Re: [Freesurfer] Selxavg3 sets high activation to zero

Dear Doug, Thanks very much for your prompt response. I tried what you suggested and the sig map looks fine now, that's probably the best that we can get for the sig map, because of the limitation of the MATLAB I guess. But for the t map, the values are still not correct for those voxels that

[Freesurfer] Different versions of FreeSurfer

Hi everyone, In our lab we use different versions of FreeSurfer on different computers. Since we share computers with other labs some updates are out of our control. We'd like to edit scans in FreeSurfer V4.5 and V5.1 and thereafter run recon -all in V5.0. Is it important to use the same

Re: [Freesurfer] Different versions of FreeSurfer

Hi Lara, The biggest consideration is that someone editing data run with v4.5 will probably have a lot more edits to do than if the same case was run with 5.0 or 5.1. It's probably best to rerun with 5.0 before editing if that's the version that you are going to work with. For your longitudinal

Re: [Freesurfer] FA interpretation from cvs registration for group analysis

Hi Antonella, Thank you very much for your answer and your help. I followed all the recommended steps (I introduced a white matter mask that will ensure that I am  only considering diffusion values in the white matter and then also I did corrected for multiple comparison running

Re: [Freesurfer] Surface-based cortical volume calculation

Actually, you are right! Most of the non-gray matter structures in the medial wall are zeroed out, but the part that goes through the hippo and amygdala are non-zero. As Mike points out, this is going to be a very small portion of the total cortical volume, but we'll find a way to remove it.

Re: [Freesurfer] Fa clusters from cvs registration for group analysis

Hi Antonella, I am doing a DTI group analysis study more exactly I am interested to see any changes in the FA values within two groups: controls versus patients (children with epilepsy). I introduced a white matter mask that will ensure that I am  only considering diffusion values in the

Re: [Freesurfer] Selxavg3 sets high activation to zero

The t is computed as the signed square root of the F (not Fsig) volume: t.vol = sqrt(Fvol.vol) .* sign(ces.vol); The Fvol (and do t) is not computed from the sig (the other way around). Are you sure that the t-value does not look right in those areas? doug Qi Zhu wrote: Dear Doug, Thanks

Re: [Freesurfer] GLM design question

Hi Martijn, sorry for the delay. Your contrast matrices look correct. The differences between demeaning and not demeaning is somewhat expected. When you do not demean, you are testing whether there is a difference between groups at age=0 (ie, birth). When you demean, you are testing for a

Re: [Freesurfer] Selxavg3 sets high activation to zero

Yes, seems weird. The image that I attached to you in the first mail is actually a t map, so the t value in those areas are also zero. And according to what I read from fast_selxavg3.m, the t value is actually calculated from the fsig, which is: t.vol = sqrt(fsig.vol).*sign(ces.vol), and fsig.vol

Re: [Freesurfer] Selxavg3 sets high activation to zero

Yes that is correct. That was fixed with version 5.1 so current distributions do the right thing. doug Qi Zhu wrote: Yes, seems weird. The image that I attached to you in the first mail is actually a t map, so the t value in those areas are also zero. And according to what I read from

[Freesurfer] error when using mri_sur2vol: has many more faces than vertices!

Dear Surfer, I was trying to project a DTI FA image onto the T1 WM surface (for now), and eventually into the fsaverage as in a recent paper: Phillips OR, Nuechterlein KH, Asarnow RF, Clark KA, Cabeen R, Yang Y, et al. Mapping corticocortical structural integrity in schizophrenia and effects of

[Freesurfer] FsFast Functional Connectivity with subject-specific surface seeds

Hi Freesurfers, We are trying to do a resting-state functional connectivity analysis using freesurfer. Instead of using the aparc+aseg segmentations as seeds, we would like to use a subject-specific surface labels that we have defined apriori. In the fcseed-config step, we then don't have a

Re: [Freesurfer] FsFast Functional Connectivity with subject-specific surface seeds

Hi Lingqiang, convert your .label file to a volume using mri_label2vol for each subject, something like cd $SUBJECTS_DIR/$subject/mri mri_label2vol --label lh.yourlabel.label --temp orig.mgz --regheader orig.mgz --subject $subject --hemi lh --proj frac 0 1 .1 --o yourlabel.mgz When you run

Re: [Freesurfer] error when using mri_sur2vol: has many more faces than vertices!

Hi Minjie, You'll want to give tksurfer the name of one of the regular surfaces (e.g., inflated, pial, etc.) as the third positional argument and then view your FA file as an overlay ( -overlay rh.fa.vol2surf2.w ). The former gives the surface geometry information (where the vertices are and