External Email - Use Caution

Hi Doug,

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

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.ukmailto:WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214-http://www.cardiff.ac.uk/people/research-students/view/482937-

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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214-

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.ukmailto:WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C1998625387cf443070c108d85e3bc629%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637362958106897728&sdata=BHtqwNrvHHYv9cEM6mNw2LbaBAw9BFLaJUswPQK4P1g%3D&reserved=0

External Email - Use Caution

Hi Bruce and Doug,

Thanks for the advice. I have the mask as a volume (atlas_dilated.label.nii.gz), which loads fine as a generic overlay on the inflated surface. However, when I run this command

mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh Atlas/atlas_dilated.nii.gz masked_func.mgh

The output still has activation outside of the mask (see attached). Am I doing something wrong here?

Also, I wondered if yourself or Doug could help with my other question in my original email? Is there a Freesurfer equivalent of fslcc? I want to run spatial cross-correlations between a probabilistic atlas (Wang 15 atlas) and my functional data.

Cheers, 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.ukmailto:WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214-http://www.cardiff.ac.uk/people/research-students/view/482937-

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.ukmailto:WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@MGH.HARVARD.EDU Sent: Tuesday, September 22, 2020 5:50 PM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

Hi Mason

mri_mask takes volumes as inputs, not label files. If you bring up your volumes and the mask looks in the right place in freeview then it should work

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Tuesday, September 22, 2020 8:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

External Email - Use Caution

Hi Doug,

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

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.ukmailto:WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214-

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.ukmailto:WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

________________________________

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 N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Sent: Monday, September 21, 2020 3:34 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214-

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.ukmailto:WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C396af653adf145ac943b08d85f17c15c%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637363902927929248&sdata=qt8oKbDIhGuGfKcQETOVqah9lk4xAzFaiw%2FefM2uUmo%3D&reserved=0

I would think that mri_mask would work, but you can also try fscalc lh_zstats_EPI_space_5mm_surface_smoothing.mgh mul Atlas/atlas_dilated.nii.gz -o masked_func.mgh

On 9/23/2020 11:18 AM, Fischl, Bruce wrote:

Hi Mason

mri_mask runs in the volume, not the surface. Are these volumes? There is a masking function in freeview I think for surface overlays – maybe Ruopeng can comment?

Thanks

Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Mason Wells *Sent:* Wednesday, September 23, 2020 10:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Cc:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

*        External Email - Use Caution *

Hi Bruce and Doug,

Thanks for the advice. I have the mask as a volume (atlas_dilated.label.nii.gz), which loads fine as a generic overlay on the inflated surface.

However, when I run this command

mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh
Atlas/atlas_dilated.nii.gz masked_func.mgh

The output still has activation outside of the mask (see attached). Am I doing something wrong here?

Also, I wondered if yourself or Doug could help with my other question in my original email? Is there a Freesurfer equivalent of fslcc? I want to run spatial cross-correlations between a probabilistic atlas (Wang 15 atlas) and my functional data.

Cheers,

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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

/*Web*/: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto:WellsMT1@caerdydd.ac.uk

*/Ffôn/*: 02920 879628

---

*From:*freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@MGH.HARVARD.EDU mailto:BFISCHL@MGH.HARVARD.EDU> *Sent:* Tuesday, September 22, 2020 5:50 PM *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

Hi Mason

mri_mask takes volumes as inputs, not label files. If you bring up your volumes and the mask looks in the right place in freeview then it should work

cheers

Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Mason Wells *Sent:* Tuesday, September 22, 2020 8:50 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

*        External Email - Use Caution *

Hi Doug,

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

*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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

/*Web*/: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto:WellsMT1@caerdydd.ac.uk

*/Ffôn/*: 02920 879628

---

*From:*freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU> *Sent:* Monday, September 21, 2020 3:34 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

/*Web*/: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

_______________________________________________

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