[Freesurfer] reference on co-registration of functional brain areas?

[Zeynep Akalin Acar]

Hi all,

I'm looking for a reference showing how the functional areas differ when
individual brains are co-registered.

Thanks,
Zeynep.
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[Freesurfer] Using FreeSurfer with 6-14 year olds

[Felipe Picon]

Dear FreeSurfer experts,

I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year
olds
So far I haven't had any errors (only 15 subjects runned so far)

My questions are:
- Should I make a template from the subjects of my whole sample, considering
their age range?
- Or FreeSurfer template would work just fine with this sample?

If I should make a average from my whole sample, should I make it separating
the sample in age ranges?

Any suggestions are welcome

Thank you!!
-- 
*Felipe Picon, MD*
Child and Adolescent Psychiatrist
Master's Degree Student - Department of Psychiatry of Federal University of
Rio Grande do Sul - UFRGS - www.ufrgs.br
Adult ADHD outpatient research program - PRODAH-A -
http://www6.ufrgs.br/prodah/prodah/equipe.html
Hospital de Clinicas de Porto Alegre - HCPA - www.hcpa.ufrgs.br
Member of the World Psychiatric Association (WPA) Early Career Psychiatrists
Council
Area Coordinator for the Americas -
http://www.wpanet.org/detail.php?section_id=22&content_id=120
Web based CV: http://lattes.cnpq.br/3896757276389918
felipepi...@gmail.com
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Re: [Freesurfer] tksurfer and viewing eccentricity data

[Douglas N Greve]

View->Configure->Functional Overlay
this will bring up a control window that you can use to change the time 
point being viewed
doug

Michelle Umali wrote:
> Hi Doug and Freesurfers,
> How does one look at each time point separately to view the eccen and  
> polar maps?
>
> Thanks.
> Michelle
>
> Quoting Douglas N Greve :
>
>   
>> No, to view the angle:
>> tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
>>
>> This will bring up an overlay with two time points. The first time
>> point is eccen, the 2nd is polar.  These are unmasked angles in radians
>> (I think). For masked use (masked by p<.01)
>>
>> tksurfer-sess -a rtopy.self.lh -s sj09 -map angle.masked
>>
>> To see the significance maps use
>>
>> tksurfer-sess -a rtopy.self.lh -s sj09 Michelle Umali wrote:
>> 
>>> Dear Freesurfers,
>>> Is this the correct command for viewing eccentricity data using tksurfer:
>>> tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen
>>>
>>> Thanks.
>>> Michelle
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>   
>> -- 
>> 
>
>
>
> maps> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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.
>> 
>
>
>
> ___
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] tksurfer and viewing eccentricity data

[Michelle Umali]

Hi Doug and Freesurfers,
How does one look at each time point separately to view the eccen and  
polar maps?

Thanks.
Michelle

Quoting Douglas N Greve :

> No, to view the angle:
> tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
>
> This will bring up an overlay with two time points. The first time
> point is eccen, the 2nd is polar.  These are unmasked angles in radians
> (I think). For masked use (masked by p<.01)
>
> tksurfer-sess -a rtopy.self.lh -s sj09 -map angle.masked
>
> To see the significance maps use
>
> tksurfer-sess -a rtopy.self.lh -s sj09 Michelle Umali wrote:
>> Dear Freesurfers,
>> Is this the correct command for viewing eccentricity data using tksurfer:
>> tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen
>>
>> Thanks.
>> Michelle
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> -- 



maps> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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.



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Re: [Freesurfer] mri_segment optional flags problem

[Christopher Luna]

Thanks for your help!

Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012
Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT



On Fri, Aug 5, 2011 at 3:22 PM, Irwin, William wrote:

> Bruce,
>
> Until it is determined if there is enough interest, how do I obtain it for
> centos4_x86_64?
>
> Thanks much,
> Wil
>
> |-Original Message-
> |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> |Sent: Friday, August 05, 2011 12:10 PM
> |To: Irwin, William
> |Cc: Christopher Luna; freesurfer@nmr.mgh.harvard.edu
> |Subject: RE: [Freesurfer] mri_segment optional flags problem
> |
> |Hi Wil
> |
> |we can certainly post it if there is enough interest.
> |
> |cheers
> |Bruce
> |On Fri, 5 Aug 2011,
> |Irwin, William wrote:
> |
> |> Hi Bruce-
> |>
> |> Is this fix going to be put on the site as a patch/fix download (e.g.,
> |ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-
> |centos4_x86_64/) or distributed on a per-user need?
> |>
> |> Thanks,
> |> Wil
> |> 
> |> William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging
> |> Center
> |> 350 Parnassus Avenue, Suite 905
> |> San Francisco  CA  94143-1207
> |> wir...@memory.ucsf.edu | memory.ucsf.edu
> |> p: 415.476.1680 | f: 415.476.1816
> |>
> |>
> |>
> |> |-Original Message-
> |> |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> |> |Sent: Thursday, August 04, 2011 12:39 PM
> |> |To: Christopher Luna
> |> |Cc: freesurfer@nmr.mgh.harvard.edu
> |> |Subject: Re: [Freesurfer] mri_segment optional flags problem
> |> |
> |> |oops, I just fixed that. If you let us know what software/hardware
> |> |env you are using we'll give you an updated binary.
> |> |
> |> |Bruce
> |> |
> |> |
> |> |On Thu, 4 Aug 2011, Christopher Luna
> |> |wrote:
> |> |
> |> |> Hello,
> |> |> I'm trying to run mri_segment with some custom values in the
> |> |> optional flags, such as -p for setting the percentage threshold with
> a float
> |value.
> |> |>
> |> |> When I run the command though,
> |> |> "mri_segment -p 0.6 brain.mgz wm.seg.mgz"
> |> |>
> |> |> The command properly sets the threshold to 60%, but also takes the
> |> |> "0.6" to
> |> |be in the input file name instead of brain.mgz.
> |> |>
> |> |> Is there another option I'm missing? Or have I unfortunately
> |> |> stumbled upon
> |> |a small bug?
> |> |>
> |> |> Thanks,
> |> |> Christopher Luna
> |> |> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab,
> |> |> McGovern Institute for Brain Research MIT Archery Club Alpha Kappa
> |> |> Psi Colony at MIT
> |> |>
> |> |>
> |> |>
> |>
> |>
> |>
> |>
> |
> |
> |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.
>
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Re: [Freesurfer] Nvidia upgrade considerations

[R Edgar]

2011/8/5 Andries R. Van Der Leij :

> For my supervisor, what kind of performance increase should I expect
> if we buy a newer nehalem system?

Freesurfer as a whole is quite keen on the improved memory subsystem
offered by Nehalem. A figure of 2x (CPU only stream) is floating in my
mind, but I don't recall the exact two setups.

Richard
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] tksurfer and viewing eccentricity data

[Douglas N Greve]

No, to view the angle:
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle

This will bring up an overlay with two time points. The first time point 
is eccen, the 2nd is polar.  These are unmasked angles in radians (I 
think). For masked use (masked by p<.01)

tksurfer-sess -a rtopy.self.lh -s sj09 -map angle.masked

To see the significance maps use

tksurfer-sess -a rtopy.self.lh -s sj09 







Michelle Umali wrote:
> Dear Freesurfers,
> Is this the correct command for viewing eccentricity data using tksurfer:
> tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen
>
> Thanks.
> Michelle
>
> ___
> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] tksurfer and viewing eccentricity data

[Michelle Umali]

Dear Freesurfers,
Is this the correct command for viewing eccentricity data using tksurfer:
tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen

Thanks.
Michelle

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Re: [Freesurfer] mri_segment optional flags problem

[Irwin, William]

Bruce,

Until it is determined if there is enough interest, how do I obtain it for 
centos4_x86_64?

