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
