Re: [Freesurfer] Cannot allocate memory

[Mayer Kristina]

Dear Bruce,

I was running:
recon-all -autorecon2-cp, after adding control points.
When I then look at the surfaces using tkmedit -surfs or inflated surfaces 
using tksurfer, everything seems to fit and I can open every output I like.
Also values for volumes seem reasonable.

Thanks in advance.

Best,
Kristina

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 12. Mai 2014 15:44
An: Freesurfer support list
Betreff: Re: [Freesurfer] Cannot allocate memory

Hi Kristina

you need to give us more context. What command is running when you get
that error?

cheers
Bruce

On Mon, 12 May 2014, Mayer Kristina wrote:

> Hi there,
>
> I am using freesurfer on MRI data of children.
> In one dataset I have following error appearing, I did not find described 
> before.
>
> MRISalloc(41043678, 76): could not allocate faces
> Cannot allocate memory
> Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
> x86_64 x86_64 x86_64 GNU/Linux
>
> Waht do I have to check or edit manually?
>
> Thanks!
>
> Best,
> Kristina
>
>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

Thank you for your reply. I was interested in looking how the thickness
changes from the posterior to the anterior side of the brain and vice
versa (the thickness gradient).

Thank you again for your time!
Panos


> Hi Panos
>
> it would certainly be possible to make that measurement, but it wouldn't
> tell you anything biologically interesting. Why would you want to do such
> a
> thing? It will reflect the (arbitrary) image slice orientation and not the
> brain.
>
> cheers
> Bruce
>
>
> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was wondering whether it would be possible to measure the average
>> cortical thickness at a specific slice (either axial, coronal, or
>> sagittal). I read in Bruce's paper: "Measuring the thickness of the
>> human
>> cerebral cortex from magnetic resonance images" that "Measuring the
>> thickness from the coronal slice at the point indicated by the green
>> cross
>> would result in an estimate in excess of 1 cm." Is that always the case,
>> or has there been a way to bypass that issue?
>>
>> Thank you for your time,
>> Panos
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>>
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Re: [Freesurfer] EM registration: brain centroid

[Mark Plantz]

Yes, I created my own atlas for use with 1-2 year olds. It seems to be
happening for all of the subjects. I am wondering if changing the recon-all
code to load the manual talairach.lta
 file for the EM_registration and CA_normalization would possibly fix the
problem. It seems strange that the wm/gm means were OK for skull stripping,
but then suddenly null for the other steps.


On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl wrote:

> Hi Mark
>
> did you create your own .gca file? If so, why? Does it happen for all your
> subjects?
> Bruce
>
>
>
>
>
> On Mon, 12 May 2014, Mark Plantz wrote:
>
>  As a quick update to this problem, it looks like the wm_mean and gm_mean
>> are reasonable
>> during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and
>> gm mean = 0 for the
>> #CA_normalize and #EM_registration steps.
>> Could this have anything to do with using a manual talairach alignment in
>> previous steps? I
>> did include the -nogcareg flag with the recon-all command.
>>
>>
>> On Mon, May 12, 2014 at 4:36 PM, Mark Plantz > northwestern.edu> wrote:
>>   Hi Freesurfers,
>>Does anyone know if it is possible to manually set the brain centroid
>> during the EM
>> Registration step of the recon-all pipeline. I am using a non-default
>> atlas, and have
>> discovered that many of my difficulties have resulted from the brain
>> centroid being
>> incorrectly assigned to a region of black space. Thank you for the help!
>>
>> Best,
>>
>> MP
>>
>>
>>
>>
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Re: [Freesurfer] EM registration: brain centroid

[Bruce Fischl]

Hi Mark

did you create your own .gca file? If so, why? Does it happen for all your 
subjects?

Bruce




On Mon, 12 May 2014, Mark Plantz wrote:


As a quick update to this problem, it looks like the wm_mean and gm_mean are 
reasonable
during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm 
mean = 0 for the
#CA_normalize and #EM_registration steps. 
Could this have anything to do with using a manual talairach alignment in 
previous steps? I
did include the -nogcareg flag with the recon-all command.


On Mon, May 12, 2014 at 4:36 PM, Mark Plantz 
 wrote:
  Hi Freesurfers,
   Does anyone know if it is possible to manually set the brain centroid during 
the EM
Registration step of the recon-all pipeline. I am using a non-default atlas, 
and have
discovered that many of my difficulties have resulted from the brain centroid 
being
incorrectly assigned to a region of black space. Thank you for the help!

