Dear Freesurfer Community;
I need to find the corresponding voxel in a functional image for a specific structural image voxel after coregistering two images. My structural image has 256*256*125 voxels and the functional image has 64*64*30 voxels.
I use the following command
tkregister2 --s subjectname --targ structural.nii --mov functional.nii --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat
Where the target is structural image and movable is the functional image
then click save to get MYregister.dat.
then take the inverse of the matrix save it as invMYregister.dat, and try to use this matrix to transform from
anatomical to functional.
However; as an example when I try to map voxel (169 , 62 ,35) of the anatomical image to the functional space using the inverse registration matrix; i get the values below
- 64.3319
-146.4394
-157.2665
as the corresponding voxels' coordinates at the functional space which is far beyond the functional volume size and is negative. It is clear I cannot manage to use the trasfer matrices appropriately.
Your help will be greatly appreciated.
Thank you;
Sinem Burcu ERDOGAN
I think this scenario applies to you (just use your structural instead of orig.mgz). doug
-------------------------------------------------------------- I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc "mov" volume and want to compute the CRS for the corresponding point in the orig.mgz:
origCRS = Torig * inv(Reg) * inv(Tmov) * [movC movR movS 1]' Torig: mri_info --vox2ras-tkr orig.mgz Tmov: mri_info --vox2ras-tkr mov.nii Reg: register.dat tkregister2 --mov mov.nii --reg register.dat
Test: click on a point in tkmedit very close to the left hemi white surface. Use the "Functional Overlay Index Coordinates" to compute origCRS (round to the nearest integer). Compare origCRS to the "Volume index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match.
--------------------------------------------------------------
On 05/17/2012 05:43 AM, Sinem Burcu Erdoğan wrote:
Dear Freesurfer Community;
I need to find the corresponding voxel in a functional image for a specific structural image voxel after coregistering two images. My structural image has 256*256*125 voxels and the functional image has 64*64*30 voxels.
I use the following command
tkregister2 --s subjectname --targ structural.nii --mov functional.nii --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat
Where the target is structural image and movable is the functional image
then click save to get MYregister.dat.
then take the inverse of the matrix
save it as invMYregister.dat, and try to use this matrix to transform from
anatomical to functional.
However; as an example when I try to map voxel (169 , 62 ,35) of the anatomical image to the functional space using the inverse registration matrix; i get the values below
- 64.3319
-146.4394
-157.2665
as the corresponding voxels' coordinates at the functional space which is far beyond the functional volume size and is negative. It is clear I cannot manage to use the trasfer matrices appropriately.
Your help will be greatly appreciated.
Thank you;
Sinem Burcu ERDOGAN
-- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan@boun.edu.tr mailto:burcu.erdogan@boun.edu.tr
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug; Thank you for your prompt reply. I have obtained Torig Tmov and Reg values as below:
mri_info --vox2ras-tkr segmentedanatomic.nii
Torig=[-0.93750 0.00000 0.00000 120.00000
0.00000 0.00000 1.20000 -75.00016
0.00000 -0.93750 0.00000 120.00000
0.00000 0.00000 0.00000 1.00000];
mri_info --vox2ras-tkr BHfunc.nii
Tmov=[-3.59375 0.00000 0.00000 115.00000
0.00000 0.00000 2.00000 -30.00000
0.00000 -3.59375 0.00000 115.00000
0.00000 0.00000 0.00000 1.00000 ];
Reg=[0.015 1,-0.017,1.62;
-0.096,-0.015,-1,-24.701;
-0.995,0.016,0.096,-0.177;
0,0,0,1];
However when i try to map lets say; voxel 32 32 15
orig=Torig*inv(Reg)*inv(Tmov)*[32 32 15 1]';
I get the below coordinates:
98.3478
-37.8002
93.9130
1.0000
which do not match at all. I wonder where i am doing the mistake.
Thank you ;
Burcu
2012/5/18 Douglas N Greve greve@nmr.mgh.harvard.edu
I think this scenario applies to you (just use your structural instead of orig.mgz). doug
I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc "mov" volume and want to compute the CRS for the corresponding point in the orig.mgz:
origCRS = Torig * inv(Reg) * inv(Tmov) * [movC movR movS 1]' Torig: mri_info --vox2ras-tkr orig.mgz Tmov: mri_info --vox2ras-tkr mov.nii Reg: register.dat tkregister2 --mov mov.nii --reg register.dat
Test: click on a point in tkmedit very close to the left hemi white surface. Use the "Functional Overlay Index Coordinates" to compute origCRS (round to the nearest integer). Compare origCRS to the "Volume index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match.
On 05/17/2012 05:43 AM, Sinem Burcu Erdoğan wrote:
Dear Freesurfer Community;
I need to find the corresponding voxel in a functional image for a specific structural image voxel after coregistering two images. My structural image has 256*256*125 voxels and the functional image has 64*64*30 voxels.
