[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. @

[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

[Freesurfer] Experience with -localGI on Mac

Hello folks, I am trying -localGI on Mac, with working Matlab2007. 1. I think that the getmatlab script is not designed to work on Mac out of the box, since it is not by default in the $PATH, so it could be caught by "which". So I uncommented the three lines and set it hard. 2. That was easy,

[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

Re: [Freesurfer] Freesurfer analysis on synthetic images

Hi Christine, Bruce is the best person to answer this but he may be out of email contact for a few more days. I think that it is probably ok, as long as your final images have a T1 contrast. doug Christine Ecker wrote: Hi, We use quantitative T1/T2 mapping to generate a variety of synthetic

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 ma

[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 s

[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

[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