Your fMRI volume and T1w image are not aligned. I have no idea why that is...
Peace, Matt. From: Leah Moreno <[email protected]<mailto:[email protected]>> Date: Tuesday, January 17, 2017 at 10:34 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "Van Essen, David" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] map data between FreeSurfer and HCP Dear David and Matt, Thank you for the specification. Please find attached the right picture now. It looks good to me. What is the problem with individual zmap volume and how could I restore the misalignment between fMRI volume and T1w image? I really appreciate your help with this. Leah ********************************** Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (646) 774-5404 email: [email protected]<mailto:[email protected]> email: [email protected]<mailto:[email protected]> [cid:[email protected]] From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Date: Monday, January 16, 2017 at 10:33 PM To: "Van Essen, David" <[email protected]<mailto:[email protected]>>, Leah Moreno <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] map data between FreeSurfer and HCP It would appear that your fMRI volume is not aligned with your T1w image. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of David Van Essen <[email protected]<mailto:[email protected]>> Date: Monday, January 16, 2017 at 9:21 PM To: Leah Moreno <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] map data between FreeSurfer and HCP Leah, I'm not sure exactly what was in your display. But I think what Matt was asking for was to see the surface contours for your individual subject surface (e.g., midthickness) overlaid on volume slices using the Vol/Surf Outline as in the attached screen capture (which is an average surface, but it suffices for the point). That will help determine whether the surfaces you are using are aligned with the volume data used for the volume-to-surface mapping. David On Jan 16, 2017, at 10:45 AM, Leah Moreno <[email protected]<mailto:[email protected]>> wrote: Dear Matt, Please find attached 2 pictures of individual z-map on brain.finalsurfs and averageT1w_restore (template). Much appreacition. -L On 1/16/17, 11:04 AM, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: What does it look like if you view the volume surface outline of your chosen surface on the functional connectivity volume in Connectome Workbench? Peace, Matt. On 1/16/17, 12:04 AM, "Leah Moreno" <[email protected]<mailto:[email protected]>> wrote: Dear Matt, Thank you very much. Here you have the output of mri_info brain.finalsurfs.mgz: Volume information for brain.finalsurfs.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 1.0000 talairach xfm : /Volumes/data3/sz/sort/x50001/FS/x50001/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.5000 0.0000 0.0000 1.0000 -102.0000 0.0000 -1.0000 0.0000 129.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.5000 -0.0000 -0.0000 -1.0000 129.0000 -0.0000 1.0000 -0.0000 102.0000 0.0000 0.0000 0.0000 1.0000 PastedGraphic-1.tiff _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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