I use the following command
tkregister2 --s subjectname --targ structural.nii --mov functional.nii --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat
Where the target is structural image and movable is the functional image
then click save to get MYregister.dat.
then take the inverse of the matrix
save it as invMYregister.dat, and try to use this matrix to transform from
anatomical to functional.
However; as an example when I try to map voxel (169 , 62 ,35) of the anatomical image to the functional space using the inverse registration matrix; i get the values below
- 64.3319
-146.4394
-157.2665
as the corresponding voxels' coordinates at the functional space which is far beyond the functional volume size and is negative. It is clear I cannot manage to use the trasfer matrices appropriately.
Your help will be greatly appreciated.
Thank you;
Sinem Burcu ERDOGAN
-- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan@boun.edu.tr mailto:burcu.erdogan@boun.edu.tr
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Sorry, I got the equation exactly backwards. Try this orig=inv(Torig)*Reg*Tmov*[32 32 15 1]';
On 05/20/2012 11:13 AM, Sinem Burcu Erdoğan wrote:
Hi Doug; Thank you for your prompt reply. I have obtained Torig Tmov and Reg values as below:
mri_info --vox2ras-tkrsegmentedanatomic.nii
Torig=[-0.93750 0.00000 0.00000 120.00000
0.00000 0.00000 1.20000 -75.00016
0.00000 -0.93750 0.00000 120.00000
0.00000 0.00000 0.00000 1.00000];
mri_info --vox2ras-tkrBHfunc.nii
Tmov=[-3.59375 0.00000 0.00000 115.00000
0.00000 0.00000 2.00000 -30.00000
0.00000 -3.59375 0.00000 115.00000
0.00000 0.00000 0.00000 1.00000 ];
Reg=[0.015 1,-0.017,1.62;
-0.096,-0.015,-1,-24.701; -0.995,0.016,0.096,-0.177; 0,0,0,1];However when i try to map lets say; voxel 32 32 15
orig=Torig*inv(Reg)*inv(Tmov)*[32 32 15 1]';
I get the below coordinates:
98.3478
-37.8002
93.9130
1.0000which do not match at all. I wonder where i am doing the mistake.
Thank you ;
Burcu
2012/5/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
I think this scenario applies to you (just use your structural instead of orig.mgz). doug -------------------------------------------------------------- I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc "mov" volume and want to compute the CRS for the corresponding point in the orig.mgz: origCRS = Torig * inv(Reg) * inv(Tmov) * [movC movR movS 1]' Torig: mri_info --vox2ras-tkr orig.mgz Tmov: mri_info --vox2ras-tkr mov.nii Reg: register.dat tkregister2 --mov mov.nii --reg register.dat Test: click on a point in tkmedit very close to the left hemi white surface. Use the "Functional Overlay Index Coordinates" to compute origCRS (round to the nearest integer). Compare origCRS to the "Volume index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match. -------------------------------------------------------------- On 05/17/2012 05:43 AM, Sinem Burcu Erdoğan wrote: > > Dear Freesurfer Community; > > I need to find the corresponding voxel in a functional image for a > specific structural image voxel after coregistering two images. My > structural image has 256*256*125 voxels and the functional image has > 64*64*30 voxels. > > I use the following command > > > tkregister2 --s subjectname --targ structural.nii --mov functional.nii > --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat > > > Where the target is structural image and movable is the functional image > > then click save to get MYregister.dat. > > > then take the inverse of the matrix > > save it as invMYregister.dat, and try to use this matrix to transform > from > > anatomical to functional. > > > However; as an example when I try to map voxel (169 , 62 ,35) of the > anatomical image to the functional space using the inverse > registration matrix; i get the values below > > - 64.3319 > > -146.4394 > > -157.2665 > > as the corresponding voxels' coordinates at the functional space which > is far beyond the functional volume size and is negative. It is clear > I cannot manage to use the trasfer matrices appropriately. > > Your help will be greatly appreciated. > > Thank you; > > Sinem Burcu ERDOGAN > > > -- > Sinem Burcu ERDOĞAN > Research Assistant > Bogazici University > Biomedical Engineering Institute > Kandilli Kampüs > 34684 Çengelköy / İSTANBUL TURKEY > Tel :+90-216-5163433 <tel:%2B90-216-5163433> > Fax :+90-216-5163479 <tel:%2B90-216-5163479> > e-mail: burcu.erdogan@boun.edu.tr <mailto:burcu.erdogan@boun.edu.tr> <mailto:burcu.erdogan@boun.edu.tr <mailto:burcu.erdogan@boun.edu.tr>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 tel:%2B90-216-5163433 Fax :+90-216-5163479 tel:%2B90-216-5163479 e-mail: burcu.erdogan@boun.edu.tr mailto:burcu.erdogan@boun.edu.tr
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Sinem Burcu Erdoğan