Caret doesn't support oblique volumes.
-------- Original Message --------
Subject: RE: [Fwd: Re: [caret-users] SPM8 - Mapping Functionals to
Volume problem]
Date: Fri, 20 Aug 2010 10:45:23 -0500
From: Coalson, Timothy Scott
To:
References:
<[email protected]><[email protected]>
<[email protected]> <[email protected]>
The problem is, the tmap volume is oblique:
[...@it tim]$ 3dinfo tmap.nii
++ 3dinfo: AFNI version=AFNI_2009_12_31_1431 (Jun 22 2010) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as tmap.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:tmap.nii is 18.303005 degrees from plumb.
Dataset File: tmap.nii
Identifier Code: NII_D9L4UP5jzpUwMw48SyNXCA Creation Date: Fri Aug 20 10:32:33
2010
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Storage Space: 665,600 (666 thousand) bytes
Geometry String:
"MATRIX(2.498272,-0.091066,0.018585,-94.97644,-0.046091,-0.779806,2.374822,78.94859,0.08071,2.373523,0.780946,-82.76968):80,80,26"
Data Axes Tilt: Oblique (18.303 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Inferior-to-Superior
third (z) = Anterior-to-Posterior [-orient RIA]
R-to-L extent: -94.976 [R] -to- 102.524 [L] -step- 2.500 mm [ 80 voxels]
A-to-P extent: 78.949 [P] -to- 141.449 [P] -step- 2.500 mm [ 26 voxels]
I-to-S extent: -82.770 [I] -to- 114.730 [S] -step- 2.500 mm [ 80 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
If you have afni and run 3dwarp -deoblique, like it suggests, it lines up in
caret. caret does not fully support loading volumes with non-plumb axes, but
sadly does not issue a warning when this happens.
Tim
-----Original Message-----
From: Donna Dierker [mailto:[email protected]]
Sent: Fri 8/20/2010 8:36 AM
To: Coalson, Timothy Scott (S&T-Student)
Subject: [Fwd: Re: [caret-users] SPM8 - Mapping Functionals to Volume problem]
Do you think you might have time to look at this today?
-------- Original Message --------
Subject: Re: [caret-users] SPM8 - Mapping Functionals to Volume problem
Date: Fri, 20 Aug 2010 11:42:19 +0200
From: Raemaekers-2, M. <[email protected]>
Reply-To: Caret, SureFit, and SuMS software users
<[email protected]>
To: Caret, SureFit, and SuMS software users
<[email protected]>
References:
<[email protected]><[email protected]>
<[email protected]>
Dear Donna,
You are absolutely right, sorry for the misunderstanding. Considering the
positioning information in niftii images, I somehow have problems when
overlaying functional images on the T1 image in Caret when the functional
images are not resliced to the volume of the T1.
I have some data made available for you on sendspace
(http://www.sendspace.com/file/sqvrcf) where I had this problem. It contains a
T1 image, a t-volume of a visual experiment, and the same t-volume -resliced to
the T1 volume. When doing checkreg in SPM, all three images are overlaying
perfectly, but in Caret only the resliced t-volume is aligned with the T1
image. Any ideas?
Regards,
Mathijs
________________________________
Van: [email protected] namens Donna Dierker
Verzonden: do 19-8-2010 17:00
Aan: Caret, SureFit, and SuMS software users
Onderwerp: Re: [caret-users] SPM8 - Mapping Functionals to Volume problem
Mathijs & Raphael,
See inline comments below.
Donna
On 08/19/2010 08:53 AM, Raemaekers-2, M. wrote:
> Dear Rafael,
>
> Not sure of this, but the results that you describe may be the result of a
> misalignment between your statistical map and your surface.
>
> It somehow seems that SPM and CARET are not using the niftii positioning
> information exactly the same,
Any details you can provide would be appreciated.
> but for me it works when I coregister&reslice a statistical map to the
> T1-image (as put in Talairach orientation before segmentation), and then map
> the resliced statistical image to the surface.
