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.hari@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 greve@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 greve@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 greve@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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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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-- 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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