Hi John, My trials with your data are detailed here:
> http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html > login pub > password download I suspect there are better ways of dealing with oblique data, and I hope others will chime in if they have alternative suggestions. (They don't have to be "better" -- just offering other perspectives, even.) This was the best I could do with the information I have. Donna On Aug 20, 2015, at 12:43 PM, j...@nbrc.ac.in wrote: >> 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 _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
