use mri_vol2vol, like
mri_vol2vol --mov CT.nii --reg v1t2.lta --fstarg --o CT-in-anat.nii
On 6/15/16 9:58 AM, HARI GURAGAIN wrote:
Dear Douglas,
With the suggestions from Zeke, the mri_coreg is working now. I have
one last question:
I got the new v1to2.lta. How to apply this transformation to the CT
image? Is it by using mri_convert?
Something like below?
mri_convert -at v1to2.lta CT.nii new_CT.nii
Any suggestion will be greatly appreciated.
Thank you again,
Hari Guragain
On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN <nuclear.h...@gmail.com
<mailto:nuclear.h...@gmail.com>> wrote:
Dear Douglas,
I have used the same file as you pointed, but it keeps on showing the
same error message. I copied the file to my
/Applications/freesurfer/bin directory but it still shows the same
error message:
‘dyld: Library not loaded:
@executable_path/../lib/gcc/lib/libgomp.1.dylib’
Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5
Does it have something to do with the library issue with mac?
Any help is appreciated.
Thank you,
On Jun 9, 2016, at 5:45 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
try
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
Dear Douglas,
The executable is not working as it says ‘Library not loaded:
@executable_path/../lib/gcc/lib/libgomp.1.dylib’
Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5
I am currently using the freeview: Version 1.0 and the operating
system is: OS X EI Captain Version: 10.11.5
I wonder if the file you pointed works for the mac? Should I
reinstall the freeview?
Any help would be greatly appreciated.
Thank you,
Hari
On Jun 9, 2016, at 4:28 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
No, it is not the same command line. If you run it without args,
it will
give you some info, but it is basically
mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
Thank you Douglas.
One more thing: Is there any syntax how to use it? I wonder if it
is same as the mri_robust_register?
On Jun 9, 2016, at 3:43 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
I don't think robust register will do cross-modal. You may be
better off
using mri_coreg, which you can get from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
Dear Freesurfer community,
I am relatively new to this community.
I was trying to register the CT image and the MRI images (MRI
as a the
target volume and CT as the movable volume). I used the
mri_robust_register to to do the registration as below:
/mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
--mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
The problem is that: after register, the new image (v1to2.nii)
is not
exactly aligned with the original MRI image (vol2.nii). It gives a
very different output. I wonder if I am missing anything here or I
need to do some extra steps after the above command in order to get
the correct alignment of the two images. I was hoping to get the
resultant image should be well orient with the target volume image
(vol2.nii image in my case).
I really appreciate any help here.
Hari Guragain
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MGH-NMR Center
gr...@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
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_______________________________________________
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
gr...@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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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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
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