> Hello Donna, Thank you for your response. I think now the functional and anatomical is aligned properly once i do a reslicing(in SPM) of functional and aligning it in par with anatomical image parameters in caret. Thank you for your kind help, john
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 > > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
