[Freesurfer] Recon-all
Dear Freesurfers. I am facing a crucial point.:)and I need your help. After examining most of our subjects, we decided that there is no need to run all the procedures- work flow, since our data is not prone to too many failures, and just start with recon-all-all, get all the data and then start editing. Usually we have to add very few cp and to do some pial edits (not in all the cases).However, our talairach looks good, no skull striping problems and wm is also ok. I was wondering if running recon-all-all, and then fixing the i.e. cp , or the pial surface when repeating autorecon2-cp, or autorecon2-pial-autorecon3, is it harmful? Does this mass my analysis , or it's ok? Thank You Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help with surface parcellation
Hello Everyone. I have a subject that throughout all the process looked pretty good, however, when I reached the final process of checking surfaces and loading the aparc.annot file, I paid attention that all my unknown area , covers my -almost fully my corpus callosum label. What should I do, is there a way to fix it? Thanks Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach
Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option which I can apply after correcting the Talairach transform? P.S following the workflow takes me almost 3-4 days for a subject (looking carefully and fixing everything,, am I on the right track? Help, Please Thank You Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Pial Surfaces
Dear FreeSurfers I have a problem editing pial surfaces. My pial borders do not include Some important brain parts i.e. amygdala. Can anybody help me? Tnx Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Manuals and Scuba
Dear FreeSurfer Team I'm a new user of freesurfer and I would like to ask you few questions. 1.Where can I find more information regarding SCUBA? 2.I read very carefully through the freesurfer website, (all the work flow and tutorials) however, I was wondering weather every time I do any kind of changes, do I have to run recon all again,, or there are any single commands that repair/edit my own revisions? 3. What is the newest version of the FreeSurfer Manual and where can I find it Thank You in advance Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
