31 Aug
2011
31 Aug
'11
3:18 p.m.
That registration appears to be ok. Remember, that is the boundary between the cortical gray and white matter, not the edge of the brain or skull, so it should be interior. doug
noam Schneck wrote:
Here are slices from the registration.
On Wed, Aug 31, 2011 at 2:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>>> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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> ------------------------------------------------------------------------ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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