You should not need to adjust the registration. The surface should follow the gray white boundary in the EPI (hard to see but there). Can you send a pic of the green surface on the EPI with the default registration (ie, without you making changes)?
noam Schneck wrote: > 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 <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel: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>> > <tel: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> > > 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> > > > > > 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 . 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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> > 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> > > > > > ------------------------------------------------------------------------ > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto: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> > FileDrop: 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
