> Hello Donna,

1.I ve tried taking the XYZ min values from .PARAMS file and transformed
the overlay. This appears very subjective and error prone.

2. "Do this in your subject directory:
>
> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
"

I am not sure i understood this step properly


I am unable to coregister the functional image and anatomical image properly.
I am sorry to trouble you again , but it would be great if you can take a
look at the dataset again, which i have uploaded in a folder " data from
john.zip" at http://pulvinar.wustl.edu/cgi-bin/upload.cgi

I doubt now that there is some issue within the procedure that we follow
in doing the analysis. So it would be best if you can check/reanalyse the
dataset from very initial step itself.

PS:
-anatomical image.hdr\img---unaltered structural T1 image.
-functional.hdr\img----basic SPM8  T2*image which is to be mapped

Thank you.




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
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
>>>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>>>> 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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