[Freesurfer] WM.mgz corrections in the ventricles & Individual Normalization

Hello - I have two questions: 1) I noticed on wm.mgz volumes that were segmented properly, that even when the ventricles were automatically filled in, on some slices they are somewhat patchy (partially filled in with white, with some black/blank voxels). Do these patchy wm fill-ins require ma

Re: [Freesurfer] FreeSurfer two atalses

Hi Guang, yes, you can read the Human Brain Mpaping (high-resolution inter-subject averaging), Neuron (whole brain segmentation) and Cerebral Cortex (parcellation) papers with me as first author. cheers Bruce On Tue, 19 Jan 2010, Guang Zeng wrote: > > Hi, there, > > Are there any place in F

[Freesurfer] Vol index to Talairach

Dear experts, I like to find Tarairach and MNI coordinate from volume index (data has been already processed with recon-all) off line using Matlab. Which transform should I use to find it ? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] brainmask

aparc+aseg.mgz is probably better. See surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your question. Satrajit Ghosh wrote: > if one wants to get at the brain only (similar to bet), is > brainmask.mgz the best file to use? on some of our data, we are > noticing a lot of eyeball

[Freesurfer] brainmask

if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg

[Freesurfer] FreeSurfer two atalses

Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s

Re: [Freesurfer] Paired Analysis, Smoothing Step

Are those backslashes ("\") in your command-line? If so, try removing them. Stidd, Reva (NIH/NIMH) [F] wrote: > Hi there, > > I've got a sample of subjects with T1 and T2 scans that I'm trying to > compare. I did the entire longitudinal stream protocol, and am now doing the > paired analysis pro

Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

If you do: $>mris_calc stats the first line reported back will be the number of vertices. So, if you want to know how many vertices on the left hemisphere: $>mris_calc lh.thickness stats and look at the Size[ XXX ] where XX will be number of vertices. Stefan Brauns wrote: > Hi

Re: [Freesurfer] a question about rebuild_gca_atlas.csh

yes, or the talairach.lta On Tue, 19 Jan 2010, Guang Zeng wrote: > > Hi, there, > > In rebuild_gca_atlas.csh, I read something like: > > # A talairach registration should be generated for this first subject as well, > # in order to align the final atlas to the Talairach space. > > Is this talair

Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

usually around 140k/hemi. If you make a label and save it as a label file it will have 1 line/vertex On Tue, 19 Jan 2010, Stefan Brauns wrote: > Hi there, > > I am running surface based analysis of cortical thickness using FreeSurfer. > Sometimes I constrain the analysis to certain regions of t

Re: [Freesurfer] a question about rebuild_gca_atlas.csh

yes. be sure to double-check it with tkregister2. On Tue, 2010-01-19 at 12:24 -0600, Guang Zeng wrote: > Hi, there, > > In rebuild_gca_atlas.csh, I read something like: > > # A talairach registration should be generated for this first subject > as well, > # in order to align the final atlas to

[Freesurfer] a question about rebuild_gca_atlas.csh

Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/tr

Re: [Freesurfer] Fw: manually specifying design matrix

It would probably be more like this: 1. 00.5000 1. 0 -0.5000 01.0.5000 01. -0.5000 The 1st col codes subject 1. The 1st row is the 1st measure of subject 1 and the 2nd row is the 2nd measure of subject 1. doug raka ma

Re: [Freesurfer] FSL and freesurfer: combine runs in volume or on surface?

I have not tested the different methods to find out. I prefer the first method because it involves one fewer resampling steps. Also, if you have a newer version of freesurfer that uses BBR, then reg-feat2anat will use BBR, which will be more accurate. And do not spatially smooth your fMRI data

Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

In the mri_glmfit.log file, there is a "SearchSpace" this will be in mm2 for surfaces and mm3 for vols. There will also be a mask.mgh file. You can run mri_segstats on this to give you the number of elements that are == 1. doug Stefan Brauns wrote: > Hi there, > > I am running surface based an

[Freesurfer] number of vertices per hemisphere using mri_glmfit

Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a pos

[Freesurfer] Fw: manually specifying design matrix

Hello Sorry for reposting again. Would really appreciate a feedback on the following mail. Thanks in advance for your time Raka - Forwarded Message From: raka maitra To: Douglas N Greve Sent: Fri, January 15, 2010 9:34:02 PM Subject: Re: [Freesurfer] manually specifying design matri

[Freesurfer] FSL and freesurfer: combine runs in volume or on surface?

Dear all, I am trying to figure out how to bring my fMRI data from FSL to the freesurfer surface. The way I understood it from the tutorial "3.0 Surface-based Group Functional Analysis"( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) There are two possibilities of combining mu