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}
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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.uk Tel: 02920
879628 |
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 |
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 Tel: 02920
879628 |
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 |
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 Tel: 02920
879628 |
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 |
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:
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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.uk
Tel: 02920 879628
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
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