[Freesurfer] Freesurfer analysis on synthetic images
Hi, We use quantitative T1/T2 mapping to generate a variety of synthetic images e.g. synthetic SPGRs/T1-weighted images. I was wondering whether Freesurfer analysis can be applied to such synthetic images and whether there is anything I need to change in the recon-all processing stream in order to make it work. Thanks, Christine - Dr. Christine Ecker Section of Brain Maturation (PO50) Department of Psychological Medicine De Crespigny Park, Denmark Hill London SE5 8AF Phone: 0207 848 0947 Email: [EMAIL PROTECTED] - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] co-regtistering a single subject to fsaverage space
Dear FreeSurfer Community... what is the best approach to co-register a single subject to fsaverage space and for the results to have identical number of vertices and faces as fsaverage??? will it work by specifying a single subject in the make_average_surface command?? in other words is the sum of two individual averages (i.e., make_average_surface --subjects subjectA and make_average_surface --subjects subjectB) equal to make_average_surface --subjects subjectA subjectB??? Any guidance is greatly appreciated. Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] lh.aparc.a2005s: S_subcentral_ant label
We recently started playing with the ?h.aparc.a2005s annotation files (fsv401). We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file. However, this variable name does *sometimes* appear in some of our study subjects. 1) Is this normal behavior? 2) Is it possible to add a FieldName index (analagous to the aseg.stats file) to facilitate detailed accountings of empty variables in the ?h.aparc.a2005s files? Many Thanks for any information you can provide, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] co-regtistering a single subject to fsaverage space
I think that will work. Dick, Rachel wrote: Dear FreeSurfer Community... what is the best approach to co-register a single subject to fsaverage space and for the results to have identical number of vertices and faces as fsaverage??? will it work by specifying a single subject in the make_average_surface command?? in other words is the sum of two individual averages (i.e., make_average_surface --subjects subjectA and make_average_surface --subjects subjectB) equal to make_average_surface --subjects subjectA subjectB??? Any guidance is greatly appreciated. Rachel ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Citation for FSFAST
Hi Doug. What's the preferred citation/reference for FSFAST? Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Citation for FSFAST
I don't really have one, the closest ref is: Marc A. Burock, Anders M. Dale. Estimation and detection of event-related fMRI signals with temporally correlated noise: A statistically efficient and unbiased approach. Human Brain Mapping, 2000, Volume 11, Issue 4 http://www3.interscience.wiley.com/journal/73504814/issue , Pages 249 - 260 or you can just site the freesurfer web site. doug Dan Dillon wrote: Hi Doug. What's the preferred citation/reference for FSFAST? Dan Dillon -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] IO with freesurfer files (.mgh in particular) from Python
Does anyone know any handy module to at least read in .mgh files from Python? Or should I simply try mri_convert them into .minc and use netcdf module within python? Thanks in advance for the ideas! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
