[Freesurfer] How to obtain sulcal depth in raw mm?
External Email - Use Caution Hi Freesurfer team, I have a quick question regarding the output of *.sulc* values in Freesurfer: From previous messages on the list, it seems as though the *.sulc* values in each hemisphere are 0-median and unit standard deviation of the original mm sulcal depth. Is this correct? Namely, I'm wondering the best way to obtain vertex-wise values for *raw sulcal depth (**mm)* from a subject's Freesurfer (recon-all) output. Perhaps this may just entail un-standardizing the .sulc values? Thank you! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Selecting vertices on label boundary for analysis
External Email - Use Caution Hi Freesurfer team, In tksurfer, it's possible to display the outline of a label. Is there is a way to obtain the list of vertices that make up the outline of a label, so that I may select them from the label file? My goal is to perform an analysis that would only involve these boundary vertices (calculating the max distance between boundary vertices in a label, as a measure of label length). Thanks again! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Avoiding or removing overlap when converting surface labels to volume
External Email - Use Caution Hi Freesurfer team, I am transforming several adjacent surface labels into volume ROIs, using *mri_label2vol*. When doing so, there seems to be some possibly unavoidable overlap in a small number of voxels in the volume ROIs. Is there any way to avoid these labels from overlapping when transformed into the volume? I see that *mri_label2vol* takes an --annot flag, would this help in avoiding overlap in the outputs? Otherwise, I can remove the overlapping voxels int he nifti file outputs, but I was wondering if the algorithm had any options to do this as part of the surface-to-volume transform. Thanks so much! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