Best,

MP 



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Re: [Freesurfer] Measuring cortical thickness at a specific location

[Bruce Fischl]

Hi Panos

it would certainly be possible to make that measurement, but it wouldn't 
tell you anything biologically interesting. Why would you want to do such a 
thing? It will reflect the (arbitrary) image slice orientation and not the 
brain.

cheers
Bruce


On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering whether it would be possible to measure the average
> cortical thickness at a specific slice (either axial, coronal, or
> sagittal). I read in Bruce's paper: "Measuring the thickness of the human
> cerebral cortex from magnetic resonance images" that "Measuring the
> thickness from the coronal slice at the point indicated by the green cross
> would result in an estimate in excess of 1 cm." Is that always the case,
> or has there been a way to bypass that issue?
>
> Thank you for your time,
> Panos
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Re: [Freesurfer] Fwd: Overinclusion of brain volume during segmentation - Question

[Bruce Fischl]

Hi Christina

it's pretty hard to diagnose from just a handful of slices. I also doubt 
that it's a huge underinclusion - probably if you move click on a point 
and change to sagittal you'll see it looks less dramatic. In any case, if 
you upload a dataset we'll take a look. Alternatively you can try the 
expert options to mris_make_surfaces to constrain the range of allowable 
intensities outside the pial surface.


cheers
Bruce
On Mon, 12 May 2014, Christina Chen 
wrote:



Hi!  
I've attached 2 pictures of some brain scans on Freesurfer -- is there any way 
we can fix
the huge underinclusion of the gray matter, hopefully without changing the 
surfaces of the
white matter?  What should be done with these scans to fix them?

Thanks!
Christina


On Thu, Mar 20, 2014 at 2:32 PM, Douglas N Greve  
wrote:

  cortical stats reported by asegstats2table use the surfaces, not the
  cortical segmentation in aseg.mgz
  doug

  On 03/20/2014 05:29 PM, Christina Chen wrote:
  > Thanks a lot!!  I have a follow up question:
  >
  > We use the command
  >
  > asegstats2table
  >
  > to output the subcortical volumes (and other whole brain volumes)  to
  > table. If the aseg is incorrect, can we still believe those values?
  >
  > Thanks,
  > Christina
  >
  >
  > On Thu, Mar 20, 2014 at 1:27 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
>     Hi Christina
>
>     if the aseg is incorrect but the surfaces are right, then you
>     don't need to worry about it. This is the reason we typically use
>     the surfaces instead of the aseg for things like brain
>     volume/cortex modeling.
>
>     cheers
>     Bruce
>
>     On Thu, 20 Mar 2014, Christina Chen wrote:
>
>         Hi!
>         If the cortical surface outlines are fine, but there is an
>         overinclusion of
>         brain volume during segmentation, how should I fix this?  Can
>         we calculate
>         brain volume based on the cortical surface outlines -- if so, how?
>
>         Thanks!
>         Christina
>
>
>
>
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Re: [Freesurfer] EM registration: brain centroid

[Mark Plantz]

As a quick update to this problem, it looks like the wm_mean and gm_mean
are reasonable during the #SkullLTA and #SkullStripping steps. However, wm
mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps.

Could this have anything to do with using a manual talairach alignment in
previous steps? I did include the -nogcareg flag with the recon-all command.


On Mon, May 12, 2014 at 4:36 PM, Mark Plantz <
markplantz2...@u.northwestern.edu> wrote:

> Hi Freesurfers,
>
>Does anyone know if it is possible to manually set the brain centroid
> during the EM Registration step of the recon-all pipeline. I am using a
> non-default atlas, and have discovered that many of my difficulties have
> resulted from the brain centroid being incorrectly assigned to a region of
> black space. Thank you for the help!
>
> Best,
>
> MP
>
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[Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi FS experts,

I was wondering whether it would be possible to measure the average
cortical thickness at a specific slice (either axial, coronal, or
sagittal). I read in Bruce's paper: "Measuring the thickness of the human
cerebral cortex from magnetic resonance images" that "Measuring the
thickness from the coronal slice at the point indicated by the green cross
would result in an estimate in excess of 1 cm." Is that always the case,
or has there been a way to bypass that issue?

Thank you for your time,
Panos
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Re: [Freesurfer] Paradigm files

[Douglas N Greve]

Yes, you can do that as long as you are not using an FIR analysis.
doug



On 05/12/2014 04:56 PM, Emily Boeke wrote:
> Hi Freesurfers,
>
> I am doing some analyses for an experiment where paradigm files were 
> automatically generated by Matlab during stimulus presentation. The script 
> was designed to make paradigm files for an older version of freesurfer, so 
> the files only have 2 columns. I am going to adjust these files so that they 
> can be read by FS 5.3 (add in the extra columns needed).
>
> I noticed that there is a line for each TR as opposed to for the onset of 
> each stimulus, for example, it looks something like this:
>
> 0 2
> 2 2   
> 4 2   
> 6 2
> 8 1
> 101
> 121
> 143
> 163   
>   
> instead of
>
> 0 2
> 8 1
> 143
>
> Is this a problem? Can I leave it as is and then just add a column of 2s and 
> a column of 1s?
>
> Thanks!
>
> Emily
>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] EM registration: brain centroid

[Mark Plantz]

Hi Freesurfers,

   Does anyone know if it is possible to manually set the brain centroid
during the EM Registration step of the recon-all pipeline. I am using a
non-default atlas, and have discovered that many of my difficulties have
resulted from the brain centroid being incorrectly assigned to a region of
black space. Thank you for the help!

Best,

MP
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Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

[Bruce Fischl]

Hi Christopher

I don't think you will be able to draw the geodesic distance in the 
ribbon in 3D as it will  cut across imaging planes unpredictably. If you 
want the true within-subject geodesic distance there are tools for doing 
this (I think it was part of Mukund Balasubramanian's Ph.D. dissertation at 
BU among other places). Rudolph might have also implemented something like 
it in his tools.


cheers
Bruce


On Mon, 12 May 2014, Milde, Christopher 
wrote:



Thanx Bruce,

I will try out your suggestion and let you know. I think I will get a good 
estimate of the degree of metric distortions, because I have a lot of subjects 
tested ;-)

If this will not work, or the distortions are to big, I will make use of the Spline 
Tool in Freeview manually drawing a line within the cortical ribbon between the peak 
voxels, whereby benefitting from the reconstructed surface brain with superimposed 
EPI (with post inflation smoothed EPI data) for visual comparison (to benefit from 
the SBR versus VBR information, to avoid the problem of guessing if an activated 
cluster belongs to Gyrus A or B when the Cluster is spread along two attached gyri). 
Maybe I can also make use of the coordinate transormations RAS <-->sphere

Greetz,

Christopher


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 12. Mai 2014 15:46
An: Freesurfer support list
Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage 
group sphere

Hi Christopher

the spherical mapping usually has on the order of 17-20% distortion in
distances, and the registration is probably significantly more. I'm not
entirely sure what are trying to do, but you can measure the difference in
great circle length between the sphere and sphere.reg to get an idea of how
much additional distortion is induced by the registration

cheers
Bruce



On Mon, 12 May 2014, Milde, Christopher wrote:



Dear Freesurfers,



In Fischl et al. 1999 it is highlighted, that the topological structure of the 
original
surface is preserved in the spherical space and due to the nature of a sphere, 
computations
(distance, area) measures are easy to make.



My question now, concerns the comparability of distance measures between 
subjects in the
group fsaverage sphere. My aim is to compare distances between peak voxels 
coordinates of
two study populations, to figure out if a systematic difference exist between 
the peak voxel
distances of the two study populations.



Can I compare the distances between peak voxels (vertices) between different 
subjects based
on the fsaverage group sphere? So, is the comparability of distances between 
vertexes of
individually spheres preserved in group fsaverage space?



Ps: I know that the distances in spherical space are not Euclidian but still 
geodesic





Best wishes and thanks in advance,





Christopher Milde, M.Sc. Biol.

Institute for Cognitive and Clinical Neuroscience

Central Institute of Mental Health Square J 5

68159 Mannheim, Germany





Christopher Milde, M.Sc. Biol.

Institute for Cognitive and Clinical Neuroscience

Central Institute of Mental Health Square J 5

68159 Mannheim, Germany



Phone:  +49-621-1703-6313

E-mail:  christopher.mi...@zi-mannheim.de

Homepage:http://www.zi-mannheim.de/

Office:  Forschungs- und Verwaltungsgebäude, Room 230







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Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

[Milde, Christopher]

Thanx Bruce,

I will try out your suggestion and let you know. I think I will get a good 
estimate of the degree of metric distortions, because I have a lot of subjects 
tested ;-)

If this will not work, or the distortions are to big, I will make use of the 
Spline Tool in Freeview manually drawing a line within the cortical ribbon 
between the peak voxels, whereby benefitting from the reconstructed surface 
brain with superimposed EPI (with post inflation smoothed EPI data) for visual 
comparison (to benefit from the SBR versus VBR information, to avoid the 
problem of guessing if an activated cluster belongs to Gyrus A or B when the 
Cluster is spread along two attached gyri). Maybe I can also make use of the 
coordinate transormations RAS <-->sphere

Greetz,

Christopher
 

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 12. Mai 2014 15:46
An: Freesurfer support list
Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage 
group sphere

Hi Christopher

the spherical mapping usually has on the order of 17-20% distortion in
distances, and the registration is probably significantly more. I'm not
entirely sure what are trying to do, but you can measure the difference in
great circle length between the sphere and sphere.reg to get an idea of how
much additional distortion is induced by the registration

cheers
Bruce



On Mon, 12 May 2014, Milde, Christopher wrote:

>
> Dear Freesurfers,
>
>
>
> In Fischl et al. 1999 it is highlighted, that the topological structure of 
> the original
> surface is preserved in the spherical space and due to the nature of a 
> sphere, computations
> (distance, area) measures are easy to make.
>
>
>
> My question now, concerns the comparability of distance measures between 
> subjects in the
> group fsaverage sphere. My aim is to compare distances between peak voxels 
> coordinates of
> two study populations, to figure out if a systematic difference exist between 
> the peak voxel
> distances of the two study populations.
>
>
>
> Can I compare the distances between peak voxels (vertices) between different 
> subjects based
> on the fsaverage group sphere? So, is the comparability of distances between 
> vertexes of
> individually spheres preserved in group fsaverage space?
>
>
>
> Ps: I know that the distances in spherical space are not Euclidian but still 
> geodesic
>
>
>
>
>
> Best wishes and thanks in advance,
>
>
>
>
>
> Christopher Milde, M.Sc. Biol.
>
> Institute for Cognitive and Clinical Neuroscience
>
> Central Institute of Mental Health Square J 5
>
> 68159 Mannheim, Germany
>
>
>
>
>
> Christopher Milde, M.Sc. Biol.
>
> Institute for Cognitive and Clinical Neuroscience
>
> Central Institute of Mental Health Square J 5
>
> 68159 Mannheim, Germany
>
>
>
> Phone:  +49-621-1703-6313
>
> E-mail:  christopher.mi...@zi-mannheim.de
>
> Homepage:http://www.zi-mannheim.de/
>
> Office:  Forschungs- und Verwaltungsgebäude, Room 230
>
>
>
>
>

