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
