[Freesurfer] White matter volume

2014-10-31 Thread Alshikho, Mohamad J.
Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the outpu

Re: [Freesurfer] White matter volume

2014-10-31 Thread Douglas N Greve
The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: > Hi Bruce, > I wanted to calculate the right and left hemispheric white matter > volume using a mask. > Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the > outpu

Re: [Freesurfer] Longitudinal prediction

2014-10-31 Thread Douglas N Greve
--osgm is for one-sample group mean which is the simplest design possible. It is probably not appropriate for your design. If you have different inputs and different labels then you will get different results On 10/30/2014 03:08 PM, Alex Hanganu wrote: > Hi Martin, > > could you please confirm

Re: [Freesurfer] White matter volume

2014-10-31 Thread Alshikho, Mohamad J.
Thanks Doug! So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday,

Re: [Freesurfer] Longitudinal prediction

2014-10-31 Thread Alex Hanganu
I see. Thank you Doug ! Now I used the command lines from the qdec output in the terminal and I constructed the next contrasts using them as a starting point. Now the results seem more reliable and I can perform the Monte-Carlo with 5000 iterations.  I'll verify them once again with LME. Alex.

Re: [Freesurfer] White matter volume

2014-10-31 Thread Douglas N Greve
I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: > Thanks Doug! > So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of > mris_volmask? > > From: freesurfer-boun...@n

Re: [Freesurfer] White matter volume

2014-10-31 Thread Bruce Fischl
Hi Mohamad this is probably due to the partial-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: > Thanks Doug, > In order to improve my understanding for the analysis that I am working on > a

Re: [Freesurfer] permission denied

2014-10-31 Thread zkaufman
Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight. -Zeke > Hi Z K, > > Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one > installed with the latest freesurfer version

Re: [Freesurfer] White matter volume

2014-10-31 Thread Alshikho, Mohamad J.
Hi Bruce, Actually I am totally confused and this is the reason for my question! What is the best and trusted approach in this case? I want to study the relationship between the FA and the right and left hemispheric white matter. I generated the DTI metrics and volume using FSL. I am sure that

Re: [Freesurfer] White matter volume

2014-10-31 Thread Bruce Fischl
yes. Partial volume correction helps both accuracy and repeatability. You can certainly use our (partial-volume) corrected WM volumes and the FA from FSL if you want cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: > Hi Bruce, > Actually I am totally confused and this is the reason

Re: [Freesurfer] White matter volume

2014-10-31 Thread Alshikho, Mohamad J.
Thanks a lot!! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] White