Tobias,
You're in luck. AFNI's 3dinfo gives me this output:
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 2.000
mm [ 91
voxels]
A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 2.000
mm [109
voxels]
I-to-S extent: -72.000 [I] -to- 108.000 [S] -step- 2.000
mm [ 91
voxels]
So you *do* need to check the right on left checkbox. Then
setting the
origin to -90,-126,-72 should work.
John's having a look at your volume.
Donna
On 03/26/2007 11:21 AM, Tobias Egner wrote:
> Donna,
>
> one last dumb question: How do I make sure that I get precisely the
> right origin parameters, since the origin I see when displaying my
> images in SPM5 is obviously not the correct one to use for
displaying
> my images in Caret?
>
> Thanks,
>
> Tobias.
>
> On 3/26/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
>> Note that when opening functional volumes in Caret, there's a
checkbox:
>>
>> Volume is an SPM2 Volume with Right on Left
>>
>> Make sure it is either selected or deselected as needed.
>>
>> On 03/26/2007 09:52 AM, Tobias Egner wrote:
>> > Donna,
>> >
>> > thanks very much indeed, I think for now I will just go with
the fix
>> > of manually re-setting the origin in the way you suggest.
>> >
>> > best wishes,
>> >
>> > Tobias.
>> >
>> > On 3/26/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
>> >> Hi Tobias,
>> >>
>> >> Your metric files were only 30 lines long -- header but no
data.
>> >> Anyway, I suspect this is a case where Caret doesn't
recognize your
>> >> nifti1 .img and .hdr format. It's reading it as Analyze, which
>> works,
>> >> except you need to then set the origin. The attached captures
>> >> overlay_bad.jpg and overlay_good.jpg show how the volume
>> intersects the
>> >> average fiducial surface before and after using Volume: Edit
Volume
>> >> Attributes: to set the origin to -90,-126,-72. (I didn't
>> double-check
>> >> that this is precisely the right origin!) Saving the volume
with the
>> >> tweaked origin results in a reasonable looking metric, as the
>> attached
>> >> capture shows.
>> >>
>> >> If you can export a flavor of NIFTI that gets along better with
>> Caret,
>> >> then perhaps a way around this problem is to do this one;
save the
>> .hdr
>> >> as something like "make_caret_happy.hdr"; and copy this .hdr
over
>> your
>> >> existing (or copied) .hdr for mapping purposes. If you do
this,
>> please
>> >> check two things: 1) The left-right orientation is good; 2)
the
>> origin
>> >> is exactly right.
>> >>
>> >> For what it's worth, I've used the .nii style NIFTI files
with good
>> >> success.
>> >>
>> >> Donna
>> >>
>> >> On 03/26/2007 08:37 AM, Tobias Egner wrote:
>> >> > Dear Donna,
>> >> >
>> >> > thanks for your help: I've uploaded a couple of volumes
>> >> > ('Tobias_feature.hdr', etc) and the metric files (note
that in the
>> >> > metric files, my volumes are referred to by different
names). I'm
>> >> > actually using Windows though, not Linux.
>> >> >
>> >> > Many thanks and best wishes,
>> >> >
>> >> > Tobias.
>> >> >
>> >> > On 3/26/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
>> >> >> Hi Tobias,
>> >> >>
>> >> >> I don't recognize this problem. Hmmm. How about if I
give it a
>> >> try on
>> >> >> my end. Can you upload one or more of your volumes here:
>> >> >>
>> >> >> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>> >> >>
>> >> >> From the "'QEventDispatcherUNIX::unregisterTimer" error,
I guess
>> >> you're
>> >> >> running Linux. We'll see if my Linux box acts the same.
>> >> >>
>> >> >> Also, would you mind also uploading one of the metric
files? Or
>> >> you can
>> >> >> just verify that it is all zeros like so:
>> >> >>
>> >> >> caret_file_convert -text my.metric
>> >> >>
>> >> >> cut -f2 -d' ' my.metric |sort -un
>> >> >>
>> >> >> If you get a bunch of lines with scalars in them, then
the metric
>> >> file
>> >> >> contains non-zero nodes; however, if you just get a bunch
of lines
>> >> with
>> >> >> alpha characters, one line with 0.000000, and one with
73730, then
>> >> it is
>> >> >> all zeroes.
>> >> >>
>> >> >> Donna
>> >> >>
>> >> >> On 03/24/2007 03:08 PM, Tobias Egner wrote:
>> >> >> > Dear all,
>> >> >> >
>> >> >> > I am trying (unsuccessfully) to display some SPM T-images
>> >> generated in
>> >> >> > SPM5 in Caret 5.5. Here's what I am doing:
>> >> >> >
>> >> >> > The T-images are in nifti1 format (with .img and .hdr
>> >> extensions), and
>> >> >> > the original functional data were converted to nifti
via the
>> DICOM
>> >> >> > import function in SPM5. The images are normalized (and
>> >> resliced) to
>> >> >> > the SPM5 MNI T1.nii template (voxel size 2x2x2,
dimensions:
>> >> 91x109x91,
>> >> >> > origin: 46 64 37).
>> >> >> >
>> >> >> > In Caret 5.5, I follow the steps indicated in the
>> >> >> > Caret_Tutorial_Sep22.pdf section 5.1. (and using the Caret
>> Tutorial
>> >> >> > Sept06 data set).
>> >> >> >
>> >> >> > 1- I open the fMRI mapping template Spec file, select
all, then
>> >> save
>> >> >> > under a new name, and load scenes.
>> >> >> > 2- Attributes: Map volumes to surface, then add my SPM
t-maps
>> >> and set
>> >> >> > thresholds.
>> >> >> > 3- Map to spec file with atlas: As output I select my
newly
>> created
>> >> >> > spec file, and then I select the SPM2 space, and the
>> corresponding
>> >> >> > SPM2 left hem atlas, then repeat those steps with the
SPM2 right
>> >> hem
>> >> >> > atlas. I accept the default settings on the next page.
>> >> >> > 4- The I name my metric files (left, right) in accrodance
>> with the
>> >> >> > left/right aspects of the 'surface family'.
>> >> >> > 5- As Mapping Algorithm, I accept the 'enclosing voxel'
>> >> default, then
>> >> >> > I press Finish and the computing starts...
>> >> >> >
>> >> >> > At the end of the number crunching, I get a little
warning sound
>> >> and
>> >> >> > in the command line window it reads:
>> >> >> >
>> >> >> > 'QEventDispatcherUNIX::unregisterTimer: invalid argument'
>> >> >> >
>> >> >> > Regardless, I next load the Scene No 4 (FLAT etc..),
and then
>> >> open the
>> >> >> > two metric files I have created. I then also load the SPM2
>> fiducial
>> >> >> > coord files. I select Metric as the Primary Overlay,
and select
>> >> L-to-L
>> >> >> > R-to-R matching. With great anticipation, I select one
of my
>> metric
>> >> >> > files, but no cigar: I don't see any surface overlays
>> whatsoever.
>> >> >> >
>> >> >> > Any idea where I am going wrong? Many thanks for any
advice!
>> >> >> > Best wishes,
>> >> >> >
>> >> >> > Tobias.
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