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.
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.
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.
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 mailto: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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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
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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
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 _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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
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,
Try this: [i,j,k]=find(mri.vol==17)
and get rid of the ind2sub call
hth d
On Tue, Sep 27, 2016 at 2:00 AM, Aziz Nanthaamornphong aziz.n@phuket.psu.ac.th wrote:
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 _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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
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
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.
I think your first argument to ind2sub needs to be size(mri.vol)
cheers Bruce On Tue, 27 Sep 2016, Aziz Nanthaamornphong wrote:
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 _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. _______________________________________________ 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
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
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Ruyuan Zhang