Dear Freesurfer Experts,
I am a happy user of freesurfer for a number of years now. And finally I managed to switch over from v3.0.5 to 4.5.0. Most of this switch was pretty straightforward only slowed down by a few self-inflicted complications. One of the consequences of switching to V4 is that most of my functional 4D volumes now are floats instead of the short we used before. And regarding the floats, I just encountered a weird issue with tkregister2 (from freesufer-linux-centos4_x86_64-stable-pub-v4.5.0-full). I try to register 2 uncompressed single file nifti files, and the target does not appear only the moveable (when I hit the target button on the gui I just the image window turns black). Interestingly this also happens when I load the same volume as target and moveable:
tkregister2 --regheader --reg tmp.reg --targ ./bold/003/f.nii --mov ./bold/003/f.nii -> nicely visible mov invisible targ, also fmo-targ does not help.
however if I convert the file to int or short the targ becomes visible again: mri_convert -i /bold/003/f.nii -o /bold/003/fi.nii -odt int tkregister2 --regheader --reg tmp.reg --targ ./bold/003/fi.nii --mov ./bold/003/fi.nii -> nicely visible mov and targ, also: tkregister2 --regheader --reg tmp.reg --targ ./bold/003/fi.nii --mov ./bold/003/f.nii -> nicely visible mov and targ,
but note: mri_convert -i /bold/003/fi.nii -o /bold/003/ff.nii -odt float tkregister2 --regheader --reg tmp.reg --targ ./bold/003/ff.nii --mov ./bold/003/ff.nii -> nicely visible mov invisible targ,
So it looks like tkregister2 does not really like floats. Is there any thing I can do to work around this problem short of mri_converting all templates to temporary ints? I would be happy to help debug this issue, so please let me know what I can do to help.
best regards & thanks for all the cool tools in freesurfer Sebastian