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
