Perhaps if this were done with wb_command -volume-resample it would work better, but Tim would have to comment on this.
Matt. From: HERACLES PANAGIOTIDES <he...@uw.edu<mailto:he...@uw.edu>> Date: Friday, March 16, 2018 at 12:11 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Fw: This is what I used: applywarp -i left_Accumbens.nii.gz -r rfMRI_REST1_LR_hp2000_clean.nii.gz -o left_Accumbens_in_FA.nii.gz The position came our not in the right place. -hp From: Glasser, Matthew Sent: Friday, March 16, 2018 9:39 AM To: HERACLES PANAGIOTIDES Subject: Re: [HCP-Users] Fw: It should work if you use applywarp with no warp or affine. Peace, Matt. From: HERACLES PANAGIOTIDES <he...@uw.edu> Date: Friday, March 16, 2018 at 11:17 AM To: Matt Glasser <glass...@wustl.edu> Subject: Re: [HCP-Users] Fw: Thanks for the reply, Matt. I did not define the problem properly. The original mask is in MNI space (198 X 263 X 212) but does not have the same number of voxels in each dimensions the rfMRI (91 X 109 X 91). Is it possible to transform the the mask to have the same dimensionality (number of voxels in each dimension) as the rfMRI? Best, -hp From: Glasser, Matthew Sent: Friday, March 16, 2018 7:22 AM To: HERACLES PANAGIOTIDES ; HCP Subject: Re: [HCP-Users] Fw: Why can’t you use an MNI space accumbens mask? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of HERACLES PANAGIOTIDES <he...@uw.edu> Date: Friday, March 16, 2018 at 8:04 AM To: HCP <hcp-users@humanconnectome.org> Subject: [HCP-Users] Fw: Could someone please help me warp a mask (left_Accumbens.nii) to an rfMRI in MNI space. I used the following FLIRT command: flirt –in left_Accumbens.nii.gz -ref rfMRI_REST1_LR_hp2000_clean.nii.gz -applyxfm -init MNI2FA.mat –out left_Accumbens_in_FA.nii.gz I am attaching the input, output and mat files. the rfMRI is too big for this email. I am also attaching an image that shows the original ROI (green) and the transformed/output ROI (red). They are not registered correctly. Alternatively, I used the fnirt command with no better luck. fnirt --ref=rfMRI_REST1_LR_hp2000_clean.nii.gz --in=left_Accumbens.nii.gz -- inmask=left_Accumbens.nii.gz --aff=MNI2FA.mat --iout=left_Accumbens_in_FA.nii.gz Any ideas or suggestions? Thanks, -hp _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
