume overlap? I would appreciate any
>> suggestion.
>>
>>
>>
>> Thank you in advance,
>>
>> Flavio.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> Enviado do meu celular
>
> ---
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> Diretor de Operações
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Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab
University of Wisconsin - Madison
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Email: jamielarshan...@gmail.com
Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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RE: [Freesurfer] mri_glmfit significiance verification outside freesurfer

[Michael Harms]

Those differences are much too large to be rounding errors.
Are you sure that you are running identical models in mris_glmfit and SAS,
and that the data that you are testing in SAS is in fact what is being
processed in mris_glmfit (e.g., same degree of smoothing)?

-Mike H.

>
> Hello Everyone,
> Thank you all for your replies.  We converted the values into -log10(p)
> and accounted for two-tailed, but the values were still off, and they are
> not even off in any consistent pattern.  For example:
> FS:   .1541   .1109   .0749   .0641   .0514   .0281   .0182   .0141
> .0132   .0025   .0007   .0006
> SAS: .3226   .0852   .2131   .0818   .0760   .2425   .6196   .0020   .0458
>   .0039   .0003   .0020
>
> Our SAS program only gives output to four digits.  Could the discrepencies
> be coming from rounding errors?
>
> Mahalo,
> Jeff
>
>> Date: Mon, 8 Jun 2009 19:21:53 -0400
>> From: gr...@nmr.mgh.harvard.edu
>> To: ni...@nmr.mgh.harvard.edu
>> CC: jsad...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_glmfit significiance verification
>> outside  freesurfer
>>
>> Also, p-values for t-tests are two-sided.
>>
>> Nick Schmansky wrote:
>> > Jeff,
>> >
>> > sig.mgh actually stores the -log10(p), not p, so to get the true
>> p-value
>> > of say, -2 (in the sig.mgh), take 10^-2  (giving you the true p-value
>> of
>> > 0.01).
>> >
>> > Nick
>> >
>> >
>> > On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
>> >
>> >> Hello Surfers,
>> >>
>> >> I am trying to verify the p-value sig.mgh maps outputted from the
>> >> mri_glmfit command as the first part of a more advanced analysis.  We
>> >> have been extracting the thickness data for a single vertex from each
>> >> of our 58 subjects in two control groups and then running a
>> >> significiance analysis is SAS.  We thought that the output from SAS
>> >> should match the p-value in the sig.mgh file, but the p-values do not
>> >> match at all.  We have tested multiple data points.  Does freesurfer
>> >> do some sort of a more advanced significance analysis that is not in
>> >> the standard documentation?
>> >>
>> >> Thank you very much,
>> >> Jeff Sadino
>> >>
>> >>
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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:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>
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[Freesurfer] Stand processing prepared for longitudinal pipeline.

[Hui Zheng]

Hi,

We are processing our data for the longitudinal pipeline. I found some
subjects' brainmask with skull/dura remaining, and a portion of the skull
was segmented as cortical gray matter in aseg. I'd like to ask if this kind
of problem will affect the longitudinal registration/template creation?

I have one more question. Is the method described in the paper by Golland P
(2003), Permutation Tests for Classification: Towards Statistical
Significance in Image-Based Studies, used in FreeSurfer?

Thanks,
Zheng Hui

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