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
