On Aug 18, 2015, at 2:19 AM, j...@nbrc.ac.in wrote:

> Hello Donna,
> Thank you for your reply.
> Two doubts i have
> 1. why even after loading metric as primary overlay it is not getting
> 'selectable' here in functional view (see attachment "capture")?

The metric is a vertex-intensity mapping.  It is not the volume.  You can load 
the volume that was mapped using File: Open Data File: Volume Functional files. 
 Then it will be selectable when you map to loaded volume.  Or you can simply 
map to file on disk without loading.  But it is not a bad idea to load the 
volume, too, to make sure everything aligns properly:  Functional with surface 
is the important one, but the anatomical volume is the link between functional 
and surface (i.e., how they get aligned).

> 2. what is the meaning of this error message (attachment 2), which appears
> on selecting the functional volumes?

Again, the funky file naming of two of the volume files (e.g., space, 
parentheses, leading dashes) impedes my ability to check them quickly.  But the 
whole brain anatomical does appear to be a NIfTI volume, rather than just an 
Analyze .hdr file.  I loaded it as a functional volume, and then tried to map 
it to your surface.  I got the same result as trying to map it from disk 
(clicking OK on the stickup you captured).

That warning never got removed after support for nifti .hdr/.img pairs was 
added, but based on my getting the same results using the two paths mentioned 
above, I think you will solve your problem when you solve the misalignment 
between your cropped volume and the whole brain anatomical volume.  
Alternatively, shift the surface to meet the whole brain / functional volume.

Ideally, get the following loaded and aligned in caret:

* whole brain anatomy volume
* functional volume overlay
* surface (probably shifted version of what you have now)

Do this in your subject directory:

find /my/subject/dir -name "*.params" |sort | xargs grep -i min

Capture it to a file if it's a lot.  One of those files has the offset you need.