Mathijs' comments here suggest, to me, that he is generating his own surfaces
and mapping individual maps to the individual's surface. this differs from
what Raphael is doing, which is mapping group results to the PALS atlas, at
least as I understand it.
But in both cases, your statistical maps do need to align with the target
surface. In Mathijs individual case, the map must align with the T1 used to
generate the segmentation and resulting surface. In Raphael's case, it must be
in MNI space (i.e., spatially normalized to the standard templates in the SPM
distribution). Now on to Raphael's comments below...
> Hope this helps.
>
> Regards,
> Mathijs
>
> ________________________________
>
> Van: [email protected] namens Raphael Hilgenstock
> Verzonden: do 19-8-2010 13:56
> Aan: [email protected]
> Onderwerp: [caret-users] SPM8 - Mapping Functionals to Volume problem
>
>
>
> Dear List,
>
> I`ve got a problem mapping SPM8 t- and F-contrasts to Caret surfaces.
> Unfortunately I even don`t know if it is possible to map SPM8 images to
> Caret as haven`t found any informationen on the compatibility of both
> programs (even on the list). Is there a difference between SPM5- and
> SPM8-space that has to be accounted for when projecting activations?!
>
We haven't yet generated SPM8 surfaces for the PALS atlas, but we should
do so. Odds are, John Ashburner made significant improvements to the
spatial normalization between the SPM5 and SPM8 revisions. Still, using
SPM5 is an acceptable substitute. I can tell you that when I compared
the SPM2 and SPM5 surfaces, differences were modest. I would just
specify which PALS_B12 target you used in your methods.
> I`m asking because I ran across the following problem:
>
> I processed data to map activations using the Tutorial_Sept_06 (provided
> on the Sumsdb site) click by click with the
> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec-file (is this
> approach still the standard of mapping functional files to volumes?).
>
Yes.
> When I mapped an F-contrast (spm_F.hdr and .nii) on an inflated brain
> there where more spots (and some spots in strange locations) on my
> MFM-image than on my SPM.
This is not unusual with MFM, which maps your volume to each of the 12
PALS subjects' surfaces, and then averages the resulting 12 maps. The
tutorial talks about the pros and cons of the MFM and AFM methods.
David feels the MFM method is more representative, but in practice many
WUSTL researchers use the AFM method, because it appears more
conservative. There is a way to constrain the display to an extent
equal to the average supra-threshold area in the contributing subjects.
The tutorial talks about that, too.
> When I mapped a t-contrast (spm_T.hdr and
> .nii) all activations were gone! When lowering the threshold also this
> (T-)map is showing activations that can be expected from my SPM but also
> "new" acitavtions.
I am confused about this. If all activity disappeared (using the same
contrast that gave positive F results) on your t-map, then I start
doubting the volume -- either it really is all zeroes, or the origin is
way off and/or not specified -- something like that. Upload your
spm_T.hdr and .img and/or .nii here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> The MFMs were thresholded with my SPM t/F-treshold
> and the treshold type in Caret set to "column" (does this acutally mean
> that just the information (t/F-values) form the the spm_T/F image is
> read without any changes to the threshold by Caret? I infered that from
> posts I read but I´m not yet definitively sure).
This gets confusing, but relates to what I mentioned earlier about the
MFM threshold that keeps the supra-threshold area equal to the mean
supra-threshold area of the 12 PALS subjects. If you select this option
and enter a threshold when you map, then Caret computes the threshold
needed to hold the area at this level, and it stores it in the user
threshold, I believe. You over-ride this with your own column threshold.
> As suggested in another
> post I also used different algorithms (e.g. Metric-Gaussian). However
> the result is still the same. I´m most concerned about strange
> activation foci that I won`t find in my SPMs.
>
This is a normal consequence of MFM mapping -- a reflection of normal
anatomical variability. It might go away with proper thresholding. But
first, try AFM mapping and see if your concerns disappear.
> Is there anything I did wrong?!
Don't know. The disappearing t activations puzzle me, which is why I
want to see your volume.
> Any hint or help would be greatly
> appreciated.
>
> Thanks & best regards
> Raphael
>
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