External Email - Use Caution Hi Doug, (having to repost without any attachments)
I did try to use mri_mask but could not get it to work. I have the mask both in label format, 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. 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: [email protected]<mailto:[email protected]> Tel: 02920 879628 Web: Cardiff University webpage<https://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: [email protected]<mailto:[email protected]> Ffôn: 02920 879628 ________________________________ From: [email protected] <[email protected]> on behalf of Douglas N. Greve <[email protected]> Sent: Monday, September 21, 2020 3:34 PM To: [email protected] <[email protected]> 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: [email protected]<mailto:[email protected]> 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: [email protected]<mailto:[email protected]> Ffôn: 02920 879628 _______________________________________________ Freesurfer mailing list [email protected]<mailto:[email protected]> 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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