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 <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 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 _______________________________________________ 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%7C1998625387cf443070c108d85e3bc629%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637362958106897728&sdata=BHtqwNrvHHYv9cEM6mNw2LbaBAw9BFLaJUswPQK4P1g%3D&reserved=0>
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