> thank you.
> 
> 
> Hi John,
>> 
>> Got your upload.  While I couldn't open the cropped volume in caret due to
>> the way it was named, I was able to view the surface contour over the
>> uncropped volume.  See attached capture, which shows an offset.
>> 
>> If you have a SureFit/Caret .params file (not included in the zip), it
>> might contain the [XYZ]min values from the cropping, which might be used
>> to either adjust the functional volume's origin, or more likely apply an
>> affine transform to the surface, to shift it back into alignment with the
>> whole brain volume.  You don't have to blow away your existing coord; just
>> rename the shifted version to indicate the offset.  This can be done via
>> command line or using the Caret: Window: Transformation Matrix editor.
>> The polarity of the shift (+ or -) depends on whether you're shifting the
>> volume or surface, and I always get confused about it.  Usually I try it
>> one way; look at the result like the capture below; and if it looks worse,
>> I try it the other way. ;-)  One of the ways usually does the trick.
>> 
>> Donna
>> 
>> 
>> 
>> On Aug 12, 2015, at 9:14 AM, Donna Dierker <do...@brainvis.wustl.edu>
>> wrote:
>> 
>>> Could you upload your dataset in a zip archive here:
>>> 
>> 
>>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>> 
>>> Specifically I need:
>>> 
>>> * functional volume being mapped
>>> * anatomical volume with which functional volume aligns
>>> * anatomical volume used to generate segmentation -- *cropped*
>>> * fiducial coord file
>>> * topology file
>>> 
>>> I am wondering if the centers of the volumes between the cropped volume
>>> used to generate the surface and the whole brain anatomical volume.
>>> 
>>> 
>>> On Aug 12, 2015, at 1:11 AM, j...@nbrc.ac.in wrote:
>>> 
>>>>> 
>>>> 
>>>> Ya, sorry for the incomplete query.
>>>> Our interest is to view and threshold fMRI/voxel correlation data over
>>>> the
>>>> fiducial brain surface created out of high res image of individual
>>>> macaques.
>>>> 1. we used CARET 5.65 for creating the fiducial surfaces(following the
>>>> caret5 tutorial guide for segmentation).we used individual already
>>>> coregistered high res images for this purpose.
>>>> 2. then we tried overlaying the fMRI data(spmT file from analysis using
>>>> spm8) on the fiducial surface (following the procedures from
>>>> http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/
>>>> and the tutorial guides).
>>>> 
>>>> we ended up having
>>>> a) fiducial surfaces with fmri data mapped onto it. But the voxel
>>>> coordinates did not match properly with the results in spm8.
>>>> I should tell you one thing that we found: when we overlay whole brain
>>>> fmri results, it matches more or less in x&y axes but not in z axis.
>>>> and
>>>> when we overlay results from explicitly masked analysis(roi), it seems
>>>> to
>>>> be shifted caudally by 2-3mm in R-C axis. same things when checked in
>>>> spm8, shows up to be well coregistered!
>>>> 
>>>> b)Another issue is we are not able to threshold the caret brain
>>>> overlays
>>>> in concordance with the thresholds that we use in spm.
>>>> The metric thresholding range (user defined) doesn't seems to represent
>>>> what we really need.
>>>> eg:we tried overlaying FDR corrected voel corrln values, thresh 0.4 on
>>>> the
>>>> brain in caet and tried a range of metric thresholds(user scale 0-1,
>>>> put
>>>> display mode-pos,thresh type -user, tried changing user pos thresh
>>>> values
>>>> to 0.4 and voxels doesn't show up!
>>>> 
>>>> Thank you donna,
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> What software was used to reconstruct the surface?
>>>>> 
>>>>> With freesurfer, there is an offset between the orig.mgz and the
>>>>> surface.
>>>>> And depending on many factors, you might have to flip/rotate the
>>>>> surface
>>>>> to be in the same orientation as the volume (or bring the volume to
>>>>> the
>>>>> surface).
>>>>> 
>>>>> See this thread:
>>>>> 
>>>>> http://www.mail-archive.com/caret-users%40brainvis.wustl.edu/msg02081.html
>>>>> 
>>>>> Also see the "Check Alignment between Normalized Volume and Surface"
>>>>> section here:
>>>>> 
>>>>> http://brainvis.wustl.edu/help/pals_volume_normalization/spm5_normalization_pals.html
>>>>> 
>>>>> Examining the surface contour overlaid on the volum in volume view All
>>>>> is
>>>>> often very enlightening.
>>>>> 
>>>>> 
>>>>> On Aug 11, 2015, at 4:42 AM, j...@nbrc.ac.in wrote:
>>>>> 
>>>>>>> 
>>>>>> yes, ours is an individual s surface reconstruction, and so we
>>>>>> checked
>>>>>> the
>>>>>> registration in spm8( using  anatomical image used for reconstruction
>>>>>> and
>>>>>> the functional image volumes used for mapping), where the volumes are
>>>>>> coregistered properly, but shows anomaly in caret.
>>>>>> 
>>>>>> thank you
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> This almost always is because the functional volume is not
>>>>>>> stereotactically registered to the anatomical volume used to
>>>>>>> generate
>>>>>>> the
>>>>>>> fiducial surface. Is this an atlas surface (e.g., one of the PALS
>>>>>>> mean
>>>>>>> midthickness surfaces), or is it an individual's surface
>>>>>>> reconstruction?
>>>>>>> If atlas, this could happen if you were trying to map SPM functional
>>>>>>> data
>>>>>>> to the AFNI mid thickness surface, for example, because there are
>>>>>>> noticeable differences between those stereotaxic spaces.
>>>>>>> 
>>>>>>> If individual, make sure the functional volume is in register with
>>>>>>> the
>>>>>>> anatomical volume used to generate the surface.
>>>>>>> 
>>>>>>> 
>>>>>>> On Aug 10, 2015, at 1:40 AM, j...@nbrc.ac.in wrote:
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> when i map the functional data onto caret fiducial surface, it
>>>>>>>> appears
>>>>>>>> that the mapping is shifted in rostrocaudal axis, caudally, by
>>>>>>>> about 2
>>>>>>>> -3 mm. anyone has idea what could be possibly wrong here?
>>>>>>>> thanks,
>>>>>>>> john
>>>>>>>> _______________________________________________
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>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>> 
>>>>>>> 
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>>>>>>> 
>>>>>>> 
>>>>>> 
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>>>>> 
>>>>> 
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>>>>> 
>>>> 
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>> 
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