[Freesurfer] postdoc opportunity

2019-03-04 Thread Bruce Fischl
see the attached job opening description. If interested contact Michael (contact info below and in attachment) Michael Zeineh, M.D.-Ph.D. Assistant Professor, Dept. of Radiology Associate Chief of Neuroradiology for Operations and IT Stanford University, Lucas Center for Imaging, Rm. P271 1201

Re: [Freesurfer] Omitting aseg regions from segmentation

2019-03-04 Thread Bruce Fischl
Hi Kody yes, there are some hidden options to recon-all for this. Take a look at the script for things like -no-cerebellum, -rh-only, and see if they are sufficient for what you are trying to do cheers Bruce On Mon, 4 Mar 2019, zalewk wrote: External Email - Use Caution

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2019-03-04 Thread zalewk
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-exchange-diagnostics: =?iso-8859-1?Q?1; CY4PR08MB3573; 23:4qVRtf+4Frk8+HkoSkWpxiBI3Aktx4BluHS3p5r?= =?iso-8859-1?Q?Y9pwKqXqpNNthdH0OWUp6OBtvK1l/YV1ElGbh7XgLoXOL3hSC0itzucGip?= =?iso-8859-1?Q?p+wDHeAm0zUT5UWpPv2w4rF

[Freesurfer] Whitening/weighting matrix in FSFAST

2019-03-04 Thread Zhi Li
External Email - Use Caution Hello Freesurfer Experts, May I ask if there is a whitening/weighting matrix used to give weighted least squares estimates (WLS) and whiten the data during the 1st-level model estimation in FSFAST? If so, how could I get it? Many thanks and kind regar

[Freesurfer] citing freesurfer

2019-03-04 Thread Daniel Callow
External Email - Use Caution Hello, How should I go about properly citing freesurfer if I am using dt_recon for dti analysis? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail

[Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

2019-03-04 Thread CAGNA Bastien
External Email - Use Caution Hi everyone, I need to convert a surfacic mask that is made from data of one subject projected onto fsaverage6 into a volumic map. To do so, I'm trying to use mri_surf2vol to take my Gifti file and create 3D version as Nifti file (using gray matter).

[Freesurfer] Group analysis

2019-03-04 Thread Hengameh Marzbani
External Email - Use Caution Hi Freesurfers, I want to do group analysis on four groups and use the volume values in aseg,stats. 1- Is it correct that each subcortical segmentation is based on a "volumetric segmentation atlas" created by Freesurfer? 2- Are the volume values expres