[Freesurfer] Vertex-wise thickness correlations

Dear FS experts We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question: Is there any tool in FS yet that is able to do that? Thanks in advance Best regards Juerge

[Freesurfer] cortical thickness: same subjects at different time points

Hello everybody, It's some time ago that I did some group analyses for cortical thickness and after glancing through the new documentation I believe (or hope) that I still know how do do a group comparison (e.g. patients vs controls). I have, however, never tried analyses of groups at differen

Re: [Freesurfer] Vertex-wise thickness correlations

Hi Juergen, qdec will certainly do this on a parcel basis. I'll leave the correlation map for Doug. cheers, Bruce On Fri, 22 Feb 2008, Juergen Haenggi wrote: Dear FS experts We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the t

Re: [Freesurfer] nu_correct error

Thomas, >From looking at the log, this appears to be v3.0.2, which is an old version. Is this the first time this has been used? That is, has this version been used on other scans and it is just now failing on this one (and the others in the set)? Can you get a more recent version? The current

[Freesurfer] finding WM hypointensities

Hello, i wonder if there is a possibility to identify the recognized WM hypointensities with tkmedit - something like labeling the WM hypointensities. Thanks for help, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] finding WM hypointensities

Hi Thomas, the aseg includes hypointensities, but there's only so much you can do with only a T1-weighted image. We do have some beta versions that use a PD/T2 dual each in addition to the T1 to label them. Bruce On Fri, 22 Feb 2008, Thomas Doering wrote: Hello, i wonder if there is a pos

[Freesurfer] QDEC

Dear FS experts I tried to open QDEC but the following error occurred: dyld: Library not loaded: /usr/X11R6/lib/libexpat.0.dylib Referenced from: /Applications/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.dylib Reason: image not found Trace/BPT trap [Macintosh-3:/usr/X11R6/lib] juerge

[Freesurfer] Subcortical calabel errors

Hello All, To begin I'm running 4.0.1 on Mac OSX Tiger (Intel). I'm having trouble with one subject in particular failing before generating the aseg.auto.mgz or aseg.mgz. I don't see anything amiss in the previously generated files and images, however, this subject has extremely large ventricles,

Re: [Freesurfer] QDEC

Juergen, I'm guessing you upgraded to Leopard. Whereas Tiger put libexpat in /usr/X11R6/lib, Leopard has it in /usr/lib. So as a fix, try this: cd /usr/X11R6/lib sudo ln -s /usr/lib/libexpat.dylib libexpat.0.dylib I can't guarantee that this will work though. A Leopard distribution of freesur

[Freesurfer] Freesurfer Citation in Paper

Is correct the statement below? FreeSurfer implementation of cortical surface-based analysis is distinct from other surface-based algorithms and conventional volume based morphometry with atlas mapping, as it does not necessarily depend on smoothing or matching to an atlas. Thanks in advance, Pe

Re: [Freesurfer] talairach striped

It just looks like an interpolation artifact and nothing to worry about, though we usually only see that kind of thing when the slices are thick. How thick are your slices? On Fri, 22 Feb 2008, Hoppmann, Fee wrote: Dear all, I performed reconall -autorecon1 on a set of images derived from to

Re: [Freesurfer] Vertex-wise thickness correlations

You can add the value you want as a continuous variable in an fsgd file, then set up a contrast to test it. On Fri, 22 Feb 2008, Juergen Haenggi wrote: Dear FS experts We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickne

Re: [Freesurfer] cortical thickness: same subjects at different time points

Hi Claus, the easiest way to do a paired t test is to run mris_preproc with the --paired-diff option. Make sure to specify time point 1 and 2 for each subject sequentially. You can do a stat test on each individual with only 2 time points. doug On Fri, 22 Feb 2008, Claus Tempelmann wrote: H

Re: [Freesurfer] Subcortical calabel errors

Marlisa, The -bigventricles flag is described in the recon-all -help output (in v4.0.2, not sure about 401). You can try including it with the - autorecon2 stage to see if it fixes the problem, although I wouldn't expect mri_ca_register to segfault w/o it. Do you have at least 2GB available for

Re: [Freesurfer] cortical thickness: same subjects at different time points

Claus, One approach to do a direct thickness comparison, as was done for a test-retest study described here: https://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility There's a link on this page to the paper that was published. That might be all you need. It is also possible to use mri_

Re: [Freesurfer] Freesurfer Citation in Paper

Hi Pedro, no, not quite. There are various atlases we use at different points, and we impose smoothness constraints on the surfaces. cheers, Bruce On Fri, 22 Feb 2008, Pedro Paulo Oliveira Jr wrote: Is correct the statement below? FreeSurfer implementation of cortical surface-based analys