External Email - Use Caution Hi Tim,
My knowledge on file format isn’t brilliant. What I would like to do is compare the spatial overlap between ROIs, which I have been doing in the volume using fslcc. This runs cross correlations between two NIFTI files. However, I wondered if Freesurfer have the facility to do these comparisons on the surface. For example, cross correlating an ICA component and a probabilistic atlas to check the spatial overlap. How I thought I would do this is to get each atlas ROI into different label files, and then use some form of freesurfer command to cross correlate the ICA component to each of the atlas regions and check which is the best "match". Any tips on how to do this would be appreciated. Thanks, 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 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 Ffôn: 02920 879628 On 15/06/2020, 12:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ts...@rcmd.org> wrote: External Email - Use Caution What would you expect to be in that NIFTI file? A vector of integers of length the number of surface vertices, in which a value of 0 means "is not part of label" and a value of 1 means "is part of label"? Or just the indices of the vertices which are part of the label? What software should be able to read the file? Tim > On June 15, 2020 at 12:15 PM Mason Wells <wells...@cardiff.ac.uk> wrote: > > > External Email - Use Caution > > Hi Bruce and Doug, > > I tried to load the overlay into Matlab, but that doesn’t work, I just get a series of letters/symbols. The surface overlay is in .mgz format. Using mri_cor2label works great for getting each roi into a label format, but I would also like them each in a .nii.gz format. Do you have any suggestions for this? > > 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> on behalf of "Fischl, Bruce" <bfis...@mgh.harvard.edu> > Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Saturday, 13 June 2020 at 03:02 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed} > > Hi Mason > > You should be able to load the overlay and the ROIs into matlab, then pick out the vertices in each ROI from the overlay and save them separately. Just be careful about the one-based indexing in matlab. That is, if your ROI is in a label file and you read the vertex indices from it, you need to add 1 to the index that point into the overlay. > > Cheers > Bruce > > From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Mason Wells > Sent: Friday, June 12, 2020 7:35 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed} > > > External Email - Use Caution > Hi Doug, > > Yes, I mean a surface overlay, it is the mgz format. It essentially has 25 visual areas, shown in the attached. I wanted to split them up, so that each ROI is its own label. I saw I could use mri_cor2label, but is there a better way? > > 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>> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> > Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, 12 June 2020 at 15:44 > 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] Splitting surface overlay into separate files > > When you say "surface" do you mean a surface overlay or a surface with xyz and neighbor relations? Assuming you mean an overlay (eg, something in an mgh or mgz file), you can try fscalc. Or do you have 25 frames in a single file and you want to split them into separate files? You might be able to convert the mgh/mgz file to nii and use FSL tools and then convert them back (sometimes works, sometimes not) > On 6/12/2020 10:24 AM, Mason Wells wrote: > > External Email - Use Caution > Hi Experts, > > Apologies if this is a rather simple question. Is there a FreeSurfer equivalent of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz file. I want to separate each atlas region into a different file, so that I end up with 25 surface atlas regions. Is there a command that could achieve this? > > My next question is whether or not there is a Freesurface command that can be used to complete surface based correlations. For example, if I want to check for the overlap between two ROIs. I have been using fslcc to do this in the volume, but perhaps freesurfer has something similar to do this on the surface? > > 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 > > > > _______________________________________________ > > 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C225f52eb98ab47bb3f9d08d8111deb66%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637278167482310020&sdata=HEnv0nWsXOJXPI2W97JETyLVe2S4xiW7JQLswxtNeZg%3D&reserved=0<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%7C225f52eb98ab47bb3f9d08d8111deb66%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637278167482310020&sdata=HEnv0nWsXOJXPI2W97JETyLVe2S4xiW7JQLswxtNeZg%3D&reserved=0> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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%7C225f52eb98ab47bb3f9d08d8111deb66%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637278167482320012&sdata=Mzm1r7clKaDxYHq%2BNHApOek5mZvbCDt5gFJDQa7lgRs%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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%7C225f52eb98ab47bb3f9d08d8111deb66%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637278167482320012&sdata=Mzm1r7clKaDxYHq%2BNHApOek5mZvbCDt5gFJDQa7lgRs%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
