Hi Dirk,
If you're on Linux or MacOSX, then you could "grep -a AFNI test.nii" to
get output like this:
<pre>
<AFNI_attributes NIfTI_nums="182,217,182,1,1,16" ni_form="ni_group"
self_idcode="16_May_2007_07_36_19_304" >
<AFNI_atr atr_name="IDCODE_DATE" ni_dimen="1" ni_type="String" >"Wed
May 16 07:36::19 2007"</AFNI_atr>
<AFNI_atr atr_name="BRICK_STATS" ni_dimen="2" ni_type="float"
>0.000000 2.000000</AFNI_atr>
<AFNI_atr atr_name="HISTORY_NOTE" ni_dimen="1" ni_type="String"
>"Volume intersected with surface:
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord"</AFNI_atr>
<AFNI_atr atr_name="BRICK_LABS" ni_dimen="1" ni_type="String"
>"volume_0~"</AFNI_atr>
<AFNI_atr atr_name="LUT_NAMES" ni_dimen="1" ni_type="String"
>"???~???_not_used~plus_cluster_area_AD10TD10_R"</AFNI_atr>
<AFNI_atr atr_name="CARET_METADATA_LINK" ni_dimen="1"
ni_type="String"
>"pubMedID=0;tableNumber=;tableSubHeaderNumber=;figureNumber=;panelNumberOrLetter=;pageNumber=;pageReferencePageNumber=;pageReferenceSubHeaderNumber="</AFNI_atr>
</AFNI_attributes>
</pre>
(Probably will be followed by some junk/binary characters the list may
not appreciate.)
Among these attributes, the LUT_NAMTES is the pertinent one: The
ordinal position of the paint name corresponds to the intensity in the
paint volume. The first paint name, corresponding to intensity=1, will
probably be "???"; in the example above, paint name
plus_cluster_area_AD10TD10_R corresponds to intensity=2. Your may be
LVE00_V1.
Donna
On 05/16/2007 07:13 AM, Dirk Neumann wrote:
Hi Donna, John,
Thank you very much for the previous suggestions. I managed to
load+fix a manual segmentation, reconstruct the surface and register
it to the f99ua1 surface.
I now deformed paint files from the atlas back to my volume (using
"copy surface paint column to volume", and saved it as nifti). What I
did not find out is which paint labels the integer numbers in the
paint volume refer to. Is there a file I can look this up? Or is there
a way to save this information in caret?
Thanks, -- Dirk
On 4/20/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
Hi Dirk,
See inline replies below.
Donna
On 04/20/2007 12:59 AM, Dirk Neumann wrote:
> Dear All,
>
> We got a high-resolution (.15 mm) T2-weighted scan of a macaque brain
> (gray matter brighter, white matter darker) and would like to
> reconstruct the cortical surfaces and align it to a standard atlas.
>
> Could this be done with any available software?
I'm sure, but the ones I know of haven't been released for public
consumption.
>
> I had a look at the caret/surefit source code. Would you recommend
> adapting the generateInnerBoundary / generateOuterBoundary /
> generateSegmentation functions ?
Let's put it this way: Even back in the days when SureFit was in
python, and it was pretty easy to just try different things, I never did
this in those "all I have is T2" (or my T1 is crummy) situations.
Instead, I'd use the equivalent of Caret's Window: Script Builder
functions to try to transform the T2 into something that looks like a
T1. This usually involved somehow getting masks of the
intracranial/extracranial voxels; reversing intensities; and
dilating/eroding to get rid of white residual voxels along the edges.
Not pretty, not ideal, not fun.
>
> Would there be an easy way of providing caret/surefit with a manually
> segmented volume or reconstructed surfaces (from amira/itk-snap) ?
Sure. You can do this. Use Volume: Open Anatomy Volume and open your
structural; then use Volume: Open Segmentation Volume and open your
amira/itk-snap output. Use D/C Overlay/Underlay volume and set anatomy
as underlay, segmentation as overlay; make sure they align. If not,
adjust orientation/origin as needed to make them align.
If you just want a surface, you can do Volume: Segmentation: Reconstruct
into surface. But if you want to carry it through to registration, then
you'll probably need to first make sure:
* The segmentation contains a single, binary object with intensities 0
or 255, no handles (or only tiny ones). Use Volume: Segmentation:
Topology error report to check number of objects, cavities, and handles.
* Both volume and segmentation are centered somewhere near the AC.
(Later, after you've generated your surface and registered to an atlas,
you can create an alternate version of your fiducial surface that is
centered on an alternate origin, e.g., interaural.) Otherwise, when you
flatten the compressed medial wall will be centered in an awkward
location. You could, however, use the very inflated surface to draw
your borders instead.
Anyway, if you're registering the surface, use Volume : SureFit
Operations: and make sure volume type is segmentation. Then turn off
all options through auto error correction, but turn on Generate fiducial
surface and everything below it.
>
> Thanks, -- Dirk
>
> ____
>
> Dirk Neumann
> Computation and Neural Systems Program
> California Institute of Technology
> (626) 395 4025 dirk @ caltech . edu
> http://emotion.caltech.edu/~dirk/
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