Thanks much,
Wil

|-Original Message-
|From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Friday, August 05, 2011 12:10 PM
|To: Irwin, William
|Cc: Christopher Luna; freesurfer@nmr.mgh.harvard.edu
|Subject: RE: [Freesurfer] mri_segment optional flags problem
|
|Hi Wil
|
|we can certainly post it if there is enough interest.
|
|cheers
|Bruce
|On Fri, 5 Aug 2011,
|Irwin, William wrote:
|
|> Hi Bruce-
|>
|> Is this fix going to be put on the site as a patch/fix download (e.g.,
|ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-
|centos4_x86_64/) or distributed on a per-user need?
|>
|> Thanks,
|> Wil
|> 
|> William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging
|> Center
|> 350 Parnassus Avenue, Suite 905
|> San Francisco  CA  94143-1207
|> wir...@memory.ucsf.edu | memory.ucsf.edu
|> p: 415.476.1680 | f: 415.476.1816
|>
|>
|>
|> |-Original Message-
|> |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|> |Sent: Thursday, August 04, 2011 12:39 PM
|> |To: Christopher Luna
|> |Cc: freesurfer@nmr.mgh.harvard.edu
|> |Subject: Re: [Freesurfer] mri_segment optional flags problem
|> |
|> |oops, I just fixed that. If you let us know what software/hardware
|> |env you are using we'll give you an updated binary.
|> |
|> |Bruce
|> |
|> |
|> |On Thu, 4 Aug 2011, Christopher Luna
|> |wrote:
|> |
|> |> Hello,
|> |> I'm trying to run mri_segment with some custom values in the
|> |> optional flags, such as -p for setting the percentage threshold with a 
float
|value.
|> |>
|> |> When I run the command though,
|> |> "mri_segment -p 0.6 brain.mgz wm.seg.mgz"
|> |>
|> |> The command properly sets the threshold to 60%, but also takes the
|> |> "0.6" to
|> |be in the input file name instead of brain.mgz.
|> |>
|> |> Is there another option I'm missing? Or have I unfortunately
|> |> stumbled upon
|> |a small bug?
|> |>
|> |> Thanks,
|> |> Christopher Luna
|> |> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab,
|> |> McGovern Institute for Brain Research MIT Archery Club Alpha Kappa
|> |> Psi Colony at MIT
|> |>
|> |>
|> |>
|>
|>
|>
|>
|
|
|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.

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Re: [Freesurfer] Nvidia upgrade considerations

[Pedro Paulo de Magalhães Oliveira Junior]

I would go for a complete new PC. You won't benefit much of a GTX590 in an
old PC

PPJ

-
Pedro Paulo de Magalhães Oliveira Junior
-- check our new iOS app:
Cargo


2011/8/5 Andries R. Van Der Leij 

> Hi pedro and Richard,
>
> Thank you for the responses! The T7400 has just one gpu slot, so I'll
> probably just buy the single 590, which itself is a dual card. The
> 2050 doesn't seem to be worth it on these older systems (ddr2, etc).
>
> For my supervisor, what kind of performance increase should I expect
> if we buy a newer nehalem system?
>
> Regards,
>
> Andries van der leij
>
> Sent from my iPhone
>
> On Aug 5, 2011, at 20:21, R Edgar  wrote:
>
> > 2011/8/5 Pedro Paulo de Magalhães Oliveira Junior  > r>:
> >> In my experience you'll have the benefit of using two cards
> >> simultaneously.
> >> That means you can run two recon-all with gpu acceleration
> >> simultaneously.
> >> The SLI is more important for graphics (cad, gaming) than for CUDA.
> >> So, I'd
> >> go for 2 GTX580
> >
> > CUDA doesn't use SLI at all - you don't want it. So long as each card
> > has enough RAM to handle one recon job, having more cards and using
> > the environment variable to select the GPU is certainly the way to go.
> > I don't think that Freesurfer is particularly heavy on the PCIe bus,
> > so you should even be able to get one of the dual GPU cards and get
> > good performance. However, Nehalem does help the data reorganisation
> > required for the GPU.
> >
> > Richard
>
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Re: [Freesurfer] Nvidia upgrade considerations

