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/*: 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: *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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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/*: 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 "Fischl,
Bruce" <bfis...@mgh.harvard.edu <mailto:bfis...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto: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
<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/*: 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://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