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[Freesurfer] Paradigm files

[Emily Boeke]

Hi Freesurfers,

I am doing some analyses for an experiment where paradigm files were 
automatically generated by Matlab during stimulus presentation. The script was 
designed to make paradigm files for an older version of freesurfer, so the 
files only have 2 columns. I am going to adjust these files so that they can be 
read by FS 5.3 (add in the extra columns needed).

I noticed that there is a line for each TR as opposed to for the onset of each 
stimulus, for example, it looks something like this:

0   2
2   2   
4   2   
6   2
8   1
10  1
12  1
14  3
16  3   
 
instead of 

0   2
8   1
14  3

Is this a problem? Can I leave it as is and then just add a column of 2s and a 
column of 1s?

Thanks!

Emily
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Re: [Freesurfer] Viewing functional data on the inflated brain

[Sherryse Corrow]

Hi Douglas,

I don’t receive any emails from anyone, I only receive the the digest which is 
what I “reply” to. So I am not sure what you mean by “try responding to the 
email that I sent.”  This is why I attempted to email you directly as I thought 
that is what you were asking for.

I hope to have straightened things out by finding each part of our conversation 
and pasting them below (in reverse order). If you have further questions, 
please let me know.

Sincerely,
Sherryse




Message: 9
Date: Fri, 09 May 2014 17:36:36 -0400
From: Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Viewing functional data on the inflated
brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
<536d4a64.5000...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


both of what? Sorry, it looks like the thread was garbled below or
somehow the digest got into it. Try responding to the email that I sent
to keep things in order




On 05/09/2014 05:09 PM, Sherryse Corrow wrote:
Thanks Douglas.  Yes, both of those exist.


Douglas N 
Greve
 Wed, 07 May 2014 12:51:02 
–0700

It is looking for subject P143 in /usr/local/freesurfer/subjects

Does it exist? If so, does
/usr/local/freesurfer/subjects/P143/mri/brainmask.mgz
Exist?


Sherryse 
Corrow
 Wed, 07 May 2014 11:00:54 
-0700

Thanks Douglas.  We tried that . . . The registration matrix that we need
is not created. Here is the output log file (attached). I am a bit new to
this so I am hoping it has the information you need. After taking a quick
glance at the log file, we noticed there are errors in the log file.

Step by step, this is what we did after we ran recon-all:
Reg-feat2anat ‹feat OurFeatDirectory.feat ‹subject P143

When we open the folder experiment.feat/reg/freesurfer, there is no
anat2exf.register.dat file.  However, there is a file called:
anat2exf.register.dat.init.

Thanks,
Sherryse



Douglas 
Greve
 Mon, 05 May 2014 19:58:31 
–0700

Run reg-feat2anat. If that does not work, then send the command line and 
terminal output. Just saying that something does not work will not get you 
closer to a solution. We need to know what you did and what happened

Doug


Sherryse 
Corrow
 Mon, 05 May 2014 16:56:58 
–0700

Hi all,


Earlier today, I posted the message listed below.   However, we discovered part
of our issue.  When we run reg-feat2anat, there is no anat2exf.register.dat
file created.  Therefore, we have no registration matrix to use.  Before, we
were inadvertently using the anat2std file instead.  Any suggestions on how to
get the anat2exf.register.dat file created?

Thanks,
Sherryse


Douglas 
Greve
 Mon, 05 May 2014 19:50:18 
–0700

Can you tell us specifically what you have done? I mean command lines …

doug


Sherryse 
Corrow
 Mon, 05 May 2014 15:58:35 
-0700

Dear FreeSurfer community,

We are having some issues registering our functional data (or masks) from FSL
to an inflated brain in FreeSurfer.  Some of our masks, when registered to the
inflated brain and viewed in FreeSurfer, are not showing up on the cortical
surface.  We have followed web-tutorials for registration but are still having
the issue.  Any suggestions?
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Re: [Freesurfer] 2x3 DODS analysis question?

[Douglas N Greve]

I think the last contrast should be of the form

1 -1  0 -1  1 0 1 -1  0 -1  1 0
1  0 -1 -1  0 1 1  0 -1 -1  0 1

but I only looked over it briefly so you should double check that it 
makes sense. The others look ok
doug

On 05/09/2014 10:44 AM, Khadka, Sabin wrote:
> Hi all,
> I am trying to run 2x3 factorial model correcting for age, sex and 
> intracranial volume. Just to give you insight in my data I have my 
> fsgd file as
>
> GroupDescriptorFile 1
> Title DODS analysis 2x3 factorial
> Class MaleGroup1Low
> Class MaleGroup1Medium
> Class MaleGroup1High
> Class MaleGroup2Low
> Class MaleGroup2Medium
> Class MaleGroup2High
> Class FemaleGroup1Low
> Class FemaleGroup1Medium
> Class FemaleGroup1High
> Class FemaleGroup2Low
> Class FemaleGroup2Medium
> Class FemaleGroup2High
> Variables Age normVol
> Input SUB001 MaleGroup1Low 18 0.4
> .
> .
> .
>
> And also my contrast files as
> Group1Group2.mtx
> [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3
> MainEffectState.mtx
> 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0
> 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5
> HighvLow.mtx
> -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5
> HighvMed.mtx
> 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5
>
> GroupxState-interaction.mtx
> 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5
> 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5
>
> I'd appreciate if anyone could please let me know that my design is 
> correct.
>
> Thanks for help.
>
> -Sabin
>
>
> ___
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Error running recon-all on hpc computers

[Natalie Garcia]

Hi all,

I'm trying to run recon-all on some data using one of the hpc clusters at
my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem
but I'm trying to rerun the data with the new version.

I keep getting this error (FreeSurfer's log file is attached here)
regarding the mni/bin folder. Could this be an error on their end? Not sure
if maybe 5.3 wasn't installed correctly on the hpc machines.

Any help is really appreciated!

Thanks,
Natalie

-- 
 Natalie V. Garcia
Graduate Fellow, Cognitive Neuroscience
Department of Psychology
The Pennsylvania State University
423 Moore Building
University Park, PA 16802
nvg...@psu.edu
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0
Actual FREESURFER_HOME /gpfs/apps/x86_64-rhel6/freesurfer/5.3.0/freesurfer
-rw-rw+ 1 nvg109 nvg109 19843 May 12 13:06 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/scripts/recon-all.log
Linux cyberstar208.hpc.rcc.psu.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 
06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
Can't locate MNI/Startup.pm in @INC (@INC contains: 
/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/ /usr/local/lib64/perl5 
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl 
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
/usr/global/freesurfer/5.3.0/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at 
/usr/global/freesurfer/5.3.0/freesurfer/mni/bin/nu_correct line 37.
#
#@# MotionCor Mon May 12 13:12:41 EDT 2014
Found 1 runs
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig/001.mgz
 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz
 

/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118

 mri_convert 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz
 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz
 --conform 

mri_convert 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz
 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz
 --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz...
TR=1700.00, TE=1.78, TI=850.00, flip angle=9.00
i_ras = (0.0196223, -0.999733, 0.0122095)
j_ras = (-0.0346559, -0.0128847, -0.999316)
k_ras = (-0.999207, -0.0191857, 0.0348995)
Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz...

 mri_add_xform_to_header -c 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/transforms/talairach.xfm
 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz
 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz
 

INFO: extension is mgz
#
#@# Talairach Mon May 12 13:12:59 EDT 2014
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz 

Linux cyberstar208.hpc.rcc.psu.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 
06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 8118 exited with ERRORS at Mon May 12 13:13:05 EDT 2014

For more details, see the log file 
/gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] bbregister to register a .annot file to MNI space

[Douglas N Greve]

The immediate problem is with permissions. The bigger problem is what 
you are trying to do. To transfer the label, use mri_label2vol and 
$FREESURFER_HOME/mni152.register.dat to map aparc+aseg.mgz to mni152 
space. But this is not going to work very well because the label is 
small. Mixing volume-based and surface-based analysis in this way is 
strongly discouraged.

doug





On 05/12/2014 01:45 PM, Paul Beach wrote:
> Nathan,
>
> I've run into problems like these before when the fsaverage directory 
> is read only. This may be behind your "permission denied" error. 
> Perhaps try to deconstruct the annotation file into your subjects_dir 
> and do the bbregister command on your label of interest from there - 
> or just copy the annotation to your subjects_dir...
>
> Cheers
>
>
> On Mon, May 12, 2014 at 1:34 PM, Nathan Hutcheson  > wrote:
>
> Hello,
>
> I am trying to use bbrestier to take an .annot file of a
> particular structure and register it to MNI space. I want to be
> able to use one of the FreeSurfer parcellations of the ACC
> (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction
> in FSL in MNI space. Below is the command I used and the error
> message I am getting. Please let me know if what I am doing makes
> any sense or if I am way off base.
>
>
> Input
>
> bbregister --s fsaverage --mov
> /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label
> --t1 --init-fsl --reg register.dat
>
>
>  Output
>
> mkdir: cannot create directory `./tmp.bbregister.6489':
> Permission denied
>
> Log file is register.dat.log
>
> register.dat.log: Permission denied.
>
>
>
>
>
>
> Take care,
> Dr. Nathan Hutcheson
> Postdoctoral Researcher
> University of California Los Angeles
> Semel Institute
> 760 Westwood Plaza C8-202
> Los Angeles, CA 90024
> T: 770.841.1694 
> nathanhutcheson.com 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> -- 
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
>  - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>
>
> ___
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> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] bbregister to register a .annot file to MNI space

[Paul Beach]

Nathan,

I've run into problems like these before when the fsaverage directory is
read only. This may be behind your "permission denied" error. Perhaps try
to deconstruct the annotation file into your subjects_dir and do the
bbregister command on your label of interest from there - or just copy the
annotation to your subjects_dir...

