You can use mri_binarize to output nii.gz files. FSL may or may not read them properly as they are surface overlays, not volume. When we convert a surface overlay to nifti, we try to repackage the dimensions to fit in the nifit standard. Depending on the subject, it sometimes works and sometimes does not.
On 6/15/2020 9:53 AM, Mason Wells wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
