[Freesurfer] Homologous Right Left ROIs

Hi all I have a ROI label on left hemisphere - I need to map this ROI onto right hemisphere to get a homologous region (for testing hemispheric differences). What is the best way for doing this? Cheers Lena -- Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( Univers

Re: [Freesurfer] normal vector in gm

Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up the wm surface by mris_convert -s 1.01 lh.white lh.white101 and then projected

Re: [Freesurfer] mri_convert Siemens Allegra Dicom problem

Can you drop 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm to me at the file drop below? doug Myriam Siefert wrote: > Hi everybody, > > We're doing a structural VBM bicentric cross cultural study, using > Freesurfer v5.0.0. on 2 computers : > FREESURFER_HOME: /Applications/freesur

[Freesurfer] mri_convert Siemens Allegra Dicom problem

Hi everybody, We're doing a structural VBM bicentric cross cultural study, using Freesurfer v5.0.0. on 2 computers : FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 9.8.0 i386 FREESURFER_HOME: /home/scnlab/Desktop/ freesu

Re: [Freesurfer] mri_mask problem

Helo Bruce, I've tryed these options you said and still not working, I must say that is not in all my subjects, I've tryed both brain.mgz and brainmask.mgz. The commands I've used are: A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader A2) mri_mask flag -keep

Re: [Freesurfer] Qdec - thickness-age correlation - Interpretation

Hi Alex, you can compute the difference in those slopes using an appropriate contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this would be an interaction between group and age). doug Alex Hanganu wrote: > Dear Freesurfer Experts, > > We have two groups at similar ages and

Re: [Freesurfer] question about the capability of qdec and using non normal distributed subjects

QDEC can do analyses with as many as two discrete variables (two levels each) and two continuous variables. More general analyses are possible with the mri_glmfit command-line. If data are not normally distributed, then you can use our permutation program (not available in QDEC but possible in

Re: [Freesurfer] Questions about GLM, Random and Fixed Effects Analysis in FsFast

Hi Gabriel, for mri_glmfit, W = diag(sqrt(1./yffxvar)), ie, it is a diagonal matrix where each element is the square root of the inverse of the variance from the lower level. This changes the equation from a simple ordinary least squares into a weighted least squares (though not quite a true

Re: [Freesurfer] mri_mask problem

Hi Gabriel, did you convert the brain.mgz so it is in the same space as the rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try mri_mask -t . The default is 1e-10 so pretty much anything non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 1). chee

Re: [Freesurfer] mri_mask problem

Hello Nick I'm wondering if you're able to verify my data today, I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked, I'm guessing you'll need my data, to see if there is something wrong on it, but I think is gonna be hard to send it to through the e-mail. Bests, Gabriel.

[Freesurfer] Qdec - thickness-age correlation - Interpretation

Dear Freesurfer Experts, We have two groups at similar ages and the thickness-age correlation shows many cluster of significant values. Pointing to this maximum the plots present similar regressions coefficients for both groups. Actually it would be intresting to have the regions were the thic