OK, I can replicate with this data. Let me see what's going on. Sebastian Moeller wrote: > Hi Doug, > > On Feb 19, 2010, at 7:16 AM, Douglas N Greve wrote: > > >> Hmmm, da stimmt etwas nicht. >> > > Ganz genau, das ist was faul im Staate Daenemark... :) > > >> I cannot replicate this. How was the original f.nii created? Can you send me >> f.nii? >> > The f.nii is in the filedrop > (https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/18898/1/a0629c2e9a52c7e1cef0915eec44fa1e). > I this case it was created by mri_vol2vol using a short as inputs. I > initially thought that maybe mri_vol2vol does something funky (I use --mov > --targ --o and --reg switches) even though the volumes look fine with > jip-display. But I can reproduce this with importing DICOMs as .nii (short) > and then run mc-sess (afni2) the resulting output is of .nii (float) and does > not display as --targ in tkregister2 but as moveable. Also if I mri_convert > the f.nii (the short, working one) to -odt float the resulting .nii float has > the reported problem. All the data is from a v17 TIM trio maybe there is > something wonky in the headers... Anything I should try to figure this out? > > Best > Sebastian > > >> doug >> >> Sebastian Moeller wrote: >> >>> 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 >>> >>> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> 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 >> >> > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
