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

Tue Sep 23 08:27:51 CDT 2008

Hi Bayle,

I removed your attachments and placed them in our upload directory, and 
I am forwarding your reply to caret-users that got held up due to 
message size constraints.  I let the first attachment you sent through, 
because it was just a bit above the limit, but this message had three 
volumes attached exceeding 2.5Mb total.  We don't want to fill up 
everyone's inbox.

I'll try to have a look at this later today, but I wanted John Harwell 
to get a look before he takes a few days off later this week.

Donna

-------- Original Message --------
Subject: 	RE: [caret-users] Problem viewing NIFTI volume file in 5.6
Date: 	Tue, 23 Sep 2008 01:21:10 +0000
From: 	Baylis Shanks <bshanks3 at hotmail.com>
To: 	Caret, SureFit, and SuMS software users 
<caret-users at brainvis.wustl.edu>

hi,

thanks for looking into it.

> When I view it in AFNI, I do see something that might be mouse cortex

yes, it's mouse cortex, and that is what it is supposed to look like :)

> 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]
> ...
> 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.

by "what is shown above", you meant this, right?

there are indeed supposed to be 58, 67, and 41 voxels along the R-L, A-P, and I-S directions. the value of the "dim" header field is [ 3   58   67   41    0    0    0    0]  (i think -- that is the value that i tried to put in there, but bear in mind that since i created the file i could have written out the header incorrectly).

on to the displacement. i was trying to make the origin be the anterior commissure, which i believe to be near 5.7, 7.8, 2.7 mm.

what are the units of the numbers 5700, 7800, 2692? my intent was for them to be microns. the values of the NIFTI header fields qoffset_x, qoffset_y, qoffset_ z are (i think) -5700, -7800, and -2700 respectively. the value of the NIFTI header field xyzt_units is (i think) NIFTI_UNITS_MICRON. but perhaps the units of the qoffset_* fields were supposed to be units of millimeters?

5700-5688.6 is 11.4, which is pretty close to 11.6 (58*.2 = 11.6) -- so it seems like 3dinfo is interpreting the 5700 as mm, and subtracting 11.4 mm from it to get the 5688.6.

so, i tried changing header fields but i haven't yet figured out how to completely fix the problem (read on for details).

before talking about that, i'd like to note something strange i noticed in the Caret's Volume Attributes Editor when viewing the original file that i included in the previous email, test.nii (when loading it as an Anatomy volume). The dialog shows the "Dimensions" as 1 in each direction, "Voxel Size" as 200, and Origin as -57, -78, and -27. This is odd, because one would think that the Voxel Size is correct and is displayed in units of microns, but one would think that Origin would be either -5700, -7800, -2700 (if the qoffset header fields are being read as microns and displayed as microns) -5700000, -7800000, -2700000 (if the qoffset header fields are being read as mm and displayed as microns), or it should be -5.7, -7.8, -2.7 (if the qoffset header fields are being read as microns and displayed as mm).

now, i will describe the results of trying to change some of the header fields, yielding new test files (attached).

first, i tried to simply scale the qoffset fields. I replaced -5700, -7800, -2700 with -5.7, -7.8, -2.7. The result is file test2_5.7.nii (attached). Caret has the same problem as before. Caret's Volume Attribute Editor shows "Dimensions" as 1 in each direction, "Voxel Size" as 200, and Origin as -0.057, -0.078, and -0.027. Again, this is odd; I would have expected one of 5700, -7800, -2700 (if the qoffsett header fields are being read as mm and displayed as microns) -5.7, -7.8, -2.7 (if the qoffset header fields are being read as microns and displayed as microns), or it should be -0.0057, -0.0078, -0.0027 (if the qoffset header fields are being read as microns and displayed as mm).

second, i tried setting the header field xyzt_units to NIFTI_UNITS_MM. I changed the pixdim header field from [200 200 200] to [.2 .2 .2], and i left the qoffset fields as -5.7, -7.8, -2.7 (test3_mm.nii, attached). Now Caret displays something, and it even looks to be centered near the origin! However, the display looks too small for some reason, and the Volume Attributes Editor shows Dimensions as 286, 331, 201, Voxel Size as .2, .2, .2, and Origin as -57, -78, -27. So, both the Dimensions and Origin field seems to be wrong.

third, i tried leaving xyzt_units as NIFTI_UNITS_MM, leaving the pixdim header field as [.2 .2 .2], and rescaling the qoffset fields by a factor of ten, to -.57, -.78, -.27, hoping to make the Origin fields in Caret's Volume Attributes Editor come out right (test4_mm_.57.nii). Loading this file into Caret, you can see something, but it is really tiny, and not centered at the origin. The Volume Attributes Editor shows Dimensions as 286, 331, 201, Voxel Size as .2, .2, .2, and Origin as -5.7, -7.8, -2.7. So, now if the units in the Volume Attributes Editor are interpreted as mm, the Voxel Size and Origin are both correct, however the Dimensions are still wrong.

thanks,
  bayle

----------------------------------------
> Date: Fri, 19 Sep 2008 08:33:33 -0500
> From: donna at brainvis.wustl.edu
> To: caret-users at brainvis.wustl.edu
> Subject: Re: [caret-users] Problem viewing NIFTI volume file in 5.6
>
> 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
>>
>

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