Dear Freesurfer experts, I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1). When I use "spmregister" as follow: spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2) Please what I am doing wrong? Thank you for any guidance Jon
Dear Freesurfer experts, I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1). When I use "spmregister" as follow: spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2) Please what I am doing wrong? Thank you for any guidance Jon
what is your freeview command?
On 07/14/2017 08:46 AM, John Anderson wrote:
Dear Freesurfer experts, I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1). When I use "spmregister" as follow: spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii
Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2)
Please what I am doing wrong? Thank you for any guidance Jon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
It is the same command left by spmregister freeview orig.mgz pcals.nii Just i excluded the flag -f /surf/?h.orig what is your freeview command?
On 07/14/2017 08:46 AM, John Anderson wrote:
Dear Freesurfer experts,
I want to derive registration matrix between pcasl image and the
structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and
the pcasl image in Freesurefr I see overlap between the images
(attached Figure1).
When I use "spmregister" as follow:
spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat
--fsvol orig --o CBF_T1.nii
Then visualize "CBF_T1" using freeview I see mis-registration
(attached Figure2)
Please what I am doing wrong?
Thank you for any guidance
Jon
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Can you try
tkregister --mov perfusion_calib.nii.gz --reg reg.dat
On 07/14/2017 06:56 PM, John Anderson wrote:
Hi Doug,
It is the same command left by spmregister freeview orig.mgz pcals.nii
Just i excluded the flag -f /surf/?h.orig
what is your freeview command?
On 07/14/2017 08:46 AM, John Anderson wrote:
Dear Freesurfer experts,
I want to derive registration matrix between pcasl image and the
structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and
the pcasl image in Freesurefr I see overlap between the images
(attached Figure1).
When I use "spmregister" as follow:
spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat
--fsvol orig --o CBF_T1.nii
Then visualize "CBF_T1" using freeview I see mis-registration
(attached Figure2)
Please what I am doing wrong?
Thank you for any guidance
Jon
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *�k��
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
John Anderson