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, [email protected] 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, [email protected] 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 <[email protected]> >>>> 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, [email protected] 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, [email protected] 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, [email protected] 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 >>>>>>>>>> [email protected] >>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> caret-users mailing list >>>>>>>>> [email protected] >>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> caret-users mailing list >>>>>>>> [email protected] >>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> caret-users mailing list >>>>>>> [email protected] >>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> [email protected] >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>> <2.PNG><Capture.PNG>_______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
