> Hi Donna, There were no steps that involved any de-obliquing, flipped, or > shifted, AC-centered "LPI" orientation. i loaded the image, anatomical and in volume attributes I checked the orientation, put the crossline at AC after shifting the image manually through co ordinate values, and selected the option to keep AC position as crossline position in main window. after this i gave coordinates of posterior comm, and middle fissure and checked voxel size etc... then i saved it as AC centered image.
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. >>>>>>>>>> >>>>>>>>>> >> >> _______________________________________________ >> 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
