I did try to use mri_mask but could not get it to work. I have the mask both in label format (attached), and as an overlay in nii.gz format. The commands below results in this error.

mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh Atlas/lh_atlas_dilated.label test.mgh

mri_read(): couldn't determine type of file Atlas/lh_atlas_dilated.label

When I try to use the nii.gz as the mask, activation outside of the mask remains (attached).

I would like to compute a correlation coeffeident between the atlas regions (1-25) and all the output ICA maps on the surface (0-~250).

Thanks for all your help.

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

E-bost: WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Monday, September 21, 2020 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations

On 9/19/2020 10:31 AM, Mason Wells wrote:

External Email - Use Caution

Hi Experts,

I wonder if anyone can give me any advice on a couple of things.

1) I have some ICA spatial maps which I have resampled to the surface using bbregister and vol2surf. I can load this data in Freeview as a generic overlay (see attched). I also have a label file which is a combination of several visual areas. What I want to do is use this label as a mask and remove any activation from the ICA map overlay which falls outside of the label/mask. Is this possible using Freesurfer? In FSL I have been using fslmaths with -mas flag.

What form are your labels in? If they are just binary masks, then you can use mri_mask

2) My next question is whether it is possible to run spatial correlations on the surface. For example, I would like to know how well my ICA component maps match with some visual areas labels I have created in Freesurfer. In FSL i have been using fslcc to run these correlations between my ROIs and the spatial maps in the volume.

You want to compute a correlation coefficient? Or a dice score?

Thanks in advance,

Mason

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

E-bost: WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628
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