[Andries R. Van Der Leij]

Hi pedro and Richard,

Thank you for the responses! The T7400 has just one gpu slot, so I'll
probably just buy the single 590, which itself is a dual card. The
2050 doesn't seem to be worth it on these older systems (ddr2, etc).

For my supervisor, what kind of performance increase should I expect
if we buy a newer nehalem system?

Regards,

Andries van der leij

Sent from my iPhone

On Aug 5, 2011, at 20:21, R Edgar  wrote:

> 2011/8/5 Pedro Paulo de Magalhães Oliveira Junior  r>:
>> In my experience you'll have the benefit of using two cards
>> simultaneously.
>> That means you can run two recon-all with gpu acceleration
>> simultaneously.
>> The SLI is more important for graphics (cad, gaming) than for CUDA.
>> So, I'd
>> go for 2 GTX580
>
> CUDA doesn't use SLI at all - you don't want it. So long as each card
> has enough RAM to handle one recon job, having more cards and using
> the environment variable to select the GPU is certainly the way to go.
> I don't think that Freesurfer is particularly heavy on the PCIe bus,
> so you should even be able to get one of the dual GPU cards and get
> good performance. However, Nehalem does help the data reorganisation
> required for the GPU.
>
> Richard

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Re: [Freesurfer] mri_segment optional flags problem

[Bruce Fischl]

Hi Wil

we can certainly post it if there is enough interest.

cheers
Bruce
On Fri, 5 Aug 2011, 
Irwin, William wrote:



Hi Bruce-

Is this fix going to be put on the site as a patch/fix download (e.g., 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/)
 or distributed on a per-user need?

Thanks,
Wil

William Irwin | Brain Imaging Coordinator
UCSF | Memory and Aging Center
350 Parnassus Avenue, Suite 905
San Francisco  CA  94143-1207
wir...@memory.ucsf.edu | memory.ucsf.edu
p: 415.476.1680 | f: 415.476.1816



|-Original Message-
|From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Thursday, August 04, 2011 12:39 PM
|To: Christopher Luna
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] mri_segment optional flags problem
|
|oops, I just fixed that. If you let us know what software/hardware env you are
|using we'll give you an updated binary.
|
|Bruce
|
|
|On Thu, 4 Aug 2011, Christopher Luna
|wrote:
|
|> Hello,
|> I'm trying to run mri_segment with some custom values in the optional
|> flags, such as -p for setting the percentage threshold with a float value.
|>
|> When I run the command though,
|> "mri_segment -p 0.6 brain.mgz wm.seg.mgz"
|>
|> The command properly sets the threshold to 60%, but also takes the "0.6" to
|be in the input file name instead of brain.mgz.
|>
|> Is there another option I'm missing? Or have I unfortunately stumbled upon
|a small bug?
|>
|> Thanks,
|> Christopher Luna
|> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern
|> Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony
|> at MIT
|>
|>
|>



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Re: [Freesurfer] Error in preprocessing

