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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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/
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.
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 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/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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/
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.
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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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/
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.
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/
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
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 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/
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.
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/
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: 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Hari,
In order to use mri_coreg on Mac, you will need to download the "Development Version" of freesurfer. See the following page under Development Version:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Once downloaded, uncompress the .tar.gz file to some directory on your machine and set the FREESURFER_HOME environment variable appropriately. Also, you will want to copy over your license file as well. Then you should be able to use the mri_coreg binary as Doug mentions below.
-Zeke
On 06/09/2016 06:53 PM, HARI GURAGAIN 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
> 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/
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.
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/
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: 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/
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
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
> 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/
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.
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/
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: 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.hari@gmail.com mailto: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 mailto: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 >> 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/ > > _______________________________________________ > 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. > _______________________________________________ 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/
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: 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/
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
freesurfer@nmr.mgh.harvard.edu
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