which ROIs are coming up zero? Have you looked at the area maps for that subject for that ROI?

On 08/16/2016 01:16 PM, A Nunes wrote:

I mean the area of an ROI

On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

please include previous correspondence. Do you mean the area of a vertex or the area of an ROI?

On 08/15/2016 06:06 PM, A Nunes wrote:

...

Hi Douglas,

I meant a surface area extracted from a surface based atlas.

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

Hi

I looked at the distribution areas with almost zero thickness and when I saw they were on one hemisphere, I checked my bash script and found out that for the left cortex it was calling the right hemisphere areas. However, I still have a few subjects which have zero thickness in some areas of my parcelled atlas. This zero thickness is it caused by a segmentation or a sphere reconstruction error/imperfection (in which case the value should be NaN), or is it capturing a brain structural characteristic worth to account for?

Thanks Adonay Date: Mon, 15 Aug 2016 16:27:24 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Zero cortical thickness To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8c1593aa-77fc-333e-e7d7-1901f9a39d71@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed

what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location?

On 8/15/16 4:13 PM, A Nunes wrote:

...

Hi,

I have read in the mailing list about zero cortical thickness, but I still have some doubts.

I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all subjects is zero, I would guess is not considered cortical, however, all my areas are cortical.

• If I compute a ttest against two groups, should I set the zeros as

NaNs? or are the zero thickness meaningful (a genuine measure or a segmentation artifact)?

-Should I use the -l ?h.cortex.label to avoid having zero thickness in some areas? If so, at which point? the commands used are:

mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h --sval-annot fsaverage/label/?h.areas.annot --tval $SUBJECTS_DIR/subjid/label/?h.areas.annot

mris_anatomical_stats -a $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h

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

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