[Douglas N Greve]

yes

tap...@nmr.mgh.harvard.edu wrote:
> Hi, is this true for FSFAST vs. 5.1 as well? -Tapsya
>
>   
>> You will need the AFNI 3dvolreg command. This is the only AFNI command
>> you'll need, but you may need to download and install AFNI to get it.
>>
>> doug
>>
>> Eiran Vadim Harel wrote:
>> 
>>> Hi,
>>> I am using stable5.0-env.
>>> I have run the pre[processing command:
>>>
>>> preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>>>
>>> I got this ERROR message:
>>>
>>> /autofs/space/shimshon_002/users/eiran/contproc/1411_MC
>>> RunList: 005 006 007
>>>  --- ** ---
>>>  --- Motion Correcting Run 005 ---
>>>  --- ** ---
>>> sess = 1411_MC
>>> Fri Aug  5 11:51:17 EDT 2011
>>> mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat
>>> 005/fmcpr.mcdat
>>> ERROR: cannot find AFNI command 3dvolreg
>>>
>>>
>>> My PROJECT DIR: /space/shimshon/2/users/eiran/contproc
>>> SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects
>>>
>>> Is there a way to solve it?
>>> Thanks,
>>> Eiran
>>> ___
>>> 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
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Nvidia upgrade considerations

[R Edgar]

2011/8/5 Pedro Paulo de Magalhães Oliveira Junior :
> In my experience you'll have the benefit of using two cards simultaneously.
> That means you can run two recon-all with gpu acceleration simultaneously.
> The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd
> go for 2 GTX580

CUDA doesn't use SLI at all - you don't want it. So long as each card
has enough RAM to handle one recon job, having more cards and using
the environment variable to select the GPU is certainly the way to go.
I don't think that Freesurfer is particularly heavy on the PCIe bus,
so you should even be able to get one of the dual GPU cards and get
good performance. However, Nehalem does help the data reorganisation
required for the GPU.

Richard

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Re: [Freesurfer] Error in preprocessing

[tapsya]

Hi, is this true for FSFAST vs. 5.1 as well? -Tapsya

>
> You will need the AFNI 3dvolreg command. This is the only AFNI command
> you'll need, but you may need to download and install AFNI to get it.
>
> doug
>
> Eiran Vadim Harel wrote:
>> Hi,
>> I am using stable5.0-env.
>> I have run the pre[processing command:
>>
>> preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>>
>> I got this ERROR message:
>>
>> /autofs/space/shimshon_002/users/eiran/contproc/1411_MC
>> RunList: 005 006 007
>>  --- ** ---
>>  --- Motion Correcting Run 005 ---
>>  --- ** ---
>> sess = 1411_MC
>> Fri Aug  5 11:51:17 EDT 2011
>> mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat
>> 005/fmcpr.mcdat
>> ERROR: cannot find AFNI command 3dvolreg
>>
>>
>> My PROJECT DIR: /space/shimshon/2/users/eiran/contproc
>> SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects
>>
>> Is there a way to solve it?
>> Thanks,
>> Eiran
>> ___
>> 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
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] Nvidia upgrade considerations

[Pedro Paulo de Magalhães Oliveira Junior]

In my experience you'll have the benefit of using two cards simultaneously.
That means you can run two recon-all with gpu acceleration simultaneously.
The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd
go for 2 GTX580

PPJ

-
Pedro Paulo de Magalhães Oliveira Junior
-- check our new iOS app:
Cargo




On Fri, Aug 5, 2011 at 14:28, Andries R. Van Der Leij <
a.r.vanderl...@gmail.com> wrote:

> Dear freesurfer team
>
> I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon
> machine's to run a large batch of fs jobs. Upgrading to Nehalem won't
> work, since it will require a new motherboard as well. However, we can
> replace our old non-fermi quadro card with a C2050.
>
> As an alternative, I was thinking about buying two GTX590 (two times 580
> and 1.5 GB ram) or two palit GTX580 (1 times 580 with 3GB ram) and running
> them in SLI. This will save quite some money, and intuitively, it feels that
> more separate cards will work better if you start batching more recon
> scripts at the same time (1 per CPU). You'll end up with 6 gb of vram in
> both cases compared to the 3 for the C2050, with 4 processors for the 590
> and 2 for the 580. As I don't understand cuda and sli well, I may very well
> be completely wrong. I'm not sure fi that running jobs under sli will work
> well. Do you have any ideas on this solution compared to a single c2050?
>
> thank you very much in advance,
>
> Andries van der Leij
>
> ___
> Freesurfer mailing list
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> 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.
>
>
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Re: [Freesurfer] Error in preprocessing

