tkregister is only for viewing and manually registering volumes. Try mri_coreg which you can get from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 11/01/2016 01:16 PM, Chiara Giacosa wrote: > The images that I see in tkregister are the original ones before any > transformations. In this way I must do all the transformations manually, > which is of course time consuming and user-driven; whereas my hope is to let > the program do the transformations automatically, so that I have only to > check if they are correct. > I am probably missing something obvious about the command usage... > > —•— > Chiara Giacosa > PhD student > Concordia University > > >> Il giorno 01 nov 2016, alle ore 12:47, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> ha scritto: >> >> what do you mean "it does nothing" ? >> >> >>> On 10/28/2016 04:41 PM, Chiara Giacosa wrote: >>> Thank you Douglas for your response. >>> >>> However I had already tried to check with tkregister without noedit >>> and it does nothing. I have to make the changes manually in order to >>> see differences in the images. It is weird that the coordinates are >>> the same because These images are relative of one subject and a >>> template that I created from our sample; I tried it also between two >>> subjects and nothing changes. What can be my mistake? >>> >>> Thanks in advance! >>> Chiara >>> >>> —•— >>> Chiara Giacosa >>> PhD student >>> Concordia University >>> >>> >>> Il giorno 28 ott 2016, alle ore 11:58, Douglas Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> ha scritto: >>> >>>> You should run tkregister2 without the --noedit to see if your >>>> registration is correct. When you use --regheader, it will compute >>>> the registration based on the scanner cooridinates in the mgz files. >>>> They apparently have the same coordinates because the matrix is the >>>> identity >>>> >>>> >>>>> On 10/17/16 11:47 AM, Chiara Giacosa wrote: >>>>> Dear experts, >>>>> >>>>> I am new to freesurfer and I am struggling making transformation of >>>>> images from one subject to another as well as to a template. I have >>>>> tried different ways, but I always end up with the original image as >>>>> if the transformation was never applied. I used tkregister2 from >>>>> command line and mri_vol2vol. >>>>> >>>>> I noticed that the transformation matrices are always the identity >>>>> matrix in the first 3 columns/rows, no matter what transformation I >>>>> tell the program to do. I don't think that this makes sense so I >>>>> wonder if I am doing something wrong or if there might be an issue >>>>> with the version of tkregister I have. >>>>> >>>>> My *commands *are: >>>>> tkregister2 --mov $subj/mri/orig.mgz --targ my_template/mri/orig.mgz >>>>> --regheader --reg $subj/reg/orig2templ_tkreg.dat --noedit >>>>> >>>>> mri_vol2vol --mov $subj/mri/rh.hand_manual.nii.gz --targ >>>>> my_template/mri/orig.mgz --o $subj/mri/rh.hand_subj_in_mytempl.mgz >>>>> --reg $subj/reg/orig2templ_tkreg.dat >>>>> >>>>> *Output Matrix *$subj/reg/orig2templ_tkreg.da: >>>>> subject-unknown >>>>> 1.000000 >>>>> 1.000000 >>>>> 0.150000 >>>>> 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 >>>>> -1.370635986328125e+00 >>>>> 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 >>>>> -4.750839233398438e+00 >>>>> 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 >>>>> -1.000000000000000e+00 >>>>> 0 0 0 1 >>>>> round >>>>> >>>>> >>>>> Contents of my $FREESURFER_HOME/build-stamp.txt file: >>>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>>>> >>>>> Any suggestion will be much appreciated! >>>>> >>>>> -- >>>>> Chiara Giacosa >>>>> Ph.D. candidate >>>>> Concordia University >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 <mailto: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
