Thanks! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 14, 2014 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prefrontal white matter
Yes, but you need to set the number of erodes. Each erode will be 1mm, and you just need to erode enough to avoid partial voluming, so 2 is probably fine. The more you erode, the smaller your ROI gets (and it can disappear).
On 11/14/2014 02:05 PM, Bruce Fischl wrote:
I think so, but I defer to Doug Bruce On Fri, 14 Nov 2014, Alshikho, Mohamad J. wrote:
Doug an Bruce thanks a lot!! I will do the following as I understood from your orientations and kindly correct me if I am wrong:
first of all I will resample my FA map into the anatomical space as the following command line : mri_vol2vol --mov fa.nii --lta dti-analysis register.lta --fstarg --o fa.anat.mgh
Then I will generate the statistics by using:
mri_segstats --seg $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh --erode --sum fa.stats
Is it correct?
Mohamad
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, November 14, 2014 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Prefrontal white matter
yes, sorry. That is what I meant Bruce On Fri, 14 Nov 2014, Douglas N Greve wrote:
I think Bruce is referring to the wmparc.mgz. Map the FA into the anatomical space. Then use it with mri_segstats, probably with the erode option.
doug
On 11/14/2014 11:41 AM, Bruce Fischl wrote:
Hi Mohamad
I would think you are better off using the wmseg for this.
cheers Bruce
cheers Bruce On Fri, 14 Nov 2014, Alshikho, Mohamad J. wrote:
Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal white matter areas. My plan is to derive a mask for that area from aseg.mgz then I will register this mask to the FA map to calculate the FA value. Is it possible to derive like this mask from aseg.mgz and can I control the dimensions of that mask?
thanks a lot Mohamad
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