Hi Doug,
great I was beginning to think that I our cluster is marginally broken (say bad
ram). But since you can reproduce I guess it is something else. For now I work
around that by converting all float targets temporary to int and thus see them
during the registration. A real fix would be much nicer though :)
Thanks for looking into this
Sebastian
On Feb 22, 2010, at 11:15 AM, Douglas N Greve wrote:
> 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
>
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