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 <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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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/ >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> 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/ >>>> >>>> _______________________________________________ >>>> 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 >> 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/ >> >> _______________________________________________ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
