[Freesurfer] better accuracy of FreeSurfer compared to SPM?

Dear FreeSurfer experts, I am searching for a publication highlighting a better accuracy of FreeSurfer compared to SPM with regard to the analysis of cortical gray matter volumes. Does anybody know one? Thanks for your help! Best, Marisa ___

Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream

Dear Martin and FS experts, I have a small follow-up question regarding the post below. Given a young sample where ICV is still growing, that I want to control for this and that the data look ok: Can I use the cross-sectional ICV as a covariate in analyses on the longitudinal data? Or will

[Freesurfer] Error when launching qdec

Hello Freesurfer Community, I am now having issues getting qdec to launch as well. The qdec window pops up momentarily but then disappears. This is the error message I get: error: xp_attach_gl_context returned: 2 X Error of failed request: 0 Major opcode of failed request: 149 (GLX)

Re: [Freesurfer] Parenchyma over CSF rartio

You probably want something like BrainSegNotVent/Sum(CSF and Ventricles) Is that what you mean? doug On 10/26/14 11:45 PM, Mahmoud wrote: Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for

Re: [Freesurfer] Parenchyma over CSF rartio

Dear Doug, The problem is that I'm not sure what those terms exactly mean ! i.e. what is exactly CSF ? ventricles contain CSF right ? Is CSF counts for subdural CSF too ? I have a the aseg.stats with all terms inside but not sure which one to pick up, that's why I'm asked here. Thank you,

Re: [Freesurfer] Parenchyma over CSF rartio

All CSF measures are ventricular, not sulcal. If you are in doubt, you can always load the aseg.mgz and see what labels correspond to what. You can also see http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats doug On 10/27/14 9:40 AM, Mahmoud wrote: Dear Doug, The problem is that

[Freesurfer] template to dicoms

Dear freesurfers, I have a bit of a strange question: does anyone know a way to write a template T1 brain (for instance fsaverage or MNI152) to dicom files? I have some very old software that only takes dicoms and it's the only software I can use to replicate previous findings, but obviously

Re: [Freesurfer] template to dicoms

We don't have tools to do this. Not sure who does, but I think there are some out there. doug On 10/27/2014 11:23 AM, Linda Douw wrote: Dear freesurfers, I have a bit of a strange question: does anyone know a way to write a template T1 brain (for instance fsaverage or MNI152) to dicom files?

[Freesurfer] Appropriate levels of surface smoothing

Hi everyone, Firstly - thank you for the excellent tools. This year has been my first foray into surfaced based analysis and I'm enjoying it very much. I don't currently have a gut instinct for an appropriate level of surface smoothing. I'm sure that can't be easily answered but would a range

Re: [Freesurfer] Appropriate levels of surface smoothing

Hi Kirstie there is no easy answer to this question, but there are some guidelines: 1. The size of the smoothing kernel depends on the size of the effect you are looking for and how well you expect it to align across subjects. For example, you would need a far smaller smoothing kernel if you

[Freesurfer] Overlay transparency

Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity1 such that I can see the curvature underneath. I am using a script for doing this and everything works, but the opacity doesn’t change when I use the command

Re: [Freesurfer] Overlay transparency

Make sure to use piecewise or linear thresholding and not linear opaque doug On 10/27/2014 12:49 PM, Roberta Santoro wrote: Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity1 such that I can see the

Re: [Freesurfer] Overlay transparency

Hi Roberta you are probably better off doing this in freeview - Ruopeng can help you there. cheers Bruce On Mon, 27 Oct 2014, Roberta Santoro wrote: Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity1

Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream

Hi Christian, Yes, you can use the ICV from the cross-sectional processing as co-variate. The longitudinal stream assumes head-size is not changing much in a few steps, but is still relatively robust in capturing large brain changes. I have never tested it thoroughly in kids and am not sure

Re: [Freesurfer] Overlay transparency

Thanks a lot for your input, I’ll give it a try. Roberta On 27 Oct 2014, at 17:58, Ruopeng Wang rpw...@nmr.mgh.harvard.edumailto:rpw...@nmr.mgh.harvard.edu wrote: Hi Roberta, not sure how well you know freeview. You can set the opacity of overlay either from 'Configure Overlay' button on the

[Freesurfer] GI analysis of single subject

Hi all, I'm trying to get gyrification information about a single subject. I've run the -localGI process but I have a few questions about the results: 1. When I try to plot the smoothed out pial surface over the brainmask in freeview, I use the command freeview -v subject/mri/brainmask.mgz -f

Re: [Freesurfer] permission denied

Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME