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
>
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