Hi Bruce,

I am using freesurfer to generate masks for fmri data from a breath hold task.

As you are probably well aware, this task activates much of the gray matter.

I have been content to consider all gray matter as one large ROI but one of my colleagues on the project (Danny Mathalon) has suggested that we might want to look at the BH response more regionally.

We have a smallish sample and don't want to go to far with data. So we thought that a reasonable comprimise might be to go for the 4 major lobes.

Does this make sense?

I do all of my fmri work in MNI space so what I have been doing is registering the freesurfer output to MNI space using SPM tools to get masks and then do the rest with afni.

Lee

-------------- Original message ---------------------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Lee,

what is your goal? Are you just trying to measure lobar volume?

Bruce

On Sat, 14 Apr 2007 lfriedman10@comcast.net wrote:

...

Burce and Rahul,

thanks so much for your help.

So I am a little new to freesurfer. I have been using lh.ribbon and rh.ribbon as neocortical masks and aseg.mgz

for

...

subcortical gray structures, with labels from FreeSurferColorLUT.txt.

What I want to do now is to further subdivide the *h.ribbon masks into

frontal, temporal,

...

occipital and parietal lobes.

How would one go about this?

Lee

-------------- Original message ---------------------- From: rahul@nmr.mgh.harvard.edu

...

Hi Lee,

Bruce is correct in that some ROIs cross two or more lobar boundaries (i.e. fusiform) while others (i.e. cingulate subdivisions) can be considered separately or can be included to follow the 4 lobes. To the best of my ability, if you are using the *h.aparc.annot, you can add up the individual ROIs as such to get the lobes:

Frontal: Superior Frontal Rostral and Caudal Middle Frontal Pars Opercularis, Pars Triangularis, and Pars Orbitalis Lateral and Medial Orbitofrontal Precentral Paracentral Frontal Pole

Parietal: Superior Parietal Inferior Parietal Supramarginal Postcentral Precuneus

Temporal Superior, Middle, and Inferior Temporal Fusiform Transverse Temporal Entorhinal Temporal Pole Parahippocampal

Occipital: Lateral Occipital Lingual Cuneus

Cingulate (if want to include in a lobe): Rostral Anterior (Frontal) Caudal Anterior (Frontal) Posterior (Parietal) Isthmus (Parietal)

Best,

rahul

...

Hi Bruce,

Are you saying that you don't think I even could build these lobar groups using the existing codes in the LUT.txt file?

Lee

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Saturday, April 14, 2007 2:21 PM To: lfriedman10@comcast.net Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] major lobes - frontal, parietal occipital and temporal

Hi Lee,

sorry, not really - we've never done a lobar parcellation, and I don't think the existing units break down that way.

Bruce On Sat, 14 Apr 2007 lfriedman10@comcast.net wrote:

...

I know that I could go thru the FreeSurferColorLUT.txt file to get codes for different cortical structures. Is there an easier way to get the major lobes: frontal, parietal occipital and temporal.

Lee _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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