Hi Doug,

No worries at all! Thanks for your input, I will go ahead and do that.

In addition to calculating the number of WM hyperintensity voxels in each adjacent cortical label, I was also interested in creating a figure depicting the potential significant correlations between regional WM hyperintensity burden and cortical thinning. Is there a way to statistically compare two surface maps (i.e., the *h.thickness surface map and the projected-to-the-cortex WM hyperintensity map) to come up with such a figure?

Thanks again!

Best,

panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Thursday, May 31, 2018 2:54:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

sorry, fell through the cracks!

The easier way to do this is to use the wmparc.mgz. This is a segmentation where the WM is labeled based on the adjacent cortical label. You can run something like

mri_segstats --i wmhyper.mgz --seg wmparc.mgz --ctab-default --accumulate --sum sum.dat

The sum.dat will have the number of voxels of wmh in each ROI. There will be a lot of ROIs in the sum.dat, so you'll have to filter through them

On 5/31/18 11:30 AM, Fotiadis, Panagiotis wrote:

Hi all,

Just wanted to re-circulate this, just in case someone had some input!

Thanks,

Panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fotiadis, Panagiotis PFOTIADIS@mgh.harvard.edumailto:PFOTIADIS@mgh.harvard.edu Sent: Friday, May 25, 2018 10:49:10 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

Hello,

I'm interested in looking into the association of cortical thickness and white matter hyperintensity from a regional perspective. Specifically, I would like to create a figure that depicts in which ROIs does cortical thinning correlate significantly with increased white matter hyperintensity volume of the underlying white matter (not just the overall white matter hyperintensity). I have created binary masks of the white matter hyperintensity burden on each patient, and I was planning on projecting them into each respective cortex. However, I didn't know what the next step should be. I was thinking about the group analysis pipeline but didn't know whether it was applicable, as I don't want to just adjust for global white matter hyperintensity volume.

Thanks in advance for any help!

Best,

Panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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

Hi Doug,

I will definitely analyze the lesion load vs mean cortical thickness for each ROI. I was just trying to think of whether there was a way to also depict those results in a figure as well. In that case though, I'll just stick with the statistical analyses!

Thanks again,

Panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Thursday, May 31, 2018 3:12:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

It is not so easy to do because you have to map the lesions to the closest cortical voxel then use the per vertex regressor (--pvr) in mri_glmfit (and the whole process might be iffy). why not just analyze the lesion load vs mean cortical thickness for an ROI?

On 5/31/18 3:07 PM, Fotiadis, Panagiotis wrote:

Hi Doug,

No worries at all! Thanks for your input, I will go ahead and do that.

In addition to calculating the number of WM hyperintensity voxels in each adjacent cortical label, I was also interested in creating a figure depicting the potential significant correlations between regional WM hyperintensity burden and cortical thinning. Is there a way to statistically compare two surface maps (i.e., the *h.thickness surface map and the projected-to-the-cortex WM hyperintensity map) to come up with such a figure?

Thanks again!

Best,

panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, May 31, 2018 2:54:57 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

sorry, fell through the cracks!

The easier way to do this is to use the wmparc.mgz. This is a segmentation where the WM is labeled based on the adjacent cortical label. You can run something like

mri_segstats --i wmhyper.mgz --seg wmparc.mgz --ctab-default --accumulate --sum sum.dat

The sum.dat will have the number of voxels of wmh in each ROI. There will be a lot of ROIs in the sum.dat, so you'll have to filter through them

On 5/31/18 11:30 AM, Fotiadis, Panagiotis wrote:

Hi all,

Just wanted to re-circulate this, just in case someone had some input!

Thanks,

Panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fotiadis, Panagiotis PFOTIADIS@mgh.harvard.edumailto:PFOTIADIS@mgh.harvard.edu Sent: Friday, May 25, 2018 10:49:10 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

Hello,

I'm interested in looking into the association of cortical thickness and white matter hyperintensity from a regional perspective. Specifically, I would like to create a figure that depicts in which ROIs does cortical thinning correlate significantly with increased white matter hyperintensity volume of the underlying white matter (not just the overall white matter hyperintensity). I have created binary masks of the white matter hyperintensity burden on each patient, and I was planning on projecting them into each respective cortex. However, I didn't know what the next step should be. I was thinking about the group analysis pipeline but didn't know whether it was applicable, as I don't want to just adjust for global white matter hyperintensity volume.

Thanks in advance for any help!

Best,

Panos

Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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

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