[caret-users] Problem viewing NIFTI volume file in 5.6

[Donna Dierker]

Hi Bayle,

Your problem replicates on my end -- i.e., I get an empty volume when I 
view test.nii in Caret (see test.nii.caret.jpg).

When I view it in AFNI, I do see something that might be mouse cortex 
(see test.nii.afni.jpg).

The header does look unusual.  Here is AFNI's 3dinfo output:

it.wustl.edu 30% 3dinfo test.nii
++ 3dinfo: AFNI version=AFNI_2007_05_29_1644 (Jan 29 2008) [64-bit]

Dataset File:    test.nii
Identifier Code: NII_-z--ofl-dASZaHy2pulrNg  Creation Date: Fri Sep 19 
08:26:32 2008
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI file
Storage Space:   637304 (637 thousand) bytes
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:  5688.600 [L] -to-  5700.000 [L] -step-     0.200 mm [ 58 
voxels]
A-to-P extent:  7786.800 [P] -to-  7800.000 [P] -step-     0.200 mm [ 67 
voxels]
I-to-S extent: -2700.000 [I] -to- -2692.000 [I] -step-     0.200 mm [ 41 
voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float

If the voxdims are really cubic .2mm, which is consistent with the mousy 
look of what AFNI shows, then the field of view should be 11.6x13.4 mm 
-- not what is shown above.

Let's start by verifying the voxdims and field of view.

Donna

On 09/18/2008 05:17 PM, Bayle Shanks wrote:
> Hi, I'm having trouble viewing the attached NIFTI functional volume
> file (test.nii) in Caret 5.56. I can view it fine in Caret 5.51.
>
> What happens is that when i open the file, there are no errors but it
> looks empty. The three coordinate selectors at the top (to the left of
> the D/C button) are each at 0 and can't be changed.
>
> I created the file
> myself so it's possible that it doesn't conform to the NIFTI standard
> in some way (of course, if so i'd like to correct that).
>
> I'm using Debian 2.6.18-6-amd64 (64-bit) (a mix of Debian stable and
> unstable).
>
> I've tried building Caret from source and also running the binary
> distribution. I've tried caret5 and also caret5_mesa. With
> caret5_mesa, some errors are displayed on the console (not sure if I was
> using CARET_DEBUG), I've copied them below.
>
> thanks,
>   bayle
>
> -----
> Time to read .caret5_preferences (0.00209236 MB) was 0 seconds.
> Caret Home Directory: /usr/local/caret
> NIFTI extension[0] 0
> Unscaled range: 0 10.9652
> Scaled range: 0 10.9652
>
> OpenGL Error: invalid enum
> At end of drawBrainModelPrivate().
> While drawing brain model VOLUME - test.nii
> In window number 0
> Projection Matrix Stack Depth 1
> Model Matrix Stack Depth 1
> Name Matrix Stack Depth 0
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>   

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