It is from an individual. I checked the registration, the green surface outline seems well within the movable EPI image. I can scale it down manually and than the zstat, with the scaled down register.dat, fits within the anatomical. Is this the only solution?
On Wed, Aug 31, 2011 at 2:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Is this a zmap from the individual run or the gfeat? If individual, double > check the registration with > tkregister2 --mov example_func.nii.gz --reg anat2exf.register.dat --surfs > If from a gfeat, then you should use anat2std.register.dat, like > > tkmedit bert orig.mgz -overlay zstat1.nii.gz -overlay-reg > anat2exf.register.dat -fthresh 2.3 -fmax 4.3 -aux brain.mgz -seg > aparc+aseg.mgz > > doug > > noam Schneck wrote: > >> Hi, >> Here is the command line for viewing the zstat from a single subject >> single run, in which I ran into the same problem. I've also attached a >> screenshot of the tkmedit image: tkmedit bert bert/mri/orig.mgz -overlay >> zstat1.nii.gz -overlay-reg anat2exf.register.dat -fthresh 2.3 -fmax 4.3 -aux >> bert/mri/brain.mgz -seg bert/mri/aparc+aseg.mgz >> Thank you so much for your help, >> Noam >> On Wed, Aug 31, 2011 at 12:04 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> >> >> noam Schneck wrote: >> >> Hi Doug >> >> Here are more detailed versions of my first two questions. >> 1) I used tkmedit to look at the mean_func produced by a gfeat >> analysis of one subject's three functional runs overlayed onto >> the anatomical image produced by recon-all on that same >> subject(bert/mri/orig.mgz). The registration matrix I used was >> the anat2std.dat that was produced by running reg-feat2anat on >> all three of the feat analyses from the individual runs. When >> I did this I saw that the mean_func image was outside the >> boundaries of the anatomical image. Correspondingly, when I >> overlayed the zstat.nii.gz from the gfeat analysis onto the >> anatomical image I had activation outside of the anatomical >> image brain. >> >> What was the command line? >> >> >> 2) Originally, I ran BBR on a subject that I had run >> Recon-all for. I used BBR to register the example_func.nii.gz >> to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then >> used ApplyXFM in fsl to apply BBR's fsl.mat to register the >> example_func.nii.gz onto a T1 image that had been created by >> converting bert/mri/brainmask.mgz into niftii with >> mri_convert. I tried it again, this time converting the >> orig.mgz to niftii. In both cases the example_func in T1 space >> image produced by ApplyXFM is rotated about 90 degrees and >> also inverted. This is viewed in fslview, I have attached a >> screenshot. The corresponding T1 images created by mri_convert >> are not. What can I do to allow me to use BBR's fsl.mat >> within ApplyXFM? >> >> Here is the header info for the T2*_T1 image attached to this >> email. sizeof_hdr 348 >> data_type FLOAT32 >> dim0 3 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> dim5 1 >> dim6 1 >> dim7 1 >> vox_units mm >> time_units s >> datatype 16 >> nbyper 4 >> bitpix 32 >> pixdim0 0.0000000000 >> pixdim1 1.0000000000 >> pixdim2 1.0000000000 >> pixdim3 1.0000000000 >> pixdim4 1.5000000000 >> pixdim5 1.0000000000 >> pixdim6 1.0000000000 >> pixdim7 1.0000000000 >> vox_offset 352 >> cal_max 0.0000 >> cal_min 0.0000 >> scl_slope 0.000000 >> scl_inter 0.000000 >> phase_dim 0 >> freq_dim 0 >> slice_dim 0 >> slice_name Unknown >> slice_code 0 >> slice_start 0 >> slice_end 0 >> slice_duration 0.000000 >> time_offset 0.000000 >> intent Unknown >> intent_code 0 >> intent_name intent_p1 0.000000 >> intent_p2 0.000000 >> intent_p3 0.000000 >> qform_name Scanner Anat >> qform_code 1 >> qto_xyz:1 -1.000000 -0.000000 -0.000000 128.678986 >> qto_xyz:2 -0.000000 0.000000 1.000000 -100.598366 >> qto_xyz:3 0.000000 -1.000000 0.000000 143.524200 >> qto_xyz:4 0.000000 0.000000 0.000000 1.000000 >> qform_xorient Right-to-Left >> qform_yorient Superior-to-Inferior >> qform_zorient Posterior-to-Anterior >> sform_name Scanner Anat >> sform_code 1 >> sto_xyz:1 -1.000000 -0.000000 0.000000 128.678986 >> sto_xyz:2 -0.000000 -0.000000 1.000000 -100.598366 >> sto_xyz:3 -0.000000 -1.000000 0.000000 143.524200 >> sto_xyz:4 0.000000 0.000000 0.000000 1.000000 >> sform_xorient Right-to-Left >> sform_yorient Superior-to-Inferior >> sform_zorient Posterior-to-Anterior >> file_type NIFTI-1+ >> file_code 1 >> descrip FreeSurfer Jun 18 2008 >> aux_file >> Thank you, >> Noam >> >> On Mon, Aug 29, 2011 at 1:16 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> Hi Noam, >> >> >> noam Schneck wrote: >> >> Hi, >> >> I am trying to use reg-feat2anat to register my Feat >> analyses >> to anatomical images and running into a number of problems. >> 1) When I check the registration of the mean_func to the >> anatomical in tkregister2 it looks fine. But when I overlay >> the fsl statmaps onto the anatomical brain they extend >> outside >> of boundaries of the anatomical brain. >> >> Need more detail. What command are you using to visualize? >> >> >> 2) Also, before using reg-feat2anat. I was trying to do the >> EPI_2_structural registration in FLIRT with the fsl.mat >> produced by BBR. When I try this the registered image is >> rotated 90 degrees from the original image. Why does >> that happen? >> >> More detail needed. What program did you run? What >> visualization >> tool? This will align the anatomical in the conformed space >> to the >> EPI, so make sure you're using the right anatomical. >> >> >> 3) I also noticed that if I look at the header >> information for >> an image in fslhd and mri_info the orientations are >> flipped. >> If the fslhd orientation is RAS it will be LPI in mri_info. >> Could this be related to what is happening in question (2)? >> >> Need more detail. What images are you looking at? >> >> In general, you have to tell us specifically what you are >> doing. >> It's going to be very hard to help with vague descriptions. >> doug >> >> >> Best, >> Noam >> ------------------------------** >> ------------------------------**------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/ >> **freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> FileDrop: >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> >> >> >> The information in this e-mail is intended only for the >> person to >> whom it is >> addressed. If you believe this e-mail was sent to you in >> error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was >> sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> ------------------------------**------------------------------** >> ------------ >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >> <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> ------------------------------**------------------------------** >> ------------ >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
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