Re: [Freesurfer] wm-hypointensities variables

It depends what you want. If you want total volume, then yes. They are typically false positives in young healthy subjects. Telling damaged white matter from say the superior-most aspect of the caudate is *very* hard on just a T1 On Sat, 13 Feb 2016, Otília wrote: Thank you for your reply.

Re: [Freesurfer] wm-hypointensities variables

Thank you for your reply. I just wasn't expecting ("high") values in healthy subjects. Of course FS just "sees" voxels, whether it's a lesion or other thing, but I was afraid it would be some segmentation issue. I have also other MRI contrasts but I really wanted to estimate possible T1w lesio

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Yes, thanks ... from my notes: This command contracts the selected surface vectors 3.0 mm and places the resultant new surface file in surf/lh.white-3: mris_expand lh.white -3.0 lh.white-3 Best regards,   Don > -Original Message- > From: freesurfer-

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

mris_expand probably On Sat, 13 Feb 2016, Krieger, Donald N. wrote: Thanks for posting back about this, Bruce. I am thinking about a different function which probably is not called --dilate. One specifies a surface, e.g. white, and gets back a new surface displaced by the distance you specify w

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Thanks for posting back about this, Bruce. I am thinking about a different function which probably is not called --dilate. One specifies a surface, e.g. white, and gets back a new surface displaced by the distance you specify whose tangent is parallel to the tangent of the starting surface at the

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Hi Don I think label2label --dilate does a morphological dilation on the surface, not a new surface. It is also independent of distance - it just uses topology - so your approach will be better if you truly want a circle (although of course if the surface is highly curved then the metric won'

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Hi Martha, A brute force but simple way to do this is to use the list of labels contained in subjects/nnn/label/lh.cortex and rh.cortex. Given a vertex x,y,z, go through the file and select the lines for which the distance to x,y,z <= 2 mm. This will give you a bunch of labels for points withi

[Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Hello Freesurfer community, I am looking for a way to automatically generate a surface label file of a specific dimension (e.g. a circle with a specific diameter, or a square), given a specific vertex and some measure of the desired size. I have considered to do so by starting with a label file c

[Freesurfer] curved Surface projection

Hello I know it is not the best place to ask this kind of question. But I don't know any place to ask a question like this. I am looking to display "curved Surface projection" for brain mri (like explained in http://www.ajnr.org/content/24/6/1045.full). Can any one suggest me a tool to do this.

Re: [Freesurfer] comparison between two hemisphere in single

Thank you Douglas for your reply. I have perforemed surfreg --s subj1 --t fsaverage_sym --lh surfreg --s subj1--t fsaverage_sym --lh --xhemi mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out lh.lh-rh.thickness.sm00.