Cheers


On Mon, May 12, 2014 at 1:34 PM, Nathan Hutcheson  wrote:

> Hello,
>
> I am trying to use bbrestier to take an .annot file of a particular
> structure and register it to MNI space. I want to be able to use one of the
> FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and
> do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used
> and the error message I am getting. Please let me know if what I am doing
> makes any sense or if I am way off base.
>
>
> Input
>
>> bbregister --s fsaverage --mov
>> /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1
>> --init-fsl --reg register.dat
>>
>>
>  Output
>
>> mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied
>>
>> Log file is register.dat.log
>>
>> register.dat.log: Permission denied.
>>
>
>
>
>
>
> Take care,
> Dr. Nathan Hutcheson
> Postdoctoral Researcher
> University of California Los Angeles
> Semel Institute
> 760 Westwood Plaza C8-202
> Los Angeles, CA 90024
> T: 770.841.1694
> nathanhutcheson.com
>  
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] bbregister to register a .annot file to MNI space

[Nathan Hutcheson]

Hello,

I am trying to use bbrestier to take an .annot file of a particular
structure and register it to MNI space. I want to be able to use one of the
FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and
do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used
and the error message I am getting. Please let me know if what I am doing
makes any sense or if I am way off base.


Input

> bbregister --s fsaverage --mov
> /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1
> --init-fsl --reg register.dat
>
>
 Output

> mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied
>
> Log file is register.dat.log
>
> register.dat.log: Permission denied.
>





Take care,
Dr. Nathan Hutcheson
Postdoctoral Researcher
University of California Los Angeles
Semel Institute
760 Westwood Plaza C8-202
Los Angeles, CA 90024
T: 770.841.1694
nathanhutcheson.com
 
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Re: [Freesurfer] nonlinear models in longitudinal analysis

[Jodie Davies-Thompson]

Hi Martin,

Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new to 
this!). Do you mean something like this?

For examining an increase between timepoint 1 and 2, but the same between 
timepoint 2 and 3?

fsid   fsid-base   years   years-to-years
Day1   base   0   0.4
Day2   base   0.4   0.4
Day3   base   0.8   0

All the best,
Jodie



Message: 6
Date: Fri, 09 May 2014 16:52:25 -0400
From: Martin Reuter 
Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <536d4009.7030...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Jodie,

'years' should contain the real time between time points (usually, 
unless you have test-retest where time is irrelevant, or different task 
that can be ordered as you like). For what you are trying to do you 
should use linear mixed effects models with a piecewise linear setup. 
This will allow you to estimate a slope before and after timepoint 2 and 
compare those slopes.
Your design matrix would probably have the column of 1, years and a 
column with
years-years(at tp2 of that subject)   if that value is positive
0 otherwise

Testing if the coef of the 3rd column is > 0 is asking if the slope 
increases in the second interval. Not exactly what you want, but close 
and of course you can test if the slope in interval 1 is different from 
zero (second column) and if the slope in interval 2 is different from 
zero ( 0 1 1, ie the sum of the last two columns).

Best, Martin

On 05/08/2014 03:48 PM, Jodie Davies-Thompson wrote:
> Dear Freesurfer experts,
>
> I am attempting to do a longitudinal analysis of cortical thickness with 3 
> timepoints. So far, I have successfully completed the analysis for 
> long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to 
> timepoint 3, and a linear increase for timepoint 1 to 2 to 3.
>
> However, I am primarily interested in finding regions which show a) an 
> increase between timepoint 1 and 2, but no difference between 2 and 3, and b) 
> no difference between timepoint 1 and 2, but an increase between 2 and 3.
>
> Would the correct way of 'modelling' these two in the qdec file be:
>
> a)
> fsid fsid-base years
> day1 base 0
> day2 base 3
> day3 base 3
>
> and b)
> fsid fsid-base years
> day1 base 0
> day2 base 0
> day3 base 3
>
> All the best,
> Jodie
>
> -
> ---
> Jodie Davies-Thompson, Postdoctoral Fellow
> Department of Ophthalmology & Visual Sciences
> UBC/VGH Eye Care Centre
> 2550 Willow Street
> Vancouver, BC, V5Z 3N9
> Canada
> Tel: 604-875-4111 ext 69003
>

-
---
Jodie Davies-Thompson, Postdoctoral Fellow
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
2550 Willow Street
Vancouver, BC, V5Z 3N9
Canada
Tel: 604-875-4111 ext 69003



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Re: [Freesurfer] Coomand not found

[Louis Nicholas Vinke]

Ok, could you send the entire terminal output?
Thanks.
-Louis

On Mon, 12 May 2014, Francesca Strappini wrote:

