[Freesurfer] recon-all issue (CSF seg as gray matter)

Hi, after running recon-all on many datasets without any manual intervention, it looks like I finally have to. As you can see in : https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%2013.16.52.png the CSF is segmented as gray matter while white+gray matters are merged.

Re: [Freesurfer] matrix ill-conditioned....

Hi Doug, Thanks! I actually thought I only had to demean variables that were not of interest. But this was indeed the problem, it now works! Thank you very much! Best Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life S

[Freesurfer] Thickness vertex by vertex

Dear all, Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? Thanks Cheers Giusy Chinnici ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] recon-all issue (CSF seg as gray matter)

Hi Alex that's pretty bad! You could start by specifying some expert options about the ranges of gray and white matter intensities to mri_segment and mris_make_surfaces. Hopefully someone will chime in with the syntax, as I don't remember it. You can also check the recon-all.log to see what ran

Re: [Freesurfer] Thickness vertex by vertex

you mean only within that ROI? I don't think so, but this would be pretty easy in matlab On Wed, 28 Aug 2013, Giusy Chinnici wrote: > Dear all, > > Is there available a function that, given a certain ROI, returns per vertex > thickness (not the average thickness)? > > Thanks > Cheers > > Giusy C

Re: [Freesurfer] Thickness vertex by vertex

Giusy, You can access vertex level info in Matlab with MRIread('SUBJECT.FILENAME'). Avram On Wed, Aug 28, 2013 at 8:42 AM, Giusy Chinnici wrote: > Dear all, > > Is there available a function that, given a certain ROI, returns per > vertex thickness (not the average thickness)? > > Thanks > Che

Re: [Freesurfer] matrix ill-conditioned....

In general, you should not need to demean. For the interaction, you need to demean before computing the interaction. doug On 08/28/2013 07:54 AM, Jacobs H (NP) wrote: > Hi Doug, > > Thanks! I actually thought I only had to demean variables that were not of > interest. > But this was indeed th

[Freesurfer] Longitudinal Processing Pipeline

Question regarding longitudinal processing pipeline. Is there a way to force the -long procedure to use an individual base template for a time point not used to create the base in the first place? David F. Tate, Ph.D. ___ Freesurfer mailing list Fre

Re: [Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

JoJo, I have not tried to recreate your issues on machine running Ubuntu 13.04 but have tried to run the commands on Ubuntu 12.04. To summarize: 1) Regarding your first issue... this is standard output to the terminal on certain OS's including Ubuntu. I got it when I tested your command but th

[Freesurfer] license error with FS5.3

I see some reports of license failures, and seem to be having a similar problem. Our installations of 4.5 and 5.1 work normally, but with 5.3 I had a mysterious error in unpacksdcmdir that ultimately traced to a license error in mri_convert. I can reproduce the error like so: *mri_convert $FREESUR

[Freesurfer] pial surface editing

Hello, I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using "shift+click" to delete voxels at a brush value of 1 and then s

Re: [Freesurfer] pial surface editing

Are you saying that edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are not showing up as affecting the actual pial surfaces themselves? I would focus on whether the pial surfaces are fixed, not whether edits to brain.finalsurfs.manedit.mgz are "back-propagated" to brainmask.mgz.  (I

Re: [Freesurfer] Thickness vertex by vertex

you can use read_label and the first column (+1) for the indices Bruce On Wed, 28 Aug 2013, Giusy Chinnici wrote: Thanks all, I opened the file subj/surf/?h.thickness with MATLAB using the function read_curv(subj/surf/lh.thickness). I obtained a vector with dimensions nverticesX1, but I need

[Freesurfer] Brainhack 2013 Invitation and Registration Link

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Brainhack 2013 is a unique workshop with the goals of fostering interdisciplinary coll

Re: [Freesurfer] pial surface editing

If you're following the instructions of the tutorial, then I don't know why your edits to brain.finalsurfs.manedit.mgz wouldn't be reflected in the pial surface. Perhaps one of the FS developers will have a thought as to what is going wrong. cheers, -MH --  Michael Harms, Ph.D. ---

Re: [Freesurfer] Thickness vertex by vertex

Thanks all, I did it :) Cheers Giusy Inviato da iPhone Il giorno 28/ago/2013, alle ore 18:40, Avram Holmes ha scritto: > check the .vol values I think they should match those from read_curv. > > Avram > > > On Wed, Aug 28, 2013 at 11:37 AM, Giusy Chinnici > wrote: >> Thanks all, >> >> I

[Freesurfer] Longitudinal processing - Surface area

Dear all, I am interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical patients. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering