Hi John,

Those tweaks were very helpful.  I looked at the volumes with the surface 
overlaid, and here's what I found:

http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
login pub
password download

I don't trust Caret to handle oblique volumes properly.  Quoting the link 
above, "Can you go back through the history of this volume's processing -- 
specifically what happened to generate anatomical_ac_centered.hdr from 
anatomical_image.hdr? Were there steps the de-obliqued, flipped, or shifted the 
anatomical to get it AC-centered and probably in "LPI" orientation, as Caret 
required to segment?"

Donna


On Aug 20, 2015, at 1:02 AM, j...@nbrc.ac.in wrote:

> Hello Donna,
> I've made the necessary changes and uploaded the file.
> 
> john.
> 
> 
> 
> If you can find your *.params file, then don't worry about the find
>> command, which was intended to help you locate it if you did not know its
>> name/location already.
>> 
>> I looked at your dataset, and you must do two things to help me help you:
>> 
>> * Remove the spaces from the filenames.  Replace them with _ characters.
>> When I try to read, move, or otherwise manipulate these files, the spaces
>> are misinterpreted by the Linux shell as separate arguments.
>> 
>> * Add the *.params file.
>> 
>> After you've made those changes, rename the directory john_renamed.  Then
>> zip it and upload it.  I'll do my best to solve it.
>> 
>> 
>> On Aug 19, 2015, at 1:23 AM, j...@nbrc.ac.in wrote:
>> 
>>>> 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.
>>>>>>>>> 
>>>>>>>>> 
> 
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