Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example one endpoint):
flirt -ref /mri/orig/T1.nii.gz -in dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init /dmri/xfms/diff2anat.bbr.mat
I then loaded the images in Freeview and they look reasonable together with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
What I don't get is how to do this:
"we projected the tract endpoints onto the gray/white matter surface by sampling along the surface normal vector, anywhere within 6 mm (3 DWI-space voxels) of the gray/white junction and then smoothing along the surface with a 2D Gaussian kernel of 6mm full width at half max." (Solsnes et al. 2016)
Any help would be greatly appreciated.
Best wishes, Barbara
Dear all,
If you have some suggestions I'd greatly appreciate them.
Thank you very much,
Best wishes,
Barbara
-------- Forwarded Message -------- Subject: TRACULA tract endpoints on cortical surface Date: Fri, 5 Aug 2016 12:03:02 +0200 From: Barbara Kreilkamp bakk.hbg@googlemail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example one endpoint):
flirt -ref /mri/orig/T1.nii.gz -in dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init /dmri/xfms/diff2anat.bbr.mat
I then loaded the images in Freeview and they look reasonable together with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
What I don't get is how to do this:
"we projected the tract endpoints onto the gray/white matter surface by sampling along the surface normal vector, anywhere within 6 mm (3 DWI-space voxels) of the gray/white junction and then smoothing along the surface with a 2D Gaussian kernel of 6mm full width at half max." (Solsnes et al. 2016)
Any help would be greatly appreciated.
Best wishes, Barbara
Hi Barbara - This can be done with mri_vol2surf. The projection that's described in that passage can be done with --projdist-max -6 6 1, and the surface smoothing with --surf-fwhm 6. There are other options in mri_vol2surf, I'd recommend playing with the settings to see what works better for your data.
Best,
a.y
On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:
Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example one endpoint):
flirt -ref /mri/orig/T1.nii.gz -in dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init /dmri/xfms/diff2anat.bbr.mat
I then loaded the images in Freeview and they look reasonable together with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
What I don't get is how to do this:
"we projected the tract endpoints onto the gray/white matter surface by sampling along the surface normal vector, anywhere within 6 mm (3 DWI-space voxels) of the gray/white junction and then smoothing along the surface with a 2D Gaussian kernel of 6mm full width at half max." (Solsnes et al. 2016)
Any help would be greatly appreciated.
Best wishes, Barbara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Anastasia, I'll try this.
Best wishes, Barbara
On 12/08/2016 23:19, Anastasia Yendiki wrote:
Hi Barbara - This can be done with mri_vol2surf. The projection that's described in that passage can be done with --projdist-max -6 6 1, and the surface smoothing with --surf-fwhm 6. There are other options in mri_vol2surf, I'd recommend playing with the settings to see what works better for your data.
Best,
a.y
On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:
Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example one endpoint):
flirt -ref /mri/orig/T1.nii.gz -in dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init /dmri/xfms/diff2anat.bbr.mat
I then loaded the images in Freeview and they look reasonable together with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
What I don't get is how to do this:
"we projected the tract endpoints onto the gray/white matter surface by sampling along the surface normal vector, anywhere within 6 mm (3 DWI-space voxels) of the gray/white junction and then smoothing along the surface with a 2D Gaussian kernel of 6mm full width at half max." (Solsnes et al. 2016)
Any help would be greatly appreciated.
Best wishes, Barbara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Anastasia Yendiki -
Barbara Kreilkamp