[Freesurfer] exporting segmented mgz file
External Email - Use Caution Hi I'm new to freesurfer. I used freesurfer to preform Thalamus segmentation, and can see the segmented volume in freeview. I would like to export the segmented volume to nii to continue analysis in MRvista. I was able to do this using mri_convert - however the values in the nifti are not those on the label list (as seen in freeview). The number of different values is similar but not the same, and the values themselves are totally different (8103-8233 in freeview, 16384 - 32767). It is possible to compare regions based on visual inspection - however that is tedious and might lead to mistakes. How can I export the labels of each region in the segmented mgz? Any suggestions? I'd appreciate to learn fro your experience Thanks Atira -- ד"ר עתירה גן-צבי ביק יחידת ההדמיה התפקודית הדסה עין-כרם האוניברסיטה העברית Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Intensity inhomogeneity messing with the wm.mgz
Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors? I am using FS6 for linux Here are some pictures: [cid:b4c23099-ffe0-4054-83b9-730a124b78e9]?[cid:35eb0541-c4de-4d31-9f85-4986e1e26661] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How is Total cortical gray matter volume calculated
External Email - Use Caution Ian, You can use the mris_anatomical_stats command with the -b option. E.g., mris_anatomical_stats -b subjectid lh will give you a tabular output containing the total gray matter volume in the 3rd column: 128449 86239 *243375 *2.588 0.876 0.123 0.026 1496 133.3 /xxx./subjects/QEN001/surf/lh.white See https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats for more information. Xiaojiang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How is Total cortical gray matter volume calculated
External Email - Use Caution Morning Freesurfers. Can you describe how the FS stat Total cortical gray matter volume is calculated from the files in the freesurfer subject directory? Is there an mgz file where each voxel has an estimated percentage grey matter here as the value... or is the volume between the surfaces calculated somehow? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