[Douglas N Greve]

You will need the AFNI 3dvolreg command. This is the only AFNI command 
you'll need, but you may need to download and install AFNI to get it.

doug

Eiran Vadim Harel wrote:
> Hi,
> I am using stable5.0-env.
> I have run the pre[processing command:
>
> preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>
> I got this ERROR message:
>
> /autofs/space/shimshon_002/users/eiran/contproc/1411_MC
> RunList: 005 006 007
>  --- ** ---
>  --- Motion Correcting Run 005 ---
>  --- ** ---
> sess = 1411_MC
> Fri Aug  5 11:51:17 EDT 2011
> mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat
> 005/fmcpr.mcdat
> ERROR: cannot find AFNI command 3dvolreg
>
>
> My PROJECT DIR: /space/shimshon/2/users/eiran/contproc
> SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects
>
> Is there a way to solve it?
> Thanks,
> Eiran
> ___
> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] skull stripping and gcut error

[Jacquelynn Nicosia Copeland]

Yes, I think this may help a lot, if possible.

Thanks,
Jacquie

Jacquelynn N. Copeland, M.A.
Doctoral Candidate
Medical/Clinical Psychology Program
Department of Psychology
University of Alabama at Birmingham
Email:jcopel...@uab.edu

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 04, 2011 11:39 AM
To: Jacquelynn Nicosia Copeland
Cc: Khoa Nguyen; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] skull stripping and gcut error

I guess it is detecting the fact that gcuts failed. Nick: is there any way
to disable the failure detection so Jacquie can see what it did?
Bruce


On Thu, 4 Aug 2011,
Jacquelynn Nicosia Copeland wrote:

> Hi Khoa,
>
> Thanks for your response. The extra dura/skull is being included in some 
> parts of the pial surface, particularly around the superior surfaces of the 
> brain (gray matter and cortical regions that we are interested in are being 
> affected). Thus, manual editing by erasing dura/skull has been taking a long 
> time (hours?) to do in on one participant.
>
> That's why I tried gcut on the original image to see if it was much 
> different, but I got the message I previously posted, where it appeared that 
> gcut did not work. I don't really care about cutting off the cerebellum, as 
> long as it takes off the extra dura/skull affecting the pial surface and thus 
> decreasing the amount of manual edits I need to make.
>
> I will try to the additional skull strip as you suggested. But why do you 
> think that gcut isn't running and I am getting the message I included in my 
> earlier post? I was really hoping gcut would be my savior rather than making 
> lots of edits. In addition, adjusting the watershed parameters hasn't really 
> helped either. Is there no saving grace?
>
> Thanks,
> Jacquie
>
>
> Jacquelynn N. Copeland, M.A.
> Doctoral Candidate
> Medical/Clinical Psychology Program
> Department of Psychology
> University of Alabama at Birmingham
> Email:jcopel...@uab.edu
> 
> From: Khoa Nguyen [k...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 04, 2011 6:38 AM
> To: Jacquelynn Nicosia Copeland
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] skull stripping and gcut error
>
> Hi,
>
> How much dura/skull is left on your subjects that you want to remove?
> Sometimes gcut takes away more than just dura, especially in the
> cerebellum region so that might be why it is much smaller.
>
> If the surfaces are not including the extra dura/skull, then it is not
> necessary that you remove them. If you want, you can try just running
> "recon-all -skullstrip -s subjid" again instead. That might improve it.
>
> -Khoa
>
> On Wed, 3 Aug 2011, Jacquelynn Nicosia Copeland wrote:
>
>> Hi Freesurfers:
>>
>> I am trying to minimize the amount of skull stripping manual edits I need to 
>> make on Freesurfer outputs due to remaining dura. I've been trying both: 
>> adjusting the watershed parameters and using gcut.
>>
>> However, I noticed the output with and without gcut for the same participant 
>> were not different. So I went to the log file, and when I searched for gcut 
>> it says:
>>
>> " rm -f brainmask.gcuts.mgz
>>
>> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz 
>> brainmask.gcuts.mgz
>>
>> INFO: Care must be taken to thoroughly inspect your data
>>  when using mri_gcut. In particular, inspect the edges of
>>  gm and cerebellum for over-aggressive cutting.
>>  Add -segmentation brainmask.gcuts.mgz to the tkmedit
>>  command string to view the voxels which gcut has removed.
>>
>> reading mask...
>> white mean: 107.529232
>> threshold set to: 107.529232*0.40=43.011693
>> calculating weights...
>> doing mincut...
>> now doing maxflow, be patient...
>> g-cut done!
>> post-processing...
>> post-processing done!
>> masking...
>> ** Gcutted brain is much smaller than the mask!
>> ** Using the mask as the output instead!
>>
>> cp brainmask.auto.mgz brainmask.mgz "
>>
>> Thus, it does not appear to be using the brainmask with gcut edits. I added 
>> the "-segmentation brainmask.gcuts.mgz" to the tkmedit command and got an 
>> error basically saying that the file does not exist. This is the case for 
>> many of our participants. Why is this occurring? Isn't the purpose of gcut 
>> is to make the brainmask smaller (b/c it has less dura in it)?
>>
>> Also, any other suggestions for reducing remaining dura/skull?
>>
>> Thanks for any help you can provide,
>> Jacquie
>>
>> Jacquelynn N. Copeland, M.A.
>> Doctoral Candidate
>> Medical/Clinical Psychology Program
>> Department of Psychology
>> University of Alabama at Birmingham
>> Email:jcopel...@uab.edu
>> ___
>> 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

