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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: 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
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/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You could also do it pretty easily in matlab or python
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, June 12, 2020 10:44 AM To: 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: 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
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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: 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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edu" 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: 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
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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
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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: 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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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
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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 WellsMT1@cardiff.ac.uk wrote:
External Email - Use CautionHi 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: 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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 CautionHi 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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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 CautionHi 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: 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
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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: WellsMT1@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: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
On 15/06/2020, 12:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@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 WellsMT1@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: 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 > > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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: 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 > > > From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> > Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> > Date: Friday, 12 June 2020 at 15:44 > To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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 > > 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.m...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.m...
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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 CautionHi 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: WellsMT1@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: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
On 15/06/2020, 12:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@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 <WellsMT1@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: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@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: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> > Ffôn: 02920 879628 > > > From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@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: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> > Ffôn: 02920 879628 > > > From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU<mailto:dgreve@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: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@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: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@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
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Hi Mason
What do you mean you “just get a series of letters/symbols”? Can you send us the commands you ran and the screen output?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Monday, June 15, 2020 6:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Saturday, 13 June 2020 at 03:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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
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Hi Bruce,
I just used the load command. See below.
load('rh.wang15_mplbl.mgz')
Error using load Unknown text on line number 1 of ASCII file rh.wang15_mplbl.mgz +u�^[1]�".
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: 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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 15 June 2020 at 15:44 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
Hi Mason
What do you mean you “just get a series of letters/symbols”? Can you send us the commands you ran and the screen output?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Monday, June 15, 2020 6:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Saturday, 13 June 2020 at 03:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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
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You can't just use the load() command. Try rh = MRIread(filename) The pixel data will be in rh.vol
On 6/16/2020 10:25 AM, Mason Wells wrote:
External Email - Use Caution
Hi Bruce,
I just used the load command. See below.
load('rh.wang15_mplbl.mgz')
Error using load
Unknown text on line number 1 of ASCII file rh.wang15_mplbl.mgz
+u�^[1]�".
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/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@MGH.HARVARD.EDU *Reply to: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, 15 June 2020 at 15:44 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
Hi Mason
What do you mean you “just get a series of letters/symbols”? Can you send us the commands you ran and the screen output?
Cheers
Bruce
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Mason Wells *Sent:* Monday, June 15, 2020 6:15 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
* 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/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
*From: *<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDU mailto:BFISCHL@MGH.HARVARD.EDU> *Reply to: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Saturday, 13 June 2020 at 03:02 *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto: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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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 mailto: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/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
*From: *<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU mailto:dgreve@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/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@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%7C290cf5e8c626465f0d4508d8113a92b5%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637278290553922850&sdata=hIZxtcjFJ%2Brz6pIAZBZGxiqmump%2B6%2FiO8BdzfMOvyck%3D&reserved=0>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You need to use load_mgh or MRIread (which we distribute)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Tuesday, June 16, 2020 10:26 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
External Email - Use Caution Hi Bruce,
I just used the load command. See below.
load('rh.wang15_mplbl.mgz')
Error using load Unknown text on line number 1 of ASCII file rh.wang15_mplbl.mgz +u�^[1]�".
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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 15 June 2020 at 15:44 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
Hi Mason
What do you mean you “just get a series of letters/symbols”? Can you send us the commands you ran and the screen output?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Mason Wells Sent: Monday, June 15, 2020 6:15 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}
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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Saturday, 13 June 2020 at 03:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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: 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
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 12 June 2020 at 15:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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: 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
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If you want to save it on label format, then mri_cor2label is the right way to go. Make sure to use the --surf option. If you want them in separate mgz files, then use mri_binarize with --match
On 6/12/20 7:35 PM, Mason Wells wrote:
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/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply to: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, 12 June 2020 at 15:44 *To: *"freesurfer@nmr.mgh.harvard.edu" 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/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@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/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@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%7C2cc182d0329f46ad8b0b08d80edf1c1e%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637275698698058308&sdata=wRFT5fuvG7ejUfN6F%2FKCn1Uw29LaO%2BOkil5i6vCwPlk%3D&reserved=0>
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Douglas N. Greve
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