I can't tell anything from that image. How do you know it is wrong? Did you look at the registration using tkregister? Does Katkov_OT_45_LH.nii.gz look ok on the surface? The problem could be in load_nii and/or save_nii. These are not our programs. You might try MRIread() and MRIwrite().
On 04/14/2016 09:54 AM, Francesca Strappini wrote:
Hi, I think that somehow my answer did not arrive... I used load_nii and save_nii to read and write out the volume. I attached a picture that shows the misalignment.
Thanks! Francesca
2016-04-08 18:31 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
can you show a pic? What were your matlab commands to read in and write out the volume? On 04/04/2016 07:36 AM, Francesca Strappini wrote: > Dear Freesurfers, > > I run the preprocessing step of some functional data with > preproc-sess, then the Fourier analysis with matlab. Now, I'm trying > to plot this data on the surface: > > mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh > --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz > > I used as registration matrix the one produced by the preprocessing > step but when I try to visualize the map on the surface it looks like > completely misaligned. > > Thank you > Best > Francesca > > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584> > E-mail: francesca.strappini@weizmann.ac.il <mailto:francesca.strappini@weizmann.ac.il> > <mailto:francesca.strappini@weizmann.ac.il <mailto:francesca.strappini@weizmann.ac.il>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <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.-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il
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