[Freesurfer] Nvidia upgrade considerations

[Andries R. Van Der Leij]

Dear freesurfer team

I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon
machine's to run a large batch of fs jobs. Upgrading to Nehalem won't work,
since it will require a new motherboard as well. However, we can replace our
old non-fermi quadro card with a C2050.

As an alternative, I was thinking about buying two GTX590 (two times 580 and
1.5 GB ram) or two palit GTX580 (1 times 580 with 3GB ram) and running them
in SLI. This will save quite some money, and intuitively, it feels that more
separate cards will work better if you start batching more recon scripts at
the same time (1 per CPU). You'll end up with 6 gb of vram in both cases
compared to the 3 for the C2050, with 4 processors for the 590 and 2 for the
580. As I don't understand cuda and sli well, I may very well be completely
wrong. I'm not sure fi that running jobs under sli will work well. Do you
have any ideas on this solution compared to a single c2050?

thank you very much in advance,

Andries van der Leij
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[Freesurfer] Error in preprocessing

[Eiran Vadim Harel]

Hi,
I am using stable5.0-env.
I have run the pre[processing command:

preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

I got this ERROR message:

/autofs/space/shimshon_002/users/eiran/contproc/1411_MC
RunList: 005 006 007
 --- ** ---
 --- Motion Correcting Run 005 ---
 --- ** ---
sess = 1411_MC
Fri Aug  5 11:51:17 EDT 2011
mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat
005/fmcpr.mcdat
ERROR: cannot find AFNI command 3dvolreg


My PROJECT DIR: /space/shimshon/2/users/eiran/contproc
SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects

Is there a way to solve it?
Thanks,
Eiran
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Re: [Freesurfer] mri_segment optional flags problem

[Irwin, William]

Hi Bruce-

Is this fix going to be put on the site as a patch/fix download (e.g., 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/)
 or distributed on a per-user need? 

