Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

aparc.a2005s.annot errors?
by Yigal Agam 25 Jun '10

25 Jun '10

Hi, There are some "holes" in fsaverage lh cingulate labels in the a2005s annotation. For example, vertex 16631, between the cingulate gyrus and sulcus is part of the superior frontal gyrus label. Same with vertices 20390 and 141081. Is that an error? This is a problem for us because it creates holes in our ACC labels. Thanks, Yigal

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saving snapshots with white background
by ythomas 25 Jun '10

25 Jun '10

Hi, Is there an option to save snapshots in tksurfer with a white background instead of the usual black? Thanks, Thomas

3 2

File input
by Michele Placci 25 Jun '10

25 Jun '10

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, DICOM format (I have NIFTI too) to calculate brain volume. I downloaded the software from your site following the instructions for a Linux CentOS 4. Now my questions are: I have a classical MRI 3D image file, how do I send the files to FreeSurfer? What are the instructions that I have to write in the bash? Is there a GUI to calculate brain volume? Any help is appreciated, Thanks! Michele.

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Freesurfer DWI
by Tina Jeon 24 Jun '10

24 Jun '10

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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Postdoctoral Research Position in Neuroimaging/Neuropsychology at VA Boston
by Scott Hayes 24 Jun '10

24 Jun '10

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 verf(a)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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Confounding variables
by Kelly Silva 24 Jun '10

24 Jun '10

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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computer shut down
by Ilana Hairston 24 Jun '10

24 Jun '10

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

3 2

Command for making a picture
by roberto toro 24 Jun '10

24 Jun '10

hello, Is there a command line tool for making a picture of a surface with labels superimposed? thanks in advance! roberto

2 1

RAS to talairach transform
by Corey Keller 23 Jun '10

23 Jun '10

Hi freesurfers, I am trying to convert electrode coordinates from RAS to talairach space. I have 128 electrodes sitting directly on the pial surface which was created from recon-all. I see that the output of each reconstruction has two transforms, talairach.xfm and talairach.auto.xfm. There seems to be a difference between the two - could you explain the difference and which one I should be using? I cannot seem to find this online. Thanks. Best, Corey

2 1

Grey Matter Density?
by Matthew Ku 23 Jun '10

23 Jun '10

Hi Freesurfer Experts, I have been running Freesurfer to calculate the grey matter volume of pediatric brains but I was wondering if there was a method to determine grey matter density using Freesurfer? I have read a question previously posted asking a similar question, but there had been no replies or answers. If there is no command to calculate the density of grey matter, is there any alternate method to determine the density from the volume data? Thanks, Matt _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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