[Freesurfer] Extracting area.pial stats

2011-12-15 Thread Robustelli, Briana (NIH/NIMH) [F]
Dear FreeSurfer team, I have been looking at area.pial differences in two groups using qdec. I would now like to extract stats for each subject at the gyral level (using the Desikan parcellation). I used aparcstats2table with the measure flag set to area. But these numbers seem off. Is

Re: [Freesurfer] Extracting area.pial stats

2011-12-15 Thread Michael Harms
You need to specify 'pial' as the surface name argument in mris_anatomical_stats cheers, -MH On Thu, 2011-12-15 at 10:52 -0500, Robustelli, Briana (NIH/NIMH) [F] wrote: Dear FreeSurfer team, I have been looking at area.pial differences in two groups using qdec. I would now like to

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

2011-12-15 Thread Antonella Kis
Dear Lilla, 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 mri_glmfit-sim

Re: [Freesurfer] GLM design question

2011-12-15 Thread Martijn Steenwijk
Dear Doug, Thanks again for your reply. Based on that I did some further work. I first demeaned the age of all subjects. Actually, I have a third group which I would like to compare to, so my contrast matrices will be [.5 .5 -.5 -.5 0 0 0 0 0 0 0 0] [0 0 .5 .5 -.5 -.5 0 0 0 0 0 0] [.5 .5 0 0 -.5

[Freesurfer] nWBV

2011-12-15 Thread Lindsay Ercole
How might we obtain nWBV from the FS data? What variables could be summed or what variable could be used individually and adjusted to create a nWBV? Does total gray include cerebellar gray, but total white volume does not include cerebellar white? Sincerest thanks! Lindsay

[Freesurfer] (no subject)

2011-12-15 Thread Adam Nitenson
Hi Doug et al, We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that

Re: [Freesurfer] ICV and regional brain volumes

2011-12-15 Thread Douglas N Greve
Hi Heather, the ICV is mostly unrelated to the other volumetric measures. what do you mean that you are having problems getting ICV to fit correctly in your sample? doug Lugar, Heather wrote: We are having a difficult time getting the ICV to fit correctly in our sample, but the segmentions

Re: [Freesurfer] Estimate Brain Volume Fraction

2011-12-15 Thread Alexopoulos, Dimitrios
Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Estimate Brain Volume Fraction

2011-12-15 Thread Douglas N Greve
Yes. Alexopoulos, Dimitrios wrote: Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct? Jim

Re: [Freesurfer] Estimate Brain Volume Fraction

2011-12-15 Thread Bruce Fischl
yes On Thu, 15 Dec 2011, Alexopoulos, Dimitrios wrote: Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct? Jim

Re: [Freesurfer] Estimate Brain Volume Fraction

2011-12-15 Thread Cheryl McCreary
Ok. So then if ventricular volume is already excluded, the brain parenchymal volume should be: Total GM + total cortical WM +cerebellar GM + cerebellar WM + brain stem - CSF? Cheryl On 11-12-15 2:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yes. Alexopoulos, Dimitrios wrote: