[Freesurfer] re-run fsaverage only
External Email - Use Caution Hello, I accidentally renamed my fsaverage directory when I was renaming my subjects' directories. Since I was still in the process of running subjects, a new fsaverage directory was automatically created. Now I have two fsaverage directories that each have a different subset of my participants, but I'd like there to be one directory that has all my participants. Is there any command that I could run that would generate a new fsaverage from subjects in the same output directory? Thanks, Ryan Wales -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Should I edit or reject?
External Email - Use Caution Hi, Although there are many ways to correct for pial, WM, and segmentation defects, it seems common in the literature to forego any edits and simply either accept or reject a subject's FreeSurfer output in order to avoid subjectivity and potential over-editing. Another group rejected subjects if their defects spanned 6 or more slices, for example. Are there any guide lines on how much editing is too much editing? Should it just be edited enough so it looks tolerable by eye? Maybe by a few different raters? The defects vary in their severity, so it's difficult to know if a subject should be considered passable or requiring edits based on a minor defect. My current plan is to conduct my analysis once with excluding subjects with poor segmentation and then again, including those subjects' edited outputs. Do you agree with this logic? Thanks for your advice, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pial surface and eTIV
External Email - Use Caution Hello, I'm using freesurfer ver 6.0.0. If there are defects with the pial surface (i.e. the pial surface does not cover all the gray matter that it should), can you also assume that the eTIV has not been estimated incorrectly, or do pial surface inaccuracies not indicate eTIV inaccuracy? I know eTIV is estimated based on the linear transform to the talairach.xfm, but I'm not sure if there's any way to determine eTIV accuracy directly. I'm quality checking my images and am curious if I should remove subjects based on poor pial surfaces or if that does not matter. Important to note, at the moment, I'm only interested in pulling hippocampal volumes and eTIV (to get relative hippocampal volumes). Similarly, would poor pial segmentation affect the reported hippocampal volumes at all? What do you recommend? Thanks, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Color LUT after coregister and reslice aparc/aseg.nii
External Email - Use Caution Hello, I'm using fmriprep's aparcaseg_dseg.nii (still FreeSurfer code, right?) to create ROI masks. I wish to coregister and reslice this segmentation file to match the native space for another image (PET), then extract SUVR values for each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
