Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30050 discussions

FW: job announcement (fwd)
by Bruce Fischl 14 May '04

14 May '04

For anyone who is interested Bruce While the FreeSurfer mailing list is provided as a public resource for academic researchers, we wanted to inform you of an opening at CorTechs Labs, Inc. Computational Imaging Scientist/Engineer - Neurosciences A full-time Computational Imaging Scientist/Engineering position to develop software for the quantification and measurement of structural 3-D MR images at CorTechs, Labs, Inc. is currently available. This is an opportunity to work with leading neuroscience researchers and scientists in an exciting medical device software company focused on developing imaging diagnostics for central nervous system diseases. Advanced theoretical abilities, creative problem solving and well-developed computational skills are required. Qualifications Experienced with Linux development environments, including with HPC's (high performance computation environments), such as clustering and optimized math libraries Advanced programming abilities with C and C++ Advanced development experience with Matlab(tm) Expert in Pattern Classification, such as Bayesian classifier design, neural network, SVM (Support Vector Machine), and signal processing Strong written and verbal communication skills Prior computational experience with neuro-MRI is required Deep experience with FreeSurfer(c) or other comparable software is a plus, as is any sequence development on any of the MR vendor platforms Duties and Responsibilities Develop software and algorithms for segmentation and quantification of neuro-MRI data Help optimize MR image acquisition protocols for quantitative analysis Generate and implement advanced computational software based upon specifications Interact and communicate effectively within the scientific engineering group Plan, schedule and execute assignments within projected timelines Education A Ph.D. in Computer Science, Imaging Processing, or related field is required, as is U.S. Citizenship or Permanent Resident status. CorTechs provides a competitive salary, health and dental benefits, as well as membership in a local health club. To apply, please email your resume to info(a)cortechs.net <mailto:info@cortechs.net> . No phone calls please. For additional information about Cortechs, please see our web site at www.cortechs.net <http://www.cortechs.net/> CorTechs Labs, Inc. is an equal opportunity employer.

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surface normal
by darren.weber＠radiology.ucsf.edu 09 May '04

09 May '04

Is the freesurfer surface tesselation consistent with the "right-hand" rule? That is, if we have a triangle of three vertex points (P1, P2 & P3), we can find 2 edges, E1 = P3 - P2 E2 = P2 - P1 and we can find the normal to this triangle surface by taking the cross product of the edge vectors N = E1 x E2 and the unit normal from this, of course. The question is, then, wether N is directed outside of the surface. Note that E1 x E2 = -1 * ( E2 x E1 ) That is, the order of the cross product is important. Also, now note that the order of the points (P1, P2 & P3) in the triangle is important. Without a consistent convention for their order, we cannot know whether the surface normal is directed inside or outside the closed brain surface. Best, Darren --------------------------------------------- This message was sent using Endymion MailMan. http://www.endymion.com/products/mailman/

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R L flipping
by Mark A. Pinsk 09 May '04

09 May '04

Hello, we are desperately in search of a way to flip our freesurfered data. There was a post a while back referring to mris_reverse but it doesn't seem to be included in the current distribution. any help would be greatly appreciated ! thanks mark _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

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mean & std. dev over an ROI
by George Papadimitriou 07 May '04

07 May '04

We would like to calculate the mean and std. deviation over a region of interest using tkmedit. The underlying image volume (on which the ROI is delignated) is a scalar map. Kevin mentioned that there might be a tool in the Freesurfer suite that will do that calculation. I would really appreciate your input. George P.

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updated tkmedit won't run..
by Wietske Van Der Zwaag 05 May '04

05 May '04

Dear Freesurfers, I've just updated my freesurfer to the 20040218 version, but now I am no longer able to run the tkmedit program. I've tried the tkmedit.static version too, but with the same result (ie none) The log file says this: /usr/local/freesurfer/bin/Linux/tkmedit blobby T1 -csurf Command Finished Does anybody know what to do about this? I don't think anything's wrong with the videocard, as I was able to run the older version of tkmedit. Thank you, Wietske

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mris_anatomical_stats thickness deviation
by Ray Fix 05 May '04

05 May '04

Hello, When you run mris_anatomical_stats it reports, among other things: average cortical thickness = x mm +- y mm y is maximum difference? standard deviation? As always, thanks for your help to these simple minded questions. Ray

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Seg fault during wm_fill
by Geoffrey Aguirre 28 Apr '04

28 Apr '04

Folks -- I'm working with a dog brain. With the help of Denis Fize, I've "tricked" freesurfer into treating my 0.47 mm voxels as 1 mm voxels, and I have manually stripped the skull. I used the automated routine to segment white matter and then manually erased the brainstem and cerebellum. Now, however, when I try and apply the automated white matter fill routine, the operation fails with "Segmentation Fault" after several minutes of processing. I've provided left and right hemisphere seed points, as well as a callosal seed point. This is a fairly unusual data set, but I would appreciate any advice... Thanks, Geoff -- Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

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How to get each value for total out and inner cortex surface area
by Akemi Tomoda 28 Apr '04

28 Apr '04

Dear list, According to the results by running FS in our subjects, I have come to realize that the cortical surface area and gray-matter volume shrinks, while the cortical thickness tends to increase with a highly localized area of cortical thickening in the left hemisphere. To my knowledge, these two variables (area, thickness) can not possibly be independent. So there must be a relationship because volume = area * thickness. In order to test it statistically and look into the problem of interaction between thickness and area, I'd like to get the values of total out cortex surface area and total inner cortex surface area, separately. I know FS use the white surface for surface area from the past ML (Pial Surface). I was wondering how I can get each value for out and inner cortex surface area. Any suggestions are very welcome. Akemi Developmental Biopsychiatry Research Program McLean Hospital atomoda(a)mclean.harvard.edu Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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subcortical parcellation
by Frederic Dick 28 Apr '04

28 Apr '04

Hi all are there any plans to release the subcortical parcellation as part of freesurfer? Or is it in another set of tools? Or is it still in-house only? Thanks! Fred

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need clarification of analyze 7.5 format orient value
by Yasunari Tosa 18 Apr '04

18 Apr '04

I need the clarification of analyze 7.5 format in sagittal flipped case. I just found that it is different from the one I used for freesurfer. I used Graham version from his web site: wideman-one.com/gw/brain/analyze/formatdoc.htm has *hist.orient* *Mayo name* *Voxel[Index0, Index1, Index2] * *Index0* *Index1* *Index2* 0 (default) transverse unflipped R-L P-A I-S 1 coronal unflipped R-L I-S P-A 2 sagittal unflipped P-A I-S R-L 3 transverse flipped R-L A-P I-S 4 coronal flipped R-L S-I P-A 5 sagittal flipped P-A S-I R-L Note: Index0 is fastest-varying (innermost-nested) index, Index2 the outermost. Index0..Index2 are often called X, Y, Z, but I am trying to avoid confusion with spatial coordinates. I found that http://nifti.nimh.nih.gov/dfwg/nifti_revised.html has * /vs./ qform_code*: The ANALYZE-7.5 format indicated 3D orientation with the 1 byte code orient, which was to be interpreted as 0 = transverse-unflipped R?L P?A I?S 1 = coronal-unflipped R?L I?S P?A 2 = sagittal-unflipped P?A I?S R?L 3 = transverse-flipped R?L A?P I?S 4 = coronal-flipped R?L S?I P?A 5 = sagittal-flipped P?A I?S L?R Note that the second and third axis of "sagittal flipped" are flipped ;-) Tosa -- Yasunari Tosa, Ph.D. R&D Engineer email: tosa(a)nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149 13th Street fax : Charlestown, MA 02129

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