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.
>>>>>>> 
>>>>>>> 
>>>>>>> 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
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
>>>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> caret-users mailing list
>>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> caret-users mailing list
>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users@brainvis.wustl.edu
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>> 
>>>> 
>>>> _______________________________________________
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>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>> 
>>> <2.PNG><Capture.PNG>_______________________________________________
>>> caret-users mailing list
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>> 
>> 
>> _______________________________________________
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>> 
>> 
> 
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