> Thanks Louis!
>
> Yes, I did run tkmedit from the same terminal window I have sourced
> freesurfer...
>
> Francesca
>
> 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke :
>> Hi Francesca,
>> Are you trying to run the tkmedit command in the same terminal window you
>> have sourced freesurfer?  You'll need to source freesurfer in any new
>> terminal window you open before being able to run any freesurfer commands.
>>
>> It's possible to set it up so that freesurfer is sourced automatically
>> when opening a new terminal or setting up an alias to make the process
>> quicker.
>> -Louis
>>
>> On Sat, 10 May 2014, Francesca Strappini wrote:
>>
>>> Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64
>>> and I have Ubuntu 12.04 LTS. I have set up the licence file and
>>> configured freesurfer:
>>>
>>> tcsh
>>> setenv FREESURFER_HOME /media/Shared_Data/freesurfer
>>> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>>>
>>>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> FREESURFER_HOME   /media/Shared_Data/freesurfer
>>> FSFAST_HOME   /media/Shared_Data/freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii.gz
>>> SUBJECTS_DIR  /media/Shared_Data/freesurfer/subjects
>>> MNI_DIR   /media/Shared_Data/freesurfer/mni
>>>
>>> When I try to run any type of command, like tkmedit bert orig.mgz, I
>>> get this error:
>>>
>>> command not found.
>>>
>>> Thanks for the help!
>>>
>>> Francesca
>>> ___
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>>>
>>>
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[Freesurfer] A question about installation

[木村一皓]

Hi,

I would like to install "Freesurfer," but I have a problem.
I now only have a PC running Windows OS.
So I am wondering if I could use "Freesurfer" by windows.(say in "VMware
Player")
Or should I buy Macintosh or somtehing because of memory problems?

Sorry for my really novice question,
Ikko Kimura
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Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

[Douglas N Greve]

For #2 you can get the average with mri_segstats passing the mask with 
the --seg command and using --id 1. If the mask is in fsaverage space, 
then just apply it to the y.mgh (i,e the input to mri_glmfit passed with 
--y). Use the --avgwf option to mri_segstats. This will give you the 
average for each subject in a single ascii file. For #1, I would not 
recommend using the data from the most significant voxel since this is 
not necessarily a stable measure

doug


On 05/09/2014 08:44 PM, charujing wrote:
> Hi FS experts and users
> I have done the each subjects' surface regestration on fsaverage 
> surface, and merge all of them into a *.mgh. Group analysis is also 
> completed.
> Now I have two questions:
> 1,I want to extract the VtxMax vertex number thickness for all 
> subjects. The VtxMax vertex number can be got in the 
> *.sig.cluster.summary file. And it represents the most significant 
> vertex in that cluster. I search my question in google and find these 
> scripts which maybe helpful for me:
> for i in `seq 1 $numsubject`
>do
>  mri_convert --frame $i y.mgh 
> $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh
>  mris_convert -c $i.mgh 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc
>done
> I got the lh.*.asc file and open it. There are five columes in this 
> file. I guess that: first colume is vertex number, the 2nd-4th columes 
> represent MNI305 coordinates in surface, and the 5th colume is 
> thickness of this vertex. If I want to deal with my 1st question, all 
> I need to get the lh.*.asc file and search the specific vertex number 
> in this file. All of above, is there anything wrong?
> 2, I created a surface mask, and want to extract the average thickness 
> value in this mask for every subject. How can I complete it? Can I 
> extract all vertex thickness in that mask, and average them in each 
> subject? If so, however, it will be a bot of inconvenience. I want to 
> some simple codes to deal with it.
> Any reply will be highly appreaciated.
> Thanks
> All the best.
> Rujing Zha
> 2014-05-10
> 
> charujing
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[Douglas N Greve]

Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table

On 05/12/2014 03:41 AM, amirhossein manzouri wrote:
> Hi again,
> I think I missed my question, How can I get the Mean Thickness of each 
> hemisphere for several subjects using the aparcstats2table command?
>
> On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri 
> mailto:a.h.manzo...@gmail.com>> wrote:
>
> Dear Doug,
> I have read this
> 
> post(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
>  regarding
> extracting Mean Cth of each hemisphere and I just get insula as
> the last and totally 34 numbers, I use
> aparcstats2table --hemi lh --subjects bert -m thickness
> --tablefile lh.Cth.bert.txt
>
>
>
> Best regards,
> Amirhossein Manzouri
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Coomand not found

[Francesca Strappini]

Thanks Louis!

Yes, I did run tkmedit from the same terminal window I have sourced
freesurfer...

Francesca

2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke :
> Hi Francesca,
> Are you trying to run the tkmedit command in the same terminal window you
> have sourced freesurfer?  You'll need to source freesurfer in any new
> terminal window you open before being able to run any freesurfer commands.
>
> It's possible to set it up so that freesurfer is sourced automatically
> when opening a new terminal or setting up an alias to make the process
> quicker.
> -Louis
>
> On Sat, 10 May 2014, Francesca Strappini wrote:
>
>> Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64
>> and I have Ubuntu 12.04 LTS. I have set up the licence file and
>> configured freesurfer:
>>
>> tcsh
>> setenv FREESURFER_HOME /media/Shared_Data/freesurfer
>> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>>
>>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /media/Shared_Data/freesurfer
>> FSFAST_HOME   /media/Shared_Data/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /media/Shared_Data/freesurfer/subjects
>> MNI_DIR   /media/Shared_Data/freesurfer/mni
>>
>> When I try to run any type of command, like tkmedit bert orig.mgz, I
>> get this error:
>>
>> command not found.
>>
>> Thanks for the help!
>>
>> Francesca
>> ___
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>>
>>
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>
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> properly
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Re: [Freesurfer] Coomand not found

[Louis Nicholas Vinke]

Hi Francesca,
Are you trying to run the tkmedit command in the same terminal window you 
have sourced freesurfer?  You'll need to source freesurfer in any new 
terminal window you open before being able to run any freesurfer commands.

