Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce, Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
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Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.