Potentially. Presumably your DWI show up “upside-down” in the A/P axis when viewed in ‘fslview’?
You could use ‘fslreorient2std’ to change to LAS (or RAS) orientation on your already converted NIFTI, but you’ll need to adjust the bvecs appropriately as well. Or, try another DICOM converter (e.g., dcm2niix) to see if that generates LAS orientation by default with your data. I’d try that on 1-2 subjects for which you are having issues, and see if it solves your problem. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: Maarten Vaessen <[email protected]<mailto:[email protected]>> Date: Wednesday, October 19, 2016 at 8:47 AM To: Michael Harms <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] alignment issues with diffusion data The data is from a 2d EPI sequence converted from DICOM with mrtrix routines. From mri_info I get: ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 3.8554 : x_a = 0.0000, y_a = -0.9285, z_a = -0.3714, c_a = -7.2492 : x_s = 0.0000, y_s = -0.3714, z_s = 0.9285, c_s = 15.6468 Orientation : LPS Primary Slice Direction: axial The issue is then with the DICOM conversion? Thx, -Maarten On Wed, Oct 19, 2016 at 3:39 PM, Harms, Michael <[email protected]<mailto:[email protected]>> wrote: Is your DWI data by any chance saved with an orientation other than LAS or RAS? -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Maarten Vaessen <[email protected]<mailto:[email protected]>> Date: Wednesday, October 19, 2016 at 6:50 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] alignment issues with diffusion data Hello experts, I have been trying to use the HCP Diffusion preprocessing pipeline for my own diffusion data. However, I run into a lot of issues at the final stage of the pipeline where the dwi data is registered to the T1w_acpc space (the freesurfer part of the pipeline runs fine on the structural images, the eddy correction also seems to run fine). So far I have not had a single subject where this alignment went smoothly and was accurate. It seems to be a problem with flirt. In the DiffusiontoStructural.sh subscript there are several calls to flirt (or epi_ref_dof) with the T1 as reference and for some reason flirt gives very wrong results like AP inverted or cerebellum to frontal lobe matching etc... I have managed to solve some cases with a call to only flirt and not epi_reg_dof and adding -useqform to the flirt options, but some I only managed by doing a rough manual alignment first. When the initial reg to T1 in ok-ish the bbregister and later parts all work very well. I don't think my dwi data is very special (1.5 mm^3 90 dir 2 shell), so I have no idea what might be the issue here or how to solve it (in a consistent way). -Maarten _______________________________________________ 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
