Re: [Freesurfer] Coordinates of particular volumes (fwd) - Freesurfer

27 Sep 2016


      the command should be
[i,j,k] = ind2sub(mri.volsize,pos);
---------- Forwarded message ----------
Date: Tue, 27 Sep 2016 13:00:51 +0700
From: Aziz Nanthaamornphong aziz.n@phuket.psu.ac.th
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Coordinates of particular volumes
I have tried to get the coordinates with following commands:
mri = MRIread('aseg.mgz');
pos = find(mri.vol == 17);
[i,j,k] = ind2sub(10213,pos);
However, I found that all values of 'j' are 1. is there something wrongs
with my strategy?
Best Regards,
Aziz.
On Mon, Sep 12, 2016 at 8:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
        Hi Aziz,
make sure $FREESURFER_HOME/matlab is in your matlab path.
cheers
        Bruce
        On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote:
Which the version of Matlab has a 'MRIread'
              function? I got this error
              message from my installed Matlab (v. 8.4.0).
              "Undefined function 'MRIread' for input arguments of
              type 'char'."
Best Regards,
              Aziz.
On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl
              fischl@nmr.mgh.harvard.edu
              wrote:
                    yup, or mri_Info called form the command line.
              If you use
                    MRIread on the aseg.mgz you can extract e.g.
              the left
                    hippocampus using matlab via:
mri = MRIread('aseg.mgz');
                    find(mri.vol == 17);
                    then compute the ras coords of those indices
              using ind2sub
cheers
                    Bruce
On Sun, 4 Sep 2016, Ruyuan Zhang wrote:
Hi, Aziz
You can use MRIread function to
              read in a
                          volume (i.e. brainmask.mgz).
                          You will get a structure, which contains
              a field
                          called ras2vox.
cheers
ruyuan
On 9/4/16 6:23 PM, Aziz Nanthaamornphong
              wrote:
                                Hi,
                          For example, I want to know the list of
              x, y, z
                          coordinates of a left
                          hippocampus volume.
As you mentioned "ras2vox" matrices, hoe
              can I see
                          or get these
                          matrices?
Thank you.
                          Aziz
On Monday, 5 September 2016, Bruce
              Fischl
                          fischl@nmr.mgh.harvard.edu
                          wrote:
                                Hi Aziz
can you elaborate? What
              coordinates do you
                          want? What are
                                you trying to do with them? The
              .mgz format
                          contains
                                ras2vox matrices that let you go
              from voxel
                          indices to RAS
                                coordinates and such.
cheers
                                Bruce
On Sun, 4 Sep 2016, Aziz
              Nanthaamornphong
                          wrote:
Dear Freesurfer experts,
                                      How can we get the
              coordinates (X, Y, Z)
                          of a
                                      particular volume? I
              couldn't
                                      find any functions or
              command to do
                          that.
Thank you in advance.
Aziz.
--
Aziz Nanthaamornphong, Ph.D.,
                          Chair of Master of Science Program in
              Information
                          Technology
                          Department of ICT
                          Faculty of Technology and Environment
                          Prince of Songkla University, Phuket
              Campus
                          +66 7627 6716 (v)
                          http://research.te.psu.ac.th/aziz
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              contains patient information, please contact the
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              e-mail was sent to you
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              but does not contain patient information, please
              contact the sender
              and properly
              dispose of the e-mail.
--
Aziz Nanthaamornphong, Ph.D.,
              Chair of Master of Science Program in Information
              Technology
              Department of ICT
              Faculty of Technology and Environment
              Prince of Songkla University, Phuket Campus
              +66 7627 6716 (v)
              http://research.te.psu.ac.th/aziz
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
--
Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz