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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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. <dgr...@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: wells...@cardiff.ac.uk<mailto:wells...@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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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: wells...@cardiff.ac.uk<mailto:wells...@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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@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: wells...@cardiff.ac.uk<mailto:wells...@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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
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