Thanks,
Wil

William Irwin | Brain Imaging Coordinator
UCSF | Memory and Aging Center
350 Parnassus Avenue, Suite 905
San Francisco  CA  94143-1207
wir...@memory.ucsf.edu | memory.ucsf.edu
p: 415.476.1680 | f: 415.476.1816



|-Original Message-
|From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Thursday, August 04, 2011 12:39 PM
|To: Christopher Luna
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] mri_segment optional flags problem
|
|oops, I just fixed that. If you let us know what software/hardware env you are
|using we'll give you an updated binary.
|
|Bruce
|
|
|On Thu, 4 Aug 2011, Christopher Luna
|wrote:
|
|> Hello,
|> I'm trying to run mri_segment with some custom values in the optional
|> flags, such as -p for setting the percentage threshold with a float value.
|>
|> When I run the command though,
|> "mri_segment -p 0.6 brain.mgz wm.seg.mgz"
|>
|> The command properly sets the threshold to 60%, but also takes the "0.6" to
|be in the input file name instead of brain.mgz.
|>
|> Is there another option I'm missing? Or have I unfortunately stumbled upon
|a small bug?
|>
|> Thanks,
|> Christopher Luna
|> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern
|> Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony
|> at MIT
|>
|>
|>


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Re: [Freesurfer] convert .annot file to lable

[Douglas N Greve]

Try mri_annotation2label
doug

ZhiLiangLong wrote:

Hi all:
Are there some FS commands that can convert .annot file to lable file?
Thanks!




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Fax: 617-726-7422


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[Freesurfer] convert .annot file to lable

[ZhiLiangLong]

Hi all:
  Are there some FS commands that can convert .annot file to lable file?



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Re: [Freesurfer] dmri_train malloc error

[David Coynel]

Hi Anastasia,

Having the same issue, I was wondering if it's possible to recompile only 
tracula from the source code ? If yes could you give some hints ?

Thanks a lot,
Dr. David Coynel
Division of Cognitive Neuroscience
University of Basel
Birmannsgasse 8
4055 Basel - Switzerland
david.coy...@unibas.ch
tel: +41(0)612.670.240


Am 22.07.2011 um 16:36 schrieb Anastasia Yendiki:

> 
> Hi Kevin - This is unfortunately a problem with the macos freesurfer 
> distribution, which is still built on leopard instead of snow leopard b/c of 
> compatibility issues with some libraries unrelated to tracula. It's possible 
> to compile tracula on snow leopard (in fact that's what I use) but you'd have 
> to download the source code.
> 
> Since several people have written about this by now, I'm considering 
> something that'd be less of a pain for users, which is to create a tarball 
> with only the tracula executables compiled on snow leopard and make it 
> available.
> 
> a.y
> 
> On Fri, 22 Jul 2011, Dabbs (Kevin) wrote:
> 
>> Freesurfer users,
>> I have ran into a malloc error running trac-all.  Looks like the same error
>> that Stijn posted to the list on 17 Jun 2011.  I did not see a solution
>> posted.  It occurs in dmr_train using trac-all  -prep –c dmrirc.txt.  Also
>> tried  using trac-all –prior –c dmrirc.txt with the same results.  Reset the
>> tcsh limits for datasize, ….  
>> *
>> Loading segmentation from
>> /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz
>> Loading cortex mask from
>> /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz
>> dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice
>> Cannot allocate memory
>> **
>> My system 
>> Model Name: Mac Pro
>>   Model Identifier: MacPro3,1
>>   Processor Name: Quad-Core Intel Xeon
>>   Processor Speed: 2.8 GHz
>>   Number Of Processors: 2
>>   Total Number Of Cores: 8
>>   L2 Cache (per processor): 12 MB
>>   Memory: 18 GB
>>   System Version: Mac OS X 10.5.8
>> Thanks for any advice or suggestions!
>> Kevin Dabbs
>> SMPH/Neurology UW-Madison
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