Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points.
Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space?
Thanks for any support and for your hints.
g.
2011/1/21 Douglas Greve greve@nmr.mgh.harvard.edu
yes, 001.mgz and the DICOM share the same space.
doug
On 1/21/11 9:08 AM, Gabriele Arnulfo wrote:
Hi all,
MRI, in this context, i was considering the original DICOM T1 MRI space before the conversion to 001.mgz file. Is your suggestion still the right way to solve my task?
2011/1/20 Douglas N Greve greve@nmr.mgh.harvard.edu
I don't know of another way to map control points. By MRI space I assume
that you mean the scanner RAS space? Eg, the space defined by the nifti qform? I think this matrix will be
L = inv(T)*Q
where Q is the scanner vox2ras of the orig volume and T is the tkregister vox2ras of the orig volume. You can get both of these matrices using mri_info.
doug
Martin Reuter wrote:
Hi Gabriele,
not sure if there is an easy way (probably Doug knows). But if there isn't, I wrote a tool mri_map_cpdat to map control points from one space to another. A control points dat file is a txt file containing coordinates. The tool will be available in 5.1 where it is used to transfer manual edits in the longitudinal stream. I could send a copy of it before. So you can:
- create a control.dat file with your coordinates
- map it using a lta file.
I am not sure how you can get the lta that you need (from native to freesurfer conform space) but probably someone else can help with that. This probably has been discussed before.
Here is the format of the control.dat:
xcoord1 ycoord1 zcoord2 xcoord2 ycoord2 zcoord2 xcoord3 ycoord3 zcoord3 info numpoints 3 useRealRAS 0
So instead of the coords put your numbers, of course you can have more than three points.
Best, Martin
On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote:
Hi all,
I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about matlab tools that could be used for this purpose is it right?
My task is really simple but i cannot figure out which is the best way. I've got a list of points (basically intra-cerebral electrodes coordinates segmented from MRI) in the MRI space and I'd like to calculate the respective points in the freesurfer space. Cheers,
gabriele
-- In a world without wall, how needs WINDOWS?? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.
-- In a world without wall, how needs WINDOWS??
-- In a world without wall, how needs WINDOWS??
Hi Gabriele,
the 001.mgz is in the original scanner coords, while the orig.mgz has been "conformed" to be in our standard coronal coordinate system.
cheers Bruce
On Sat, 22 Jan 2011, Gabriele Arnulfo wrote:
Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points.
Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space?
Thanks for any support and for your hints.
g.
2011/1/21 Douglas Greve greve@nmr.mgh.harvard.edu
yes, 001.mgz and the DICOM share the same space.
doug
On 1/21/11 9:08 AM, Gabriele Arnulfo wrote:
Hi all,
MRI, in this context, i was considering the original DICOM T1 MRI space before the conversion to 001.mgz file. Is your suggestion still the right way to solve my task?
2011/1/20 Douglas N Greve greve@nmr.mgh.harvard.edu
I don't know of another way to map control points. By MRI space I assume
that you mean the scanner RAS space? Eg, the space defined by the nifti qform? I think this matrix will be
L = inv(T)*Q
where Q is the scanner vox2ras of the orig volume and T is the tkregister vox2ras of the orig volume. You can get both of these matrices using mri_info.
doug
Martin Reuter wrote:
Hi Gabriele,
not sure if there is an easy way (probably Doug knows). But if there isn't, I wrote a tool mri_map_cpdat to map control points from one space to another. A control points dat file is a txt file containing coordinates. The tool will be available in 5.1 where it is used to transfer manual edits in the longitudinal stream. I could send a copy of it before. So you can:
- create a control.dat file with your coordinates
- map it using a lta file.
I am not sure how you can get the lta that you need (from native to freesurfer conform space) but probably someone else can help with that. This probably has been discussed before.
Here is the format of the control.dat:
xcoord1 ycoord1 zcoord2 xcoord2 ycoord2 zcoord2 xcoord3 ycoord3 zcoord3 info numpoints 3 useRealRAS 0
So instead of the coords put your numbers, of course you can have more than three points.
Best, Martin
On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote:
Hi all,
I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about matlab tools that could be used for this purpose is it right?
My task is really simple but i cannot figure out which is the best way. I've got a list of points (basically intra-cerebral electrodes coordinates segmented from MRI) in the MRI space and I'd like to calculate the respective points in the freesurfer space. Cheers,
gabriele
-- In a world without wall, how needs WINDOWS?? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.
-- In a world without wall, how needs WINDOWS??
-- In a world without wall, how needs WINDOWS??
To elaborate, the 001.mgz and the orig.mgz have a different number of voxels and are (generally) sliced differently, so they do not share a voxel space. The do share an RAS space. The qform (and matrix given by --vox2ras) is the matrix that converts a voxel coordinates to RAS. This matrix must be different because they have different voxel spaces.
doug
On 1/22/11 10:40 AM, Bruce Fischl wrote:
Hi Gabriele,
the 001.mgz is in the original scanner coords, while the orig.mgz has been "conformed" to be in our standard coronal coordinate system.
cheers Bruce
On Sat, 22 Jan 2011, Gabriele Arnulfo wrote:
Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points.
Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space?
Thanks for any support and for your hints.
g.
2011/1/21 Douglas Greve greve@nmr.mgh.harvard.edu
yes, 001.mgz and the DICOM share the same space.
doug
On 1/21/11 9:08 AM, Gabriele Arnulfo wrote:
Hi all,
MRI, in this context, i was considering the original DICOM T1 MRI space before the conversion to 001.mgz file. Is your suggestion still the right way to solve my task?
2011/1/20 Douglas N Greve greve@nmr.mgh.harvard.edu
I don't know of another way to map control points. By MRI space I assume
that you mean the scanner RAS space? Eg, the space defined by the nifti qform? I think this matrix will be
L = inv(T)*Q
where Q is the scanner vox2ras of the orig volume and T is the tkregister vox2ras of the orig volume. You can get both of these matrices using mri_info.
doug
Martin Reuter wrote:
Hi Gabriele,
not sure if there is an easy way (probably Doug knows). But if there isn't, I wrote a tool mri_map_cpdat to map control points from one space to another. A control points dat file is a txt file containing coordinates. The tool will be available in 5.1 where it is used to transfer manual edits in the longitudinal stream. I could send a copy of it before. So you can:
- create a control.dat file with your coordinates
- map it using a lta file.
I am not sure how you can get the lta that you need (from native to freesurfer conform space) but probably someone else can help with that. This probably has been discussed before.
Here is the format of the control.dat:
xcoord1 ycoord1 zcoord2 xcoord2 ycoord2 zcoord2 xcoord3 ycoord3 zcoord3 info numpoints 3 useRealRAS 0
So instead of the coords put your numbers, of course you can have more than three points.
Best, Martin
On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote:
> Hi all, > > I'm a new freesurfer user and I've a small question for you all. > Which > the faster and reliable way to map a list of points into the > freesurfer > geometrical space? > I've already read the pdf/ppt but there's no suggestion in there > about > which command should be used (if any). I've read about matlab tools > that > could be used for this purpose is it right? > > My task is really simple but i cannot figure out which is the best > way. > I've got a list of points (basically intra-cerebral electrodes > coordinates segmented from MRI) in the MRI space and I'd like to > calculate the respective points in the freesurfer space. > Cheers, > > gabriele > > -- > In a world without wall, how needs WINDOWS?? > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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
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.
-- In a world without wall, how needs WINDOWS??
-- In a world without wall, how needs WINDOWS??
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Gabriele Arnulfo