Re: [Freesurfer] New way of installing and running Freesurfer - containers

Hi Dan, Users are asked to provide their license key they received from MGH after registration as a command line parameter. I also added links to the registration form. Best, Chris On Tue, Aug 9, 2016 at 12:24 PM, dgw wrote: > Hi Chris, > > This sounds great! How does it deal with the FreeSurfe

Re: [Freesurfer] New way of installing and running Freesurfer - containers

Hi Chris, This sounds great! How does it deal with the FreeSurfer license? I know that the FreeSurfer team depends on licenses to keep track of the number of users (a key component to justifying their work when applying for grants). I'm looking forward to trying it out! Thanks, Dan On Tue, Aug 9

[Freesurfer] Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both h

Re: [Freesurfer] brain mask and T1 are not the same size

To try to understand the problem as to why the brainmask.mgz and T1.mgz files are not the same size, I decided to skip that step and make edits to the white matter only. At this point, all files (i.e. T1.mgz, brainmask.mgz and the wm.mgz) have the same dimensions 256^3.  I removed offending v

[Freesurfer] Error running hippocampal segmentation with FS6

-centos6_x86_64-stable-v6-beta-20160805 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160809 INFO: SUBJECTS_DIR is /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6 -rw-rw-r-- 1 ljt22 dinahgp 490999 Aug 9

Re: [Freesurfer] hippocampus question

Thanks Bruce! On Tue, Aug 9, 2016 at 10:06 AM, Bruce Fischl wrote: > HI Jasmin > > we use the definition from various papers from the Center for Morphometric > Analysis (CMA) such as: > > Filipek, P.A., Richelme, C., Kennedy, D.N., and Caviness, V.S., Jr. > (1994). The young adult human brain: a

Re: [Freesurfer] hippocampus question

HI Jasmin we use the definition from various papers from the Center for Morphometric Analysis (CMA) such as: Filipek, P.A., Richelme, C., Kennedy, D.N., and Caviness, V.S., Jr. (1994). The young adult human brain: an MRI-based morphometric analysis. Cereb. Cortex 4, 344–360 You can find the

[Freesurfer] New way of installing and running Freesurfer - containers

Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies). Features: - Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug

[Freesurfer] Average Hippocampal Subfield Maps

Hello, I am wondering if it is possible to make average .mgz for the hippocampal subfields for a set of control images? Thanks, Jessica Sevick T: 403.944.8652 C: 587.576. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] Linking surface and volume coordinates in Freeview

Dear Freesurfer experts, In May 2016, one of the high priority on the Freeview Development board was to "Link the surfaces together (i.e. when you click on a vertex in the inflated surface, it should go to that vertex on the white and pial) & show identical vertex information in the Voxel Info

Re: [Freesurfer] resample structural ROI in functional space?

Never mind - for some inexplicable reason, I did not consider using mri_convert, which works splendidly for doing this. Sorry for posting when tired and before thoroughly exploring my options. -kami From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Kami Koldewyn mailto:k.ko

[Freesurfer] problem with Qdecrc file

Dear FreeSurfer experts, I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab when I want to chose a measure. the file is in the same directory the table.dat file is in. What might be the pr