[Freesurfer] Freesurfer DWI

[Tina Jeon]

Hello all, 

Can freesurfer be run on diffusion weighted images and/or B0 images? I am 
trying to obtain segmentation of the gray/white surfaces. 

Thanks, 
Tina Jeon

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[Freesurfer] Postdoctoral Research Position in Neuroimaging/Neuropsychology at VA Boston

[Scott Hayes]

Preliminary Announcement for Neuroimaging/Neuropsychology Postdoctoral 
Research Position
Memory Disorders Research Center and Neuroimaging Research Center
VA Boston Healthcare System

The Boston University Memory Disorders Research Center and Neuroimaging 
Research Center at VA Boston Healthcare System (VABHCS) anticipate an 
opening for a postdoctoral fellow with expertise in neuroimaging and 
neuropsychology and are seeking potential applicants for the position. 
The postdoctoral fellow will work closely with neuropsychologists and 
neuroscientists on a clinical research program aimed at elucidating the 
neural and cognitive sequelae of blast-induced traumatic brain injury, 
with Dr. David Salat and Dr. Mieke Verfaellie as primary mentors. The 
candidate will receive advanced training in diffusion tensor imaging, 
volumetric and surface-based MRI analyses, functional connectivity MRI 
analyses, and structure-function correlational approaches. The 
successful candidate will have a doctoral degree in neuropsychology, 
cognitive/behavioral neuroscience, or a closely related field, and 
experience in neuroimaging and data analysis. Candidate should have 
expertise working with MRI analysis software such as AFNI, FSL, SPM, or 
FreeSurfer, as well as familiarity with unix or Matlab.   Experience 
interpreting neuropsychological data, and previous work with clinical 
populations are highly desirable. The postdoctoral fellow will interact 
with several research groups at VABHCS studying TBI and PTSD in 
returning veterans, and will be part of a rich and stimulating 
intellectual environment. The candidate should have a keen interest in 
developing an independent research career.

The opening is expected for October, 2010, but the starting date is 
flexible. A minimum two year commitment is required.

An official job posting and formal application instructions are expected 
to be accessible at www.usajobs.gov in August.

Potential applicants are encouraged to immediately submit a CV and a 
letter describing research interests and experience and should arrange 
to have three letters of recommendation sent to:
Mieke Verfaellie, Ph.D.
Memory Disorders Research Center
VA Boston Healthcare System (151A)
150 S Huntington Avenue
Boston MA 02130
v...@bu.edu
857-364-4031

The Department of Veterans Affairs is an Equal Opportunity Employer.

-- 
Scott M. Hayes, Ph.D.
Memory Disorders Research Center
Neuroimaging Research Center
VA Boston Healthcare System

Assistant Professor
Department of Psychiatry
Boston University School of Medicine

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[Freesurfer] Confounding variables

[Kelly Silva]

Hello,
We are doing some analyses with one region of interest. We controlled (as 
possible
confounding variable) for the volume of the region of interest. Are we
correct? If no, should we put the total volume of the images as confounding 
variable?
Thanks and best regards, Kelly



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Re: [Freesurfer] computer shut down

[Pedro Paulo de Magalhães Oliveira Junior]

Now we entered this in the FAQ:
Q. I had a [Power Outage|Computer Failure|Spilled coffee on computer|etc],
how can I resume the
recon-all?

thanks
Doug.

cheers
--
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- For mobile: http://www.netfilter.com.br/mobile




On Thu, Jun 24, 2010 at 11:59, Douglas N Greve wrote:

> You can try
>
> recon-all -make all -s subject
>
> Also, depending on your version, there might be a file in the scripts
> directory called "IsRunning". You should delete this if it is there.
>
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Re: [Freesurfer] computer shut down

[Douglas N Greve]

You can try

recon-all -make all -s subject

Also, depending on your version, there might be a file in the scripts 
directory called "IsRunning". You should delete this if it is there.

doug

Ilana Hairston wrote:
> Hi There,
> If a recon stopped half way, because of a power outage. Is there a way 
> to continue the process, rather than start from scratch?
> thanks
> ilana 
> 
>
> ___
> 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] computer shut down

[Ilana Hairston]

Hi There,
If a recon stopped half way, because of a power outage. Is there a way to
continue the process, rather than start from scratch?
thanks
ilana
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Re: [Freesurfer] Command for making a picture

[Bruce Fischl]

Hi Roberto,

you can do this in tksurfer using the GUI, or you can use a tcl script 
with -tcl