Re: [Freesurfer] ICV/brain volume

Hi Mike, Thanks for your suggestions. I have learned this idea from previous posts (including yours), but found that there is an issue for this approach when I checked the pial surface with tkmedit (tkmedit subjid T1.mgz lh.pial -aux-surface rh.pial): part of two important brain structures, amygda

Re: [Freesurfer] Smoothing BOLD on the surface

Yes, create a registration file with bbregister, then use mri_vol2surf to map it to the surface. You can do surface-based smoothing mri_vol2surf (with the --surf-fwhm option) or using mri_surf2surf. doug Oya, Hiroyuki wrote: > Dear Experts, > > I would like to first analyze the BOLD response wi

[Freesurfer] Smoothing BOLD on the surface

Dear Experts, I would like to first analyze the BOLD response without smoothing in the functional volume, and apply smoothing on the surface and map it. Would this be possible? Thank you in advance. Hiroyuki ___ Freesurfer mailing list Freesurfer@n

Re: [Freesurfer] ICV/brain volume

Here is an approach that will be easier, and involves less back and forth between the surface and volume-based streams (and thus should be more accurate): Just use 'mris_volume' to get the volume of everything enclosed by the pial surface, which if I recall correctly will include the lateral vent

[Freesurfer] ANN : aparcstats2table. asegstats2table fixes

The following mis-feature highlighted by Nathan is fixed and the fixes are available from the following location. Replacing your existing aseg/aparcstats2table is highly recommended. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ Please copy the files to your $FREESURFE

[Freesurfer] ICV/brain volume

Dear FreeSurfer experts, After searching on FreeSurfer wiki and mailing list, I know that the ICV reported in aseg.stats is an estimated value based on talairach transformation. So, if the talairach transformation for a subject's head is not good, the ICV for this subject is not accurate, am I rig

[Freesurfer] Lose Keyboard

Dear all, I am running freesurfer 4.5 on Ubuntu9.10(64bit). Is anybody experiencing " lost keyboard " problem? I cannot put any number in tkmedit and tksurfer using keyboard. Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] Ubuntu FreeSurf VirtualBox root password

The password is in the README file. I think it's brain2009 cheers --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business 2010/1

[Freesurfer] Ubuntu FreeSurf VirtualBox root password

Hi all and Pedro Paulo Oliveira, I have installed Ubuntu VirtualBox on Windows. I would like to thank Pedro Paulo Oliveira for for making this convenient solution for Windows OS. What I am missing is the root password (without root password it's impossible to install guest additions, make shared f

[Freesurfer] annot to label to gm thickness map

Hello All, I want to create a gm thickness map from central sulcus and precentral gyrus. I plotted the lh.aparc.a2005s.annot on the inflated surface and I see the sulci and gyri. Is there a way to create a binary label of the central sulcus and precentral gyrus ? Can that label be then used

Re: [Freesurfer] Retinotopic mapping of only polar data

You can generate a register.dat with either fslregister-sess or spmregister-sess, or, if you have it in your version, use bbregister (note that there is not a -sess version for this yet). You can then use mri_vol2surf to resample the h.nii file to the surface, then view it in tksurfer. You can

Re: [Freesurfer] erroneous segmentation of white matter and cortical thickness...

Hi Gonzalo, the thickness is only dependent on the surfaces, not the segmentation. cheers Bruce On Fri, 8 Jan 2010, Gonzalo Rojas Costa wrote: > Hi: > > In the temporal lobe I got a white matter "erroneous" segmentation (that I > know that I could correct it using control points)... In the aseg

[Freesurfer] erroneous segmentation of white matter and cortical thickness...

Hi: In the temporal lobe I got a white matter "erroneous" segmentation (that I know that I could correct it using control points)... In the aseg.auto.mgz file the white matter appears as cerebral cortex... The cortical thickness computation is related to that segmentation ?... Or the segmentatio