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}
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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.mghThe 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}
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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://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>