It's possible to set it up so that freesurfer is sourced automatically 
when opening a new terminal or setting up an alias to make the process 
quicker.
-Louis

On Sat, 10 May 2014, Francesca Strappini wrote:

> Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64
> and I have Ubuntu 12.04 LTS. I have set up the licence file and
> configured freesurfer:
>
> tcsh
> setenv FREESURFER_HOME /media/Shared_Data/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /media/Shared_Data/freesurfer
> FSFAST_HOME   /media/Shared_Data/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /media/Shared_Data/freesurfer/subjects
> MNI_DIR   /media/Shared_Data/freesurfer/mni
>
> When I try to run any type of command, like tkmedit bert orig.mgz, I
> get this error:
>
> command not found.
>
> Thanks for the help!
>
> Francesca
> ___
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>
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Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

[Bruce Fischl]

Hi Christopher

the spherical mapping usually has on the order of 17-20% distortion in 
distances, and the registration is probably significantly more. I'm not 
entirely sure what are trying to do, but you can measure the difference in 
great circle length between the sphere and sphere.reg to get an idea of how 
much additional distortion is induced by the registration


cheers
Bruce



On Mon, 12 May 2014, Milde, Christopher wrote:



Dear Freesurfers,

 

In Fischl et al. 1999 it is highlighted, that the topological structure of the 
original
surface is preserved in the spherical space and due to the nature of a sphere, 
computations
(distance, area) measures are easy to make.

 

My question now, concerns the comparability of distance measures between 
subjects in the
group fsaverage sphere. My aim is to compare distances between peak voxels 
coordinates of
two study populations, to figure out if a systematic difference exist between 
the peak voxel
distances of the two study populations.

 

Can I compare the distances between peak voxels (vertices) between different 
subjects based
on the fsaverage group sphere? So, is the comparability of distances between 
vertexes of
individually spheres preserved in group fsaverage space?

 

Ps: I know that the distances in spherical space are not Euclidian but still 
geodesic

 

 

Best wishes and thanks in advance,

 

 

Christopher Milde, M.Sc. Biol.

Institute for Cognitive and Clinical Neuroscience

Central Institute of Mental Health Square J 5

68159 Mannheim, Germany

 

 

Christopher Milde, M.Sc. Biol.

Institute for Cognitive and Clinical Neuroscience

Central Institute of Mental Health Square J 5

68159 Mannheim, Germany

 

Phone:  +49-621-1703-6313

E-mail:  christopher.mi...@zi-mannheim.de

Homepage:    http://www.zi-mannheim.de/

Office:  Forschungs- und Verwaltungsgebäude, Room 230

 


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Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Kristina

you need to give us more context. What command is running when you get 
that error?

cheers
Bruce

On Mon, 12 May 2014, Mayer Kristina wrote:

> Hi there,
>
> I am using freesurfer on MRI data of children.
> In one dataset I have following error appearing, I did not find described 
> before.
>
> MRISalloc(41043678, 76): could not allocate faces
> Cannot allocate memory
> Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
> x86_64 x86_64 x86_64 GNU/Linux
>
> Waht do I have to check or edit manually?
>
> Thanks!
>
> Best,
> Kristina
>
>
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[Freesurfer] distance comparisons across subjects in fsaverage group sphere

[Milde, Christopher]

Dear Freesurfers,

In Fischl et al. 1999 it is highlighted, that the topological structure of the 
original surface is preserved in the spherical space and due to the nature of a 
sphere, computations (distance, area) measures are easy to make.

My question now, concerns the comparability of distance measures between 
subjects in the group fsaverage sphere. My aim is to compare distances between 
peak voxels coordinates of two study populations, to figure out if a systematic 
difference exist between the peak voxel distances of the two study populations.

Can I compare the distances between peak voxels (vertices) between different 
subjects based on the fsaverage group sphere? So, is the comparability of 
distances between vertexes of individually spheres preserved in group fsaverage 
space?

Ps: I know that the distances in spherical space are not Euclidian but still 
geodesic


Best wishes and thanks in advance,


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230

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[Freesurfer] Cannot allocate memory

[Mayer Kristina]

Hi there,

I am using freesurfer on MRI data of children.
In one dataset I have following error appearing, I did not find described 
before.

MRISalloc(41043678, 76): could not allocate faces
Cannot allocate memory
Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

Waht do I have to check or edit manually?

Thanks!

Best,
Kristina


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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

[amirhossein manzouri]

Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table command?

On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri  wrote:

> Dear Doug,
> I have read this post(
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) 
> regarding
> extracting Mean Cth of each hemisphere and I just get insula as the last
> and totally 34 numbers, I use
> aparcstats2table --hemi lh --subjects bert -m thickness --tablefile
> lh.Cth.bert.txt
>
>
>
> Best regards,
> Amirhossein Manzouri
>
>
>
>
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