Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote:
Hi Doug,
Thank you for your reply.
I tried FreeView and have attached screenshots of results.
freeview_native_brain.jpg - snapshot of native brain
freeview_aseg.jpg - aseg.mgz added. This appears to correspond with native brain
freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar to aseg.mgz. Slightly different, as I'd expect, corresponds well to native brain.
freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. This is the FreeSurfer output, ie not reoriented. It corresponds well to aseg.mgz and native brain
freeview_native_brain_lh_pial_native.jpg - The pial (left) surface that I created using register.dat and mri_surf2surf is shown. This does not correspond to the native brain.
I wonder if there are some FreeView options that I should be using?
Best regards, -Tim
On Thu, 7 Mar 2013, Douglas N Greve wrote:
Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit rigid and expects things to be a certain way (ie, not in native space). Try using freeview instead. doug
On 03/07/2013 03:19 PM, Timothy Brown wrote:
Dear FreeSurfer users,
I wish to view volumes and surfaces in native space.
I used the information at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
to convert volumes.
I then used:
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached)
Can you let me know the steps/procedure to do this?
Many thanks,
-Tim
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
Hi Doug,
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat
mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
For the previous snapshot, I ran FreeView, and loaded volume and surface using mouse/menu selection.
I just ran
freeview -v brain-in-rawavg_tb.mgz -f lh.pial.native
with snapshot attached.
-Tim
On Fri, 8 Mar 2013, Douglas N Greve wrote:
Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote:
Hi Doug,
Thank you for your reply.
I tried FreeView and have attached screenshots of results.
freeview_native_brain.jpg - snapshot of native brain
freeview_aseg.jpg - aseg.mgz added. This appears to correspond with native brain
freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar to aseg.mgz. Slightly different, as I'd expect, corresponds well to native brain.
freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. This is the FreeSurfer output, ie not reoriented. It corresponds well to aseg.mgz and native brain
freeview_native_brain_lh_pial_native.jpg - The pial (left) surface that I created using register.dat and mri_surf2surf is shown. This does not correspond to the native brain.
I wonder if there are some FreeView options that I should be using?
Best regards, -Tim
On Thu, 7 Mar 2013, Douglas N Greve wrote:
Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit rigid and expects things to be a certain way (ie, not in native space). Try using freeview instead. doug
On 03/07/2013 03:19 PM, Timothy Brown wrote:
Dear FreeSurfer users,
I wish to view volumes and surfaces in native space.
I used the information at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
to convert volumes.
I then used:
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached)
Can you let me know the steps/procedure to do this?
Many thanks,
-Tim
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
Try running mri_surf2surf like this (added rawavg.mgz after register.dat)
mri_surf2surf --sval-xyz pial --reg register.dat rawavg.mgz --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
On 03/08/2013 12:38 PM, Timothy Brown wrote:
Hi Doug,
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat
mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
For the previous snapshot, I ran FreeView, and loaded volume and surface using mouse/menu selection.
I just ran
freeview -v brain-in-rawavg_tb.mgz -f lh.pial.native
with snapshot attached.
-Tim
On Fri, 8 Mar 2013, Douglas N Greve wrote:
Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote:
Hi Doug,
Thank you for your reply.
I tried FreeView and have attached screenshots of results.
freeview_native_brain.jpg - snapshot of native brain
freeview_aseg.jpg - aseg.mgz added. This appears to correspond with native brain
freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar to aseg.mgz. Slightly different, as I'd expect, corresponds well to native brain.
freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. This is the FreeSurfer output, ie not reoriented. It corresponds well to aseg.mgz and native brain
freeview_native_brain_lh_pial_native.jpg - The pial (left) surface that I created using register.dat and mri_surf2surf is shown. This does not correspond to the native brain.
I wonder if there are some FreeView options that I should be using?
Best regards, -Tim
On Thu, 7 Mar 2013, Douglas N Greve wrote:
Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit rigid and expects things to be a certain way (ie, not in native space). Try using freeview instead. doug
On 03/07/2013 03:19 PM, Timothy Brown wrote:
Dear FreeSurfer users,
I wish to view volumes and surfaces in native space.
I used the information at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
to convert volumes.
I then used:
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached)
Can you let me know the steps/procedure to do this?
Many thanks,
-Tim
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
Hi Doug,
I ran that command line. It did produce a different surface. Screenshot attached.
Terminal output below.
cis/project/biocard/work/timothy/freesurfer_conversion/fs_output/1158119_3_6/1158119_3_6/surf$ mri_surf2surf --sval-xyz pial --reg register.dat rawavg.mgz --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6 Reading header for rawavg.mgz srcsubject = 1158119_3_6 srcval = (null) srctype = trgsubject = 1158119_3_6 trgval = pial.native trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /cis/project/biocard/work/timothy/freesurfer_conversion/fs_output/1158119_3_6/1158119_3_6/surf/lh.sphere.reg Loading source data Reading surface file /cis/project/biocard/work/timothy/freesurfer_conversion/fs_output/1158119_3_6/1158119_3_6/surf/lh.pial Applying linear registration transform 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 0.000 1.000; INFO: trgsubject = srcsubject Saving target data
-Tim
On Fri, 8 Mar 2013, Douglas N Greve wrote:
Try running mri_surf2surf like this (added rawavg.mgz after register.dat)
mri_surf2surf --sval-xyz pial --reg register.dat rawavg.mgz --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
On 03/08/2013 12:38 PM, Timothy Brown wrote:
Hi Doug,
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat
mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
For the previous snapshot, I ran FreeView, and loaded volume and surface using mouse/menu selection.
I just ran
freeview -v brain-in-rawavg_tb.mgz -f lh.pial.native
with snapshot attached.
-Tim
On Fri, 8 Mar 2013, Douglas N Greve wrote:
Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote:
Hi Doug,
Thank you for your reply.
I tried FreeView and have attached screenshots of results.
freeview_native_brain.jpg - snapshot of native brain
freeview_aseg.jpg - aseg.mgz added. This appears to correspond with native brain
freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar to aseg.mgz. Slightly different, as I'd expect, corresponds well to native brain.
freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. This is the FreeSurfer output, ie not reoriented. It corresponds well to aseg.mgz and native brain
freeview_native_brain_lh_pial_native.jpg - The pial (left) surface that I created using register.dat and mri_surf2surf is shown. This does not correspond to the native brain.
I wonder if there are some FreeView options that I should be using?
Best regards, -Tim
On Thu, 7 Mar 2013, Douglas N Greve wrote:
Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit rigid and expects things to be a certain way (ie, not in native space). Try using freeview instead. doug
On 03/07/2013 03:19 PM, Timothy Brown wrote:
Dear FreeSurfer users,
I wish to view volumes and surfaces in native space.
I used the information at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
to convert volumes.
I then used:
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached)
Can you let me know the steps/procedure to do this?
Many thanks,
-Tim
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Timothy Brown