Hi Aimi, this is not possible with nifti since 163842 > 32768 (2^15) which is the limit for nifti. It should have worked with mgh output and --noreshape. Can you confirm that it does not? doug
On 10/10/2012 11:15 AM, Aimi Watanabe wrote: > Hello, > > My input to freesurfer is: > > mri_surf2surf > --cortex --fwhm-src 5 --noreshape --hemi rh --tval [$output file] --sval > [$input file] --srcsubject [$subject id] --trgsubject fsaverage --tfmt nii > > When I reopen the resulting image with Nibabel, the dimensions are 27307 > x 1 x 6 x 296. While 296 is the time axis, I was hoping to get 27307*6 = > 163842 vertices. > > I have replaced '--noreshape' with '--reshape', '--reshape_factor=6' > > and the bash output looks proper: > > 121010-16:49:28,430 interface INFO: > stdout 2012-10-10T16:49:28.429912:Saving target data > 121010-16:49:28,430 interface INFO: > stdout 2012-10-10T16:49:28.429912:Reshaping 6 (nvertices = 163842) > 121010-16:49:28,430 interface INFO: > stdout 2012-10-10T16:49:28.429912:Saving to [$output file] > > However, it does not change the resulting image. > > I have also tried other file types that are not 'nii', like 'mgh', but > this does not help either. > > Please advise? > > Also, I could easily make a work-around, and reshape the image from > a(27307, 1, 6, 296) to b(163842, 1, 296) in FORTRAN (column-major) > order. I.E.: 0~27306 then add the next set 27307~54613. If I do this, > would the original vertex map be preserved? > > Thank you! > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
