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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