Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

Semi-Inflated Surfaces
by Liang, Kelvin 02 Nov '09

02 Nov '09

Hi FS Folks, I've often seen articles present their data on semi-inflated cortical surfaces, and I'd like to display my regions of interest in such a format. However, I've only found inflated, pial, and white surface options in qdec or tksurfer. Am I overlooking an option somewhere? Thank you for your assistance, Kelvin -- Kelvin Y. Liang MSTP, School of Medicine Washington University in St. Louis The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Surface area of subcortical structures
by Elizabeth Selgrade 02 Nov '09

02 Nov '09

Hi Nick, Why do you use 128 as the value for mri_tessellate in your suggestion below? Should this value be used for all ROIs, regardless of hemisphere? Thank you, Liz Selgrade -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, September 16, 2009 3:16 PM To: Douglas N Greve Cc: Elizabeth Selgrade; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Surface area of subcortical structures or use mri_extract_label instead of mri_binarize, like this, to get the left hippocampus: mri_extract_label aseg.mgz 17 lh.hippo.mgz mri_tessellate lh.hippo.mgz 128 lh.hippo.unsmoothed mris_smooth lh.hippo.unsmoothed lh.hippo mris_info lh.hippo |& grep total_area this seems to work. '17' is the index for left hippocampus, as found in $FREESURFER_HOME/FreeSurferColorLUT.txt Nick On Wed, 2009-09-16 at 15:05 -0400, Douglas N Greve wrote: > There's not an easy way. You could binarize the structure > (mri_binarize), then build a surface around it (mri_tessellate), maybe > smooth it (mris_smooth), then compute the surface area (mris_info). > This would be a completely untested method though:). > > Elizabeth Selgrade wrote: > > Hello, > > > > Is there a way to get the surface area of FreeSurfer subcortical structures? > > > > Thanks, > > Liz Selgrade > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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Job announcement
by Derin Cobia 02 Nov '09

02 Nov '09

Posted on behalf of a colleague: FACULTY POSITION, MEG-fMRI NEUROIMAGING Saint Louis University, is a Jesuit, Catholic university dedicated to teaching, research, health care and community service and is seeking a scientist at an open rank level for a non-tenure track, grant-funded faculty position in the Division of Neurosurgery, Department of Surgery at St. Louis University School of Medicine. The successful candidate will head the Division’s imaging research using the installed 275 channel magnetoencephalography (MEG) system and 3 Tesla MRI and manage a multimillion dollar research grant funded by the Department of Defense. This project will span 4 years and study traumatic brain injury in combat veterans using MEG, positron emission tomography (PET/CT) and functional MRI with diffusion tensor imaging (fMRI with DTI). ). A team of research staff members has been assembled to perform the study assisted by graduate and post-graduate students assigned to the project. The ideal candidate would hold a Ph.D. in any of the following areas: biomedical engineering, physiology, experimental/cognitive psychology, neuroscience, MEG, or other applicable disciplines. Candidates should be familiar with standard computational software packages for neuro-imaging such as Curry, Unix, MatLab, Slicer, and C/C++, and have at least five (5) years of clinical research experience, preferably in the neurosciences. Previous experience in neurological functional imaging is expected. Preferred candidates will have proficiency in epidemiology, biostatistics, registration techniques using deformable templates to create standardized atlases, and training/certification in clinical research. Salary will be commensurate with academic credentials and experience. Candidates will be expected to apply and obtain funding from external agencies to continue the work of the Division within the area of neuroimaging using the installed base of equipment. Interested candidates should submit a cover letter, application, relevant reprints, and current curriculum vitae to http:// jobs.slu.edu. An initial letter of interest describing current research interests and future research goals should be sent along with a curriculum vitae to: Richard Bucholz, MD, FACS Director and Professor, Division of Neurosurgery Department of Surgery Saint Louis University 3635 Vista Ave. St. Louis, MO 63110-0250 Phone: 314-577-8795 Email: Richard(a)bucholz.org Saint Louis University is an affirmative action, equal opportunity employer, and encourages nominations and applications of women and minorities.

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comparison of mean thickness of gyri in two groups
by Mehul Sampat 02 Nov '09

02 Nov '09

Hi Folks, If am comparing the mean thickness for certain gyri (pre-central, post-central) in a controls versus patients. I obtain the thickness measurements from lh.aparc.a2009s.stats and rh.aparc.a2009s.stats I was wondering if I need to normalize these thickness measurement with the estimated total intracranial volume (eTIV) ? Or has anyone reported that the these are independent of eTIV ? If so then as I understand I would only need to account for age and gender in any subsequent analysis using GLM. Thanks Mehul

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Making nice images using FreeSurfer
by Estephan Moana 01 Nov '09

01 Nov '09

Hello FreeSurfer experts, I am playing with displaying FEAT output over the 3D pial surface provided by FS. I was wondering if somebody knows how to: 1. See both hemispheres side-by-side at the same time (both pial and inflated, if possible); 2. Make a video of the output 3D brain rotating at a certain axis (x,y or z), and maybe transitioning from pial to inflated surface. This may not really matters for scientific purposes, but it should produce some "wows" during lectures and thesis defense (my goal). AFNI does it, but its rendering option makes the image grainy, resulting in a video with poor resolution. Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 moana(a)email.unc.edu

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